Starting phenix.real_space_refine on Wed Feb 12 02:39:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7r4t_14316/02_2025/7r4t_14316.cif Found real_map, /net/cci-nas-00/data/ceres_data/7r4t_14316/02_2025/7r4t_14316.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.75 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7r4t_14316/02_2025/7r4t_14316.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7r4t_14316/02_2025/7r4t_14316.map" model { file = "/net/cci-nas-00/data/ceres_data/7r4t_14316/02_2025/7r4t_14316.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7r4t_14316/02_2025/7r4t_14316.cif" } resolution = 2.75 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 6 5.16 5 C 2172 2.51 5 N 642 2.21 5 O 648 1.98 5 H 3606 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 7074 Number of models: 1 Model: "" Number of chains: 6 Chain: "F" Number of atoms: 1179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 1179 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "A" Number of atoms: 1179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 1179 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "B" Number of atoms: 1179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 1179 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "C" Number of atoms: 1179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 1179 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "D" Number of atoms: 1179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 1179 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "E" Number of atoms: 1179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 1179 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Time building chain proxies: 4.48, per 1000 atoms: 0.63 Number of scatterers: 7074 At special positions: 0 Unit cell: (132.664, 112.888, 40.376, 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 648 8.00 N 642 7.00 C 2172 6.00 H 3606 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.61 Conformation dependent library (CDL) restraints added in 643.4 milliseconds 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 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, 49.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.76 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'B' and resid 306 through 310 removed outlier: 6.595A pdb=" N GLN F 307 " --> pdb=" O ILE D 308 " (cutoff:3.500A) removed outlier: 7.720A pdb=" N TYR D 310 " --> pdb=" O GLN F 307 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N VAL F 309 " --> pdb=" O TYR D 310 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 313 through 314 removed outlier: 6.708A pdb=" N VAL F 313 " --> pdb=" O ASP D 314 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 317 through 324 removed outlier: 6.178A pdb=" N LYS F 317 " --> pdb=" O VAL D 318 " (cutoff:3.500A) removed outlier: 7.826A pdb=" N SER D 320 " --> pdb=" O LYS F 317 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N THR F 319 " --> pdb=" O SER D 320 " (cutoff:3.500A) removed outlier: 8.199A pdb=" N CYS D 322 " --> pdb=" O THR F 319 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N LYS F 321 " --> pdb=" O CYS D 322 " (cutoff:3.500A) removed outlier: 7.810A pdb=" N SER D 324 " --> pdb=" O LYS F 321 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N GLY F 323 " --> pdb=" O SER D 324 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 328 through 330 removed outlier: 6.368A pdb=" N ILE F 328 " --> pdb=" O HIS B 329 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 336 through 341 removed outlier: 6.467A pdb=" N GLN F 336 " --> pdb=" O VAL D 337 " (cutoff:3.500A) removed outlier: 7.797A pdb=" N VAL D 339 " --> pdb=" O GLN F 336 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N GLU F 338 " --> pdb=" O VAL D 339 " (cutoff:3.500A) removed outlier: 7.986A pdb=" N SER D 341 " --> pdb=" O GLU F 338 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N LYS F 340 " --> pdb=" O SER D 341 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 345 through 346 removed outlier: 6.593A pdb=" N ASP F 345 " --> pdb=" O PHE D 346 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 350 through 354 removed outlier: 6.364A pdb=" N GLN F 351 " --> pdb=" O SER D 352 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N ILE D 354 " --> pdb=" O GLN F 351 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N LYS F 353 " --> pdb=" O ILE D 354 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 357 through 362 removed outlier: 6.532A pdb=" N LEU F 357 " --> pdb=" O ASP B 358 " (cutoff:3.500A) removed outlier: 7.757A pdb=" N ILE B 360 " --> pdb=" O LEU F 357 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N ASN F 359 " --> pdb=" O ILE B 360 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N HIS B 362 " --> pdb=" O ASN F 359 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N THR F 361 " --> pdb=" O HIS B 362 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N ASP F 358 " --> pdb=" O ASN D 359 " (cutoff:3.500A) removed outlier: 7.738A pdb=" N THR D 361 " --> pdb=" O ASP F 358 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N ILE F 360 " --> pdb=" O THR D 361 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'B' and resid 368 through 378 removed outlier: 6.509A pdb=" N LYS F 369 " --> pdb=" O LYS D 370 " (cutoff:3.500A) removed outlier: 7.844A pdb=" N GLU D 372 " --> pdb=" O LYS F 369 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N ILE F 371 " --> pdb=" O GLU D 372 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N HIS D 374 " --> pdb=" O ILE F 371 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N THR F 373 " --> pdb=" O HIS D 374 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N LEU D 376 " --> pdb=" O THR F 373 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N LYS F 375 " --> pdb=" O LEU D 376 " (cutoff:3.500A) removed outlier: 7.779A pdb=" N PHE D 378 " --> pdb=" O LYS F 375 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N THR F 377 " --> pdb=" O PHE D 378 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 306 through 310 Processing sheet with id=AB2, first strand: chain 'C' and resid 313 through 314 removed outlier: 6.723A pdb=" N VAL A 313 " --> pdb=" O ASP E 314 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 317 through 324 removed outlier: 6.169A pdb=" N LYS A 317 " --> pdb=" O VAL E 318 " (cutoff:3.500A) removed outlier: 7.804A pdb=" N SER E 320 " --> pdb=" O LYS A 317 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N THR A 319 " --> pdb=" O SER E 320 " (cutoff:3.500A) removed outlier: 8.224A pdb=" N CYS E 322 " --> pdb=" O THR A 319 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N LYS A 321 " --> pdb=" O CYS E 322 " (cutoff:3.500A) removed outlier: 7.939A pdb=" N SER E 324 " --> pdb=" O LYS A 321 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N GLY A 323 " --> pdb=" O SER E 324 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 328 through 330 removed outlier: 6.404A pdb=" N ILE A 328 " --> pdb=" O HIS C 329 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 336 through 338 removed outlier: 6.501A pdb=" N GLN A 336 " --> pdb=" O VAL E 337 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 345 through 346 removed outlier: 6.605A pdb=" N ASP A 345 " --> pdb=" O PHE E 346 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 350 through 354 removed outlier: 6.377A pdb=" N GLN A 351 " --> pdb=" O SER E 352 " (cutoff:3.500A) removed outlier: 7.847A pdb=" N ILE E 354 " --> pdb=" O GLN A 351 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N LYS A 353 " --> pdb=" O ILE E 354 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 357 through 362 removed outlier: 6.503A pdb=" N LEU A 357 " --> pdb=" O ASP C 358 " (cutoff:3.500A) removed outlier: 7.720A pdb=" N ILE C 360 " --> pdb=" O LEU A 357 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N ASN A 359 " --> pdb=" O ILE C 360 " (cutoff:3.500A) removed outlier: 7.843A pdb=" N HIS C 362 " --> pdb=" O ASN A 359 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N THR A 361 " --> pdb=" O HIS C 362 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 368 through 378 removed outlier: 6.440A pdb=" N LYS A 369 " --> pdb=" O LYS E 370 " (cutoff:3.500A) removed outlier: 7.775A pdb=" N GLU E 372 " --> pdb=" O LYS A 369 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N ILE A 371 " --> pdb=" O GLU E 372 " (cutoff:3.500A) removed outlier: 7.835A pdb=" N HIS E 374 " --> pdb=" O ILE A 371 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N THR A 373 " --> pdb=" O HIS E 374 " (cutoff:3.500A) removed outlier: 7.786A pdb=" N LEU E 376 " --> pdb=" O THR A 373 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N LYS A 375 " --> pdb=" O LEU E 376 " (cutoff:3.500A) removed outlier: 7.793A pdb=" N PHE E 378 " --> pdb=" O LYS A 375 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N THR A 377 " --> pdb=" O PHE E 378 " (cutoff:3.500A) 74 hydrogen bonds defined for protein. 222 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.41 Time building geometry restraints manager: 1.96 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: 3600 1.12 - 1.29: 576 1.29 - 1.47: 1176 1.47 - 1.64: 1770 1.64 - 1.82: 6 Bond restraints: 7128 Sorted by residual: bond pdb=" N GLU F 338 " pdb=" H GLU F 338 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.70e+01 bond pdb=" N GLY F 335 " pdb=" H GLY F 335 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.70e+01 bond pdb=" N SER F 341 " pdb=" H SER F 341 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.70e+01 bond pdb=" NE2 HIS D 374 " pdb=" HE2 HIS D 374 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.69e+01 bond pdb=" CD2 PHE B 346 " pdb=" HD2 PHE B 346 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.69e+01 ... (remaining 7123 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.65: 11940 3.65 - 7.31: 1001 7.31 - 10.96: 38 10.96 - 14.62: 2 14.62 - 18.27: 3 Bond angle restraints: 12984 Sorted by residual: angle pdb=" C VAL C 339 " pdb=" N LYS C 340 " pdb=" H LYS C 340 " ideal model delta sigma weight residual 123.83 105.55 18.27 3.00e+00 1.11e-01 3.71e+01 angle pdb=" C VAL A 339 " pdb=" N LYS A 340 " pdb=" H LYS A 340 " ideal model delta sigma weight residual 123.83 106.86 16.96 3.00e+00 1.11e-01 3.20e+01 angle pdb=" C VAL E 339 " pdb=" N LYS E 340 " pdb=" H LYS E 340 " ideal model delta sigma weight residual 123.83 108.19 15.63 3.00e+00 1.11e-01 2.71e+01 angle pdb=" CB HIS F 362 " pdb=" CG HIS F 362 " pdb=" CD2 HIS F 362 " ideal model delta sigma weight residual 131.20 125.02 6.18 1.30e+00 5.92e-01 2.26e+01 angle pdb=" CB HIS A 329 " pdb=" CG HIS A 329 " pdb=" CD2 HIS A 329 " ideal model delta sigma weight residual 131.20 125.11 6.09 1.30e+00 5.92e-01 2.20e+01 ... (remaining 12979 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.45: 2806 13.45 - 26.89: 253 26.89 - 40.34: 103 40.34 - 53.78: 46 53.78 - 67.23: 74 Dihedral angle restraints: 3282 sinusoidal: 1878 harmonic: 1404 Sorted by residual: dihedral pdb=" CA VAL E 350 " pdb=" C VAL E 350 " pdb=" N GLN E 351 " pdb=" CA GLN E 351 " ideal model delta harmonic sigma weight residual 180.00 153.90 26.10 0 5.00e+00 4.00e-02 2.72e+01 dihedral pdb=" CA VAL D 350 " pdb=" C VAL D 350 " pdb=" N GLN D 351 " pdb=" CA GLN D 351 " ideal model delta harmonic sigma weight residual 180.00 154.93 25.07 0 5.00e+00 4.00e-02 2.51e+01 dihedral pdb=" CA VAL F 350 " pdb=" C VAL F 350 " pdb=" N GLN F 351 " pdb=" CA GLN F 351 " ideal model delta harmonic sigma weight residual 180.00 155.76 24.24 0 5.00e+00 4.00e-02 2.35e+01 ... (remaining 3279 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.070: 310 0.070 - 0.138: 174 0.138 - 0.207: 31 0.207 - 0.276: 10 0.276 - 0.345: 3 Chirality restraints: 528 Sorted by residual: chirality pdb=" CA LYS F 340 " pdb=" N LYS F 340 " pdb=" C LYS F 340 " pdb=" CB LYS F 340 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.97e+00 chirality pdb=" CA LYS A 340 " pdb=" N LYS A 340 " pdb=" C LYS A 340 " pdb=" CB LYS A 340 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.08e+00 chirality pdb=" CA LYS B 340 " pdb=" N LYS B 340 " pdb=" C LYS B 340 " pdb=" CB LYS B 340 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.99e+00 ... (remaining 525 not shown) Planarity restraints: 1032 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A 339 " 0.059 2.00e-02 2.50e+03 1.13e-01 1.29e+02 pdb=" N LYS A 340 " -0.196 2.00e-02 2.50e+03 pdb=" CA LYS A 340 " 0.059 2.00e-02 2.50e+03 pdb=" H LYS A 340 " 0.078 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL C 339 " 0.059 2.00e-02 2.50e+03 1.12e-01 1.26e+02 pdb=" N LYS C 340 " -0.194 2.00e-02 2.50e+03 pdb=" CA LYS C 340 " 0.060 2.00e-02 2.50e+03 pdb=" H LYS C 340 " 0.076 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL E 339 " 0.053 2.00e-02 2.50e+03 1.02e-01 1.03e+02 pdb=" N LYS E 340 " -0.176 2.00e-02 2.50e+03 pdb=" CA LYS E 340 " 0.053 2.00e-02 2.50e+03 pdb=" H LYS E 340 " 0.069 2.00e-02 2.50e+03 ... (remaining 1029 not shown) Histogram of nonbonded interaction distances: 1.56 - 2.17: 592 2.17 - 2.78: 11959 2.78 - 3.38: 18274 3.38 - 3.99: 25297 3.99 - 4.60: 34258 Nonbonded interactions: 90380 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 A 314 " pdb=" HG SER A 316 " model vdw 1.567 2.450 nonbonded pdb=" OD1 ASP F 314 " pdb=" HG SER F 316 " model vdw 1.570 2.450 nonbonded pdb=" OD1 ASP B 314 " pdb=" HG SER B 316 " model vdw 1.573 2.450 nonbonded pdb=" OD1 ASP E 314 " pdb=" HG SER E 316 " model vdw 1.594 2.450 ... (remaining 90375 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.820 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: 0.140 Extract box with map and model: 0.210 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 19.590 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 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 0.035 3522 Z= 0.721 Angle : 1.775 6.178 4710 Z= 1.174 Chirality : 0.085 0.345 528 Planarity : 0.009 0.050 600 Dihedral : 11.858 51.239 1350 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.02 (0.34), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.53 (0.26), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.002 HIS D 330 PHE 0.047 0.018 PHE F 378 TYR 0.032 0.008 TYR D 310 ARG 0.005 0.001 ARG F 349 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 136 time to evaluate : 0.631 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 347 LYS cc_start: 0.8346 (ttpt) cc_final: 0.7938 (mptt) REVERT: A 347 LYS cc_start: 0.8450 (ttpt) cc_final: 0.7989 (mptt) REVERT: B 347 LYS cc_start: 0.8339 (ttpt) cc_final: 0.7944 (mmtm) REVERT: B 349 ARG cc_start: 0.8218 (mtt180) cc_final: 0.6371 (mmp-170) REVERT: C 347 LYS cc_start: 0.8400 (ttpt) cc_final: 0.7966 (mmtm) REVERT: C 349 ARG cc_start: 0.8156 (mtt180) cc_final: 0.6382 (mmp-170) REVERT: D 347 LYS cc_start: 0.8483 (ttpt) cc_final: 0.8240 (mptt) REVERT: D 348 ASP cc_start: 0.8537 (t70) cc_final: 0.8029 (t0) REVERT: D 349 ARG cc_start: 0.7334 (mtt180) cc_final: 0.5925 (pmt-80) REVERT: E 347 LYS cc_start: 0.8447 (ttpt) cc_final: 0.8122 (mptt) REVERT: E 348 ASP cc_start: 0.8595 (t70) cc_final: 0.8148 (t0) REVERT: E 349 ARG cc_start: 0.7266 (mtt180) cc_final: 0.5882 (pmt-80) outliers start: 0 outliers final: 0 residues processed: 136 average time/residue: 3.1532 time to fit residues: 438.3373 Evaluate side-chains 88 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 88 time to evaluate : 0.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 10 optimal weight: 5.9990 chunk 21 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 20 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 307 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.133047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.122835 restraints weight = 13532.638| |-----------------------------------------------------------------------------| r_work (start): 0.3883 rms_B_bonded: 1.60 r_work: 0.3796 rms_B_bonded: 1.65 restraints_weight: 0.5000 r_work: 0.3711 rms_B_bonded: 2.88 restraints_weight: 0.2500 r_work (final): 0.3711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8730 moved from start: 0.4087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3522 Z= 0.201 Angle : 0.565 4.596 4710 Z= 0.290 Chirality : 0.051 0.145 528 Planarity : 0.003 0.021 600 Dihedral : 5.923 19.682 468 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 0.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Rotamer: Outliers : 2.53 % Allowed : 14.39 % Favored : 83.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (0.36), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.09 (0.27), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 329 PHE 0.010 0.001 PHE D 378 TYR 0.007 0.001 TYR D 310 ARG 0.004 0.000 ARG F 349 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 95 time to evaluate : 0.526 Fit side-chains REVERT: A 338 GLU cc_start: 0.7996 (OUTLIER) cc_final: 0.7500 (mp0) REVERT: A 347 LYS cc_start: 0.8549 (ttpt) cc_final: 0.8307 (mptt) REVERT: A 349 ARG cc_start: 0.7825 (mtt180) cc_final: 0.7465 (mtt180) REVERT: B 349 ARG cc_start: 0.8249 (mtt180) cc_final: 0.6580 (mmp80) REVERT: C 338 GLU cc_start: 0.8056 (OUTLIER) cc_final: 0.7525 (mp0) REVERT: C 349 ARG cc_start: 0.8211 (mtt180) cc_final: 0.6530 (mmp-170) REVERT: D 338 GLU cc_start: 0.7989 (OUTLIER) cc_final: 0.7739 (mp0) REVERT: D 348 ASP cc_start: 0.8391 (t70) cc_final: 0.8144 (t0) REVERT: D 349 ARG cc_start: 0.7536 (mtt180) cc_final: 0.6402 (pmt-80) REVERT: E 338 GLU cc_start: 0.7996 (OUTLIER) cc_final: 0.7630 (mp0) REVERT: E 340 LYS cc_start: 0.8601 (ptpp) cc_final: 0.8355 (ptpt) REVERT: E 348 ASP cc_start: 0.8417 (t70) cc_final: 0.8148 (t0) REVERT: E 349 ARG cc_start: 0.7376 (mtt180) cc_final: 0.6368 (pmt-80) outliers start: 10 outliers final: 0 residues processed: 96 average time/residue: 3.1723 time to fit residues: 311.4146 Evaluate side-chains 71 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 67 time to evaluate : 0.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain C residue 338 GLU Chi-restraints excluded: chain D residue 338 GLU Chi-restraints excluded: chain E residue 338 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 17 optimal weight: 5.9990 chunk 10 optimal weight: 7.9990 chunk 28 optimal weight: 0.0980 chunk 21 optimal weight: 5.9990 chunk 5 optimal weight: 0.9990 chunk 11 optimal weight: 5.9990 chunk 15 optimal weight: 7.9990 chunk 39 optimal weight: 2.9990 chunk 9 optimal weight: 4.9990 chunk 34 optimal weight: 6.9990 chunk 0 optimal weight: 0.6980 overall best weight: 1.9586 ------------------------------------------------------------------------------- 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 = 0.3959 r_free = 0.3959 target = 0.125562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.116070 restraints weight = 14395.503| |-----------------------------------------------------------------------------| r_work (start): 0.3836 rms_B_bonded: 1.60 r_work: 0.3772 rms_B_bonded: 1.62 restraints_weight: 0.5000 r_work: 0.3697 rms_B_bonded: 2.83 restraints_weight: 0.2500 r_work (final): 0.3697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8778 moved from start: 0.5148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3522 Z= 0.209 Angle : 0.500 3.797 4710 Z= 0.251 Chirality : 0.051 0.137 528 Planarity : 0.002 0.015 600 Dihedral : 4.965 17.039 468 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 0.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 3.79 % Allowed : 16.16 % Favored : 80.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.40 (0.36), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.06 (0.27), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 329 PHE 0.009 0.001 PHE B 378 TYR 0.007 0.001 TYR D 310 ARG 0.003 0.000 ARG A 349 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 69 time to evaluate : 0.546 Fit side-chains REVERT: F 349 ARG cc_start: 0.7991 (OUTLIER) cc_final: 0.7736 (mtt180) REVERT: A 338 GLU cc_start: 0.8006 (OUTLIER) cc_final: 0.7602 (mp0) REVERT: A 349 ARG cc_start: 0.7923 (mtt180) cc_final: 0.7608 (mtt180) REVERT: B 349 ARG cc_start: 0.8285 (mtt180) cc_final: 0.6697 (mmp-170) REVERT: C 338 GLU cc_start: 0.8043 (OUTLIER) cc_final: 0.7535 (mp0) REVERT: C 349 ARG cc_start: 0.8240 (mtt180) cc_final: 0.6608 (mmp-170) REVERT: D 338 GLU cc_start: 0.7980 (OUTLIER) cc_final: 0.7757 (mp0) REVERT: D 348 ASP cc_start: 0.8457 (t70) cc_final: 0.8234 (t0) REVERT: D 349 ARG cc_start: 0.7783 (mtt180) cc_final: 0.6538 (pmt-80) REVERT: E 338 GLU cc_start: 0.7967 (OUTLIER) cc_final: 0.7250 (mp0) REVERT: E 348 ASP cc_start: 0.8455 (t70) cc_final: 0.8206 (t0) REVERT: E 349 ARG cc_start: 0.7665 (mtt180) cc_final: 0.6448 (pmt-80) outliers start: 15 outliers final: 3 residues processed: 73 average time/residue: 2.8891 time to fit residues: 216.4441 Evaluate side-chains 72 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 64 time to evaluate : 0.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 311 LYS Chi-restraints excluded: chain F residue 349 ARG Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain C residue 338 GLU Chi-restraints excluded: chain D residue 338 GLU Chi-restraints excluded: chain E residue 311 LYS Chi-restraints excluded: chain E residue 324 SER Chi-restraints excluded: chain E residue 338 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 1 optimal weight: 7.9990 chunk 24 optimal weight: 5.9990 chunk 31 optimal weight: 5.9990 chunk 21 optimal weight: 0.8980 chunk 11 optimal weight: 7.9990 chunk 20 optimal weight: 1.9990 chunk 40 optimal weight: 5.9990 chunk 10 optimal weight: 0.9990 chunk 39 optimal weight: 0.9990 chunk 14 optimal weight: 3.9990 chunk 28 optimal weight: 4.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- 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 = 0.3966 r_free = 0.3966 target = 0.126453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.116202 restraints weight = 12634.997| |-----------------------------------------------------------------------------| r_work (start): 0.3836 rms_B_bonded: 1.58 r_work: 0.3758 rms_B_bonded: 1.62 restraints_weight: 0.5000 r_work: 0.3672 rms_B_bonded: 2.86 restraints_weight: 0.2500 r_work (final): 0.3672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8773 moved from start: 0.5397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 3522 Z= 0.186 Angle : 0.478 3.455 4710 Z= 0.238 Chirality : 0.051 0.133 528 Planarity : 0.002 0.013 600 Dihedral : 4.633 15.844 468 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 0.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 3.03 % Allowed : 17.17 % Favored : 79.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.35 (0.36), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.02 (0.28), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS B 329 PHE 0.008 0.001 PHE B 378 TYR 0.006 0.001 TYR D 310 ARG 0.003 0.000 ARG A 349 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 68 time to evaluate : 0.567 Fit side-chains REVERT: A 338 GLU cc_start: 0.8064 (OUTLIER) cc_final: 0.7673 (mp0) REVERT: A 349 ARG cc_start: 0.7949 (mtt180) cc_final: 0.7642 (mtt180) REVERT: B 349 ARG cc_start: 0.8361 (mtt180) cc_final: 0.6718 (mmp-170) REVERT: C 338 GLU cc_start: 0.8064 (OUTLIER) cc_final: 0.7632 (mp0) REVERT: C 349 ARG cc_start: 0.8233 (mtt180) cc_final: 0.6630 (mmp-170) REVERT: D 338 GLU cc_start: 0.7965 (OUTLIER) cc_final: 0.7763 (mp0) REVERT: D 348 ASP cc_start: 0.8422 (t70) cc_final: 0.8218 (t0) REVERT: D 349 ARG cc_start: 0.7795 (mtt180) cc_final: 0.6487 (pmt-80) REVERT: E 311 LYS cc_start: 0.9025 (OUTLIER) cc_final: 0.8706 (ptmt) REVERT: E 348 ASP cc_start: 0.8446 (t70) cc_final: 0.8201 (t0) REVERT: E 349 ARG cc_start: 0.7744 (mtt180) cc_final: 0.6394 (pmt-80) outliers start: 12 outliers final: 1 residues processed: 72 average time/residue: 2.8073 time to fit residues: 207.6007 Evaluate side-chains 68 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 63 time to evaluate : 0.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain C residue 338 GLU Chi-restraints excluded: chain D residue 338 GLU Chi-restraints excluded: chain E residue 311 LYS Chi-restraints excluded: chain E residue 324 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 12 optimal weight: 2.9990 chunk 13 optimal weight: 5.9990 chunk 30 optimal weight: 0.0170 chunk 25 optimal weight: 5.9990 chunk 26 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 chunk 20 optimal weight: 2.9990 chunk 5 optimal weight: 6.9990 chunk 3 optimal weight: 6.9990 chunk 15 optimal weight: 2.9990 overall best weight: 1.5824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 351 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.126848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.116661 restraints weight = 12529.834| |-----------------------------------------------------------------------------| r_work (start): 0.3848 rms_B_bonded: 1.57 r_work: 0.3771 rms_B_bonded: 1.61 restraints_weight: 0.5000 r_work: 0.3683 rms_B_bonded: 2.85 restraints_weight: 0.2500 r_work (final): 0.3683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8771 moved from start: 0.5505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 3522 Z= 0.174 Angle : 0.465 3.497 4710 Z= 0.231 Chirality : 0.051 0.128 528 Planarity : 0.002 0.013 600 Dihedral : 4.377 14.832 468 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 0.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 2.53 % Allowed : 17.42 % Favored : 80.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.33 (0.37), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.01 (0.28), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS B 329 PHE 0.006 0.001 PHE D 378 TYR 0.005 0.001 TYR A 310 ARG 0.002 0.000 ARG B 379 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 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: 10 poor density : 59 time to evaluate : 0.580 Fit side-chains REVERT: F 345 ASP cc_start: 0.8494 (m-30) cc_final: 0.8292 (m-30) REVERT: A 349 ARG cc_start: 0.7957 (mtt180) cc_final: 0.7624 (mtt180) REVERT: B 349 ARG cc_start: 0.8349 (mtt180) cc_final: 0.6736 (mmp80) REVERT: C 338 GLU cc_start: 0.8077 (OUTLIER) cc_final: 0.7854 (mp0) REVERT: C 349 ARG cc_start: 0.8232 (mtt180) cc_final: 0.6708 (mmp-170) REVERT: D 338 GLU cc_start: 0.7994 (OUTLIER) cc_final: 0.7774 (mp0) REVERT: D 348 ASP cc_start: 0.8447 (t70) cc_final: 0.8128 (t0) REVERT: D 349 ARG cc_start: 0.7876 (mtt180) cc_final: 0.6382 (pmt-80) REVERT: E 311 LYS cc_start: 0.9014 (OUTLIER) cc_final: 0.8653 (ptmt) REVERT: E 348 ASP cc_start: 0.8445 (t70) cc_final: 0.8199 (t0) REVERT: E 349 ARG cc_start: 0.7794 (mtt180) cc_final: 0.6422 (pmt-80) outliers start: 10 outliers final: 4 residues processed: 64 average time/residue: 2.8435 time to fit residues: 186.8718 Evaluate side-chains 63 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 56 time to evaluate : 0.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 311 LYS Chi-restraints excluded: chain B residue 341 SER Chi-restraints excluded: chain C residue 338 GLU Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain D residue 338 GLU Chi-restraints excluded: chain E residue 311 LYS Chi-restraints excluded: chain E residue 324 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 18 optimal weight: 4.9990 chunk 16 optimal weight: 0.0970 chunk 30 optimal weight: 3.9990 chunk 36 optimal weight: 0.5980 chunk 4 optimal weight: 3.9990 chunk 24 optimal weight: 5.9990 chunk 37 optimal weight: 2.9990 chunk 7 optimal weight: 5.9990 chunk 20 optimal weight: 3.9990 chunk 32 optimal weight: 0.9990 chunk 5 optimal weight: 3.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 351 GLN B 351 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.125920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 23)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.115740 restraints weight = 12548.174| |-----------------------------------------------------------------------------| r_work (start): 0.3836 rms_B_bonded: 1.56 r_work: 0.3758 rms_B_bonded: 1.60 restraints_weight: 0.5000 r_work: 0.3670 rms_B_bonded: 2.83 restraints_weight: 0.2500 r_work (final): 0.3670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8777 moved from start: 0.5627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 3522 Z= 0.183 Angle : 0.463 3.470 4710 Z= 0.230 Chirality : 0.050 0.130 528 Planarity : 0.002 0.013 600 Dihedral : 4.259 13.906 468 Min Nonbonded Distance : 2.632 Molprobity Statistics. All-atom Clashscore : 0.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 2.53 % Allowed : 16.41 % Favored : 81.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.36 (0.37), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.02 (0.28), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS C 329 PHE 0.006 0.001 PHE D 378 TYR 0.005 0.001 TYR A 310 ARG 0.002 0.000 ARG D 349 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 57 time to evaluate : 0.617 Fit side-chains REVERT: F 345 ASP cc_start: 0.8485 (m-30) cc_final: 0.8278 (m-30) REVERT: A 338 GLU cc_start: 0.8013 (OUTLIER) cc_final: 0.7614 (mp0) REVERT: A 349 ARG cc_start: 0.7965 (mtt180) cc_final: 0.7661 (mtt180) REVERT: B 349 ARG cc_start: 0.8381 (mtt180) cc_final: 0.6749 (mmp-170) REVERT: C 349 ARG cc_start: 0.8238 (mtt180) cc_final: 0.6762 (mmp-170) REVERT: D 338 GLU cc_start: 0.7947 (OUTLIER) cc_final: 0.7633 (mp0) REVERT: D 348 ASP cc_start: 0.8454 (t70) cc_final: 0.8126 (t0) REVERT: D 349 ARG cc_start: 0.7942 (mtt180) cc_final: 0.6405 (pmt-80) REVERT: E 311 LYS cc_start: 0.9017 (OUTLIER) cc_final: 0.8640 (ptmt) REVERT: E 348 ASP cc_start: 0.8440 (t70) cc_final: 0.8188 (t0) REVERT: E 349 ARG cc_start: 0.7933 (mtt180) cc_final: 0.6405 (pmt-80) outliers start: 10 outliers final: 4 residues processed: 61 average time/residue: 2.7184 time to fit residues: 170.5411 Evaluate side-chains 63 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 56 time to evaluate : 0.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 311 LYS Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain B residue 341 SER Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain D residue 338 GLU Chi-restraints excluded: chain E residue 311 LYS Chi-restraints excluded: chain E residue 324 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 36 optimal weight: 5.9990 chunk 4 optimal weight: 7.9990 chunk 27 optimal weight: 4.9990 chunk 8 optimal weight: 1.9990 chunk 39 optimal weight: 5.9990 chunk 22 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 13 optimal weight: 0.9990 chunk 15 optimal weight: 0.8980 chunk 2 optimal weight: 3.9990 chunk 23 optimal weight: 3.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- 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 = 0.3954 r_free = 0.3954 target = 0.124989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.114914 restraints weight = 12473.676| |-----------------------------------------------------------------------------| r_work (start): 0.3821 rms_B_bonded: 1.55 r_work: 0.3743 rms_B_bonded: 1.59 restraints_weight: 0.5000 r_work: 0.3656 rms_B_bonded: 2.81 restraints_weight: 0.2500 r_work (final): 0.3656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8783 moved from start: 0.5661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 3522 Z= 0.199 Angle : 0.467 3.572 4710 Z= 0.232 Chirality : 0.050 0.131 528 Planarity : 0.002 0.013 600 Dihedral : 4.249 13.450 468 Min Nonbonded Distance : 2.637 Molprobity Statistics. All-atom Clashscore : 0.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 2.02 % Allowed : 17.17 % Favored : 80.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.40 (0.37), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.06 (0.28), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS B 329 PHE 0.007 0.001 PHE D 378 TYR 0.005 0.001 TYR A 310 ARG 0.002 0.000 ARG B 379 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 59 time to evaluate : 0.690 Fit side-chains revert: symmetry clash REVERT: F 345 ASP cc_start: 0.8471 (m-30) cc_final: 0.8253 (m-30) REVERT: B 349 ARG cc_start: 0.8392 (mtt180) cc_final: 0.6734 (mmp-170) REVERT: C 349 ARG cc_start: 0.8274 (mtt180) cc_final: 0.6755 (mmp-170) REVERT: D 348 ASP cc_start: 0.8443 (t70) cc_final: 0.8112 (t0) REVERT: D 349 ARG cc_start: 0.8061 (mtt180) cc_final: 0.6452 (pmt-80) REVERT: E 338 GLU cc_start: 0.8016 (OUTLIER) cc_final: 0.7294 (mp0) REVERT: E 349 ARG cc_start: 0.8034 (mtt180) cc_final: 0.6494 (pmt-80) outliers start: 8 outliers final: 4 residues processed: 63 average time/residue: 2.7877 time to fit residues: 180.4016 Evaluate side-chains 62 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 57 time to evaluate : 0.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 311 LYS Chi-restraints excluded: chain B residue 341 SER Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain E residue 324 SER Chi-restraints excluded: chain E residue 338 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 14 optimal weight: 0.2980 chunk 33 optimal weight: 5.9990 chunk 4 optimal weight: 6.9990 chunk 15 optimal weight: 3.9990 chunk 30 optimal weight: 0.9980 chunk 11 optimal weight: 6.9990 chunk 2 optimal weight: 0.3980 chunk 1 optimal weight: 3.9990 chunk 29 optimal weight: 0.8980 chunk 3 optimal weight: 0.5980 chunk 13 optimal weight: 4.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 351 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.129143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.119128 restraints weight = 12307.750| |-----------------------------------------------------------------------------| r_work (start): 0.3885 rms_B_bonded: 1.54 r_work: 0.3811 rms_B_bonded: 1.58 restraints_weight: 0.5000 r_work: 0.3726 rms_B_bonded: 2.81 restraints_weight: 0.2500 r_work (final): 0.3726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8752 moved from start: 0.5803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 3522 Z= 0.120 Angle : 0.443 3.392 4710 Z= 0.220 Chirality : 0.051 0.125 528 Planarity : 0.002 0.013 600 Dihedral : 3.919 12.378 468 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 0.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 0.76 % Allowed : 18.18 % Favored : 81.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.35 (0.38), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.02 (0.29), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 374 PHE 0.005 0.001 PHE D 378 TYR 0.005 0.001 TYR A 310 ARG 0.004 0.000 ARG C 349 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 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: 3 poor density : 62 time to evaluate : 0.593 Fit side-chains revert: symmetry clash REVERT: F 345 ASP cc_start: 0.8468 (m-30) cc_final: 0.8260 (m-30) REVERT: B 338 GLU cc_start: 0.7406 (mp0) cc_final: 0.7073 (mt-10) REVERT: B 349 ARG cc_start: 0.8305 (mtt180) cc_final: 0.6728 (mmp-170) REVERT: C 349 ARG cc_start: 0.8206 (mtt180) cc_final: 0.6621 (mmp-170) REVERT: D 348 ASP cc_start: 0.8432 (t70) cc_final: 0.8124 (t0) REVERT: D 349 ARG cc_start: 0.8108 (mtt180) cc_final: 0.6457 (pmt-80) REVERT: E 348 ASP cc_start: 0.8285 (t70) cc_final: 0.8083 (t0) REVERT: E 349 ARG cc_start: 0.8026 (mtt180) cc_final: 0.6501 (pmt-80) outliers start: 3 outliers final: 3 residues processed: 64 average time/residue: 2.7051 time to fit residues: 178.4710 Evaluate side-chains 61 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 58 time to evaluate : 0.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 311 LYS Chi-restraints excluded: chain B residue 341 SER Chi-restraints excluded: chain D residue 324 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 10 optimal weight: 6.9990 chunk 7 optimal weight: 6.9990 chunk 6 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 9 optimal weight: 5.9990 chunk 18 optimal weight: 1.9990 chunk 2 optimal weight: 4.9990 chunk 12 optimal weight: 0.7980 chunk 27 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 307 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.126033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.115899 restraints weight = 12733.914| |-----------------------------------------------------------------------------| r_work (start): 0.3837 rms_B_bonded: 1.58 r_work: 0.3759 rms_B_bonded: 1.62 restraints_weight: 0.5000 r_work: 0.3672 rms_B_bonded: 2.85 restraints_weight: 0.2500 r_work (final): 0.3672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8780 moved from start: 0.5775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 3522 Z= 0.184 Angle : 0.458 3.403 4710 Z= 0.227 Chirality : 0.050 0.131 528 Planarity : 0.002 0.013 600 Dihedral : 4.006 12.621 468 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 0.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 0.76 % Allowed : 17.42 % Favored : 81.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.35 (0.37), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.02 (0.29), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS E 329 PHE 0.006 0.001 PHE D 378 TYR 0.005 0.001 TYR A 310 ARG 0.001 0.000 ARG B 379 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 59 time to evaluate : 0.626 Fit side-chains revert: symmetry clash REVERT: F 345 ASP cc_start: 0.8483 (m-30) cc_final: 0.8255 (m-30) REVERT: B 338 GLU cc_start: 0.7425 (mp0) cc_final: 0.7096 (mt-10) REVERT: B 349 ARG cc_start: 0.8390 (mtt180) cc_final: 0.6746 (mmp-170) REVERT: C 349 ARG cc_start: 0.8228 (mtt180) cc_final: 0.6713 (mmp-170) REVERT: D 348 ASP cc_start: 0.8437 (t70) cc_final: 0.8204 (t0) REVERT: D 349 ARG cc_start: 0.8155 (mtt180) cc_final: 0.6485 (pmt-80) REVERT: E 349 ARG cc_start: 0.8106 (mtt180) cc_final: 0.6425 (pmt-80) outliers start: 3 outliers final: 3 residues processed: 61 average time/residue: 2.7888 time to fit residues: 174.9407 Evaluate side-chains 60 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 57 time to evaluate : 0.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 311 LYS Chi-restraints excluded: chain B residue 341 SER Chi-restraints excluded: chain D residue 324 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 18 optimal weight: 2.9990 chunk 12 optimal weight: 5.9990 chunk 13 optimal weight: 7.9990 chunk 35 optimal weight: 4.9990 chunk 37 optimal weight: 4.9990 chunk 5 optimal weight: 4.9990 chunk 14 optimal weight: 0.6980 chunk 11 optimal weight: 4.9990 chunk 16 optimal weight: 0.2980 chunk 39 optimal weight: 2.9990 chunk 8 optimal weight: 5.9990 overall best weight: 2.3986 ------------------------------------------------------------------------------- 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 = 0.3969 r_free = 0.3969 target = 0.126153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.116342 restraints weight = 13431.495| |-----------------------------------------------------------------------------| r_work (start): 0.3804 rms_B_bonded: 1.61 r_work: 0.3726 rms_B_bonded: 1.61 restraints_weight: 0.5000 r_work: 0.3635 rms_B_bonded: 2.87 restraints_weight: 0.2500 r_work (final): 0.3635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8799 moved from start: 0.5792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3522 Z= 0.229 Angle : 0.486 3.845 4710 Z= 0.244 Chirality : 0.050 0.136 528 Planarity : 0.002 0.013 600 Dihedral : 4.177 12.952 468 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 0.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Rotamer: Outliers : 1.01 % Allowed : 16.92 % Favored : 82.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.40 (0.37), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.06 (0.28), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 329 PHE 0.007 0.001 PHE D 378 TYR 0.005 0.001 TYR A 310 ARG 0.001 0.000 ARG B 379 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 58 time to evaluate : 0.566 Fit side-chains revert: symmetry clash REVERT: F 345 ASP cc_start: 0.8484 (m-30) cc_final: 0.8255 (m-30) REVERT: B 338 GLU cc_start: 0.7458 (mp0) cc_final: 0.7155 (mt-10) REVERT: B 349 ARG cc_start: 0.8430 (mtt180) cc_final: 0.6724 (mmp-170) REVERT: C 349 ARG cc_start: 0.8286 (mtt180) cc_final: 0.6824 (mmp-170) REVERT: D 348 ASP cc_start: 0.8430 (t70) cc_final: 0.8100 (t0) REVERT: D 349 ARG cc_start: 0.8242 (mtt180) cc_final: 0.6435 (pmt-80) REVERT: E 349 ARG cc_start: 0.8173 (mtt180) cc_final: 0.6408 (pmt-80) outliers start: 4 outliers final: 3 residues processed: 61 average time/residue: 2.6473 time to fit residues: 166.2560 Evaluate side-chains 61 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 58 time to evaluate : 0.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 311 LYS Chi-restraints excluded: chain B residue 341 SER Chi-restraints excluded: chain D residue 324 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 18 optimal weight: 0.0870 chunk 11 optimal weight: 6.9990 chunk 24 optimal weight: 5.9990 chunk 20 optimal weight: 3.9990 chunk 1 optimal weight: 8.9990 chunk 16 optimal weight: 4.9990 chunk 41 optimal weight: 3.9990 chunk 10 optimal weight: 0.9980 chunk 0 optimal weight: 4.9990 chunk 4 optimal weight: 0.8980 chunk 19 optimal weight: 0.6980 overall best weight: 1.3360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 351 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.126005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.115930 restraints weight = 12645.965| |-----------------------------------------------------------------------------| r_work (start): 0.3835 rms_B_bonded: 1.58 r_work: 0.3759 rms_B_bonded: 1.60 restraints_weight: 0.5000 r_work: 0.3671 rms_B_bonded: 2.85 restraints_weight: 0.2500 r_work (final): 0.3671 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8777 moved from start: 0.5856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 3522 Z= 0.152 Angle : 0.466 3.604 4710 Z= 0.234 Chirality : 0.050 0.125 528 Planarity : 0.002 0.016 600 Dihedral : 3.990 12.467 468 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 0.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 0.76 % Allowed : 17.17 % Favored : 82.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.41 (0.37), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.07 (0.29), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS C 329 PHE 0.005 0.001 PHE D 378 TYR 0.005 0.001 TYR A 310 ARG 0.002 0.000 ARG B 379 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6322.04 seconds wall clock time: 111 minutes 49.45 seconds (6709.45 seconds total)