Starting phenix.real_space_refine on Fri Jun 6 02:52:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7r4t_14316/06_2025/7r4t_14316.cif Found real_map, /net/cci-nas-00/data/ceres_data/7r4t_14316/06_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_14316/06_2025/7r4t_14316.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7r4t_14316/06_2025/7r4t_14316.map" model { file = "/net/cci-nas-00/data/ceres_data/7r4t_14316/06_2025/7r4t_14316.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7r4t_14316/06_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-5710/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: 5.06, per 1000 atoms: 0.72 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: 1.80 Conformation dependent library (CDL) restraints added in 713.4 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: 0.79 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: 2.30 Time building geometry restraints manager: 2.21 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: 5.570 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: 0.310 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 21.090 Find NCS groups from input model: 0.190 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:15.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.480 ------------------------------------------------------------------------------- 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= 0.658 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 Details of bonding type rmsd hydrogen bonds : bond 0.07107 ( 74) hydrogen bonds : angle 8.06672 ( 222) covalent geometry : bond 0.01059 ( 3522) covalent geometry : angle 1.77467 ( 4710) *********************** 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 : 0.609 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: 3.0086 time to fit residues: 418.3727 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 : 0.654 ------------------------------------------------------------------------------- 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: 2.9990 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 = 34)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.122836 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: 0.3710 rms_B_bonded: 2.89 restraints_weight: 0.2500 r_work (final): 0.3710 ------------------------------------------------------------------------------- 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= 0.126 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 Details of bonding type rmsd hydrogen bonds : bond 0.02730 ( 74) hydrogen bonds : angle 5.70979 ( 222) covalent geometry : bond 0.00297 ( 3522) covalent geometry : angle 0.56494 ( 4710) *********************** 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 : 0.613 Fit side-chains REVERT: A 338 GLU cc_start: 0.8002 (OUTLIER) cc_final: 0.7506 (mp0) REVERT: A 347 LYS cc_start: 0.8549 (ttpt) cc_final: 0.8310 (mptt) REVERT: A 349 ARG cc_start: 0.7826 (mtt180) cc_final: 0.7468 (mtt180) REVERT: B 349 ARG cc_start: 0.8250 (mtt180) cc_final: 0.6584 (mmp80) REVERT: C 338 GLU cc_start: 0.8060 (OUTLIER) cc_final: 0.7530 (mp0) REVERT: C 349 ARG cc_start: 0.8212 (mtt180) cc_final: 0.6535 (mmp-170) REVERT: D 338 GLU cc_start: 0.7993 (OUTLIER) cc_final: 0.7742 (mp0) REVERT: D 348 ASP cc_start: 0.8389 (t70) cc_final: 0.8144 (t0) REVERT: D 349 ARG cc_start: 0.7538 (mtt180) cc_final: 0.6405 (pmt-80) REVERT: E 338 GLU cc_start: 0.8002 (OUTLIER) cc_final: 0.7635 (mp0) REVERT: E 340 LYS cc_start: 0.8602 (ptpp) cc_final: 0.8355 (ptpt) REVERT: E 348 ASP cc_start: 0.8417 (t70) cc_final: 0.8149 (t0) REVERT: E 349 ARG cc_start: 0.7379 (mtt180) cc_final: 0.6372 (pmt-80) outliers start: 10 outliers final: 0 residues processed: 96 average time/residue: 3.0018 time to fit residues: 294.7108 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 : 0.580 ------------------------------------------------------------------------------- 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: 4.9990 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: 5.9990 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 = 0.125572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 23)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.116057 restraints weight = 14399.875| |-----------------------------------------------------------------------------| r_work (start): 0.3827 rms_B_bonded: 1.61 r_work: 0.3764 rms_B_bonded: 1.61 restraints_weight: 0.5000 r_work: 0.3688 rms_B_bonded: 2.84 restraints_weight: 0.2500 r_work (final): 0.3688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8777 moved from start: 0.5127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3522 Z= 0.138 Angle : 0.500 3.845 4710 Z= 0.250 Chirality : 0.051 0.137 528 Planarity : 0.002 0.015 600 Dihedral : 5.005 17.196 468 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 0.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 3.28 % Allowed : 16.67 % 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 0.006 0.001 TYR D 310 ARG 0.003 0.000 ARG A 349 Details of bonding type rmsd hydrogen bonds : bond 0.02026 ( 74) hydrogen bonds : angle 4.97098 ( 222) covalent geometry : bond 0.00319 ( 3522) covalent geometry : angle 0.50023 ( 4710) *********************** 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 81 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 68 time to evaluate : 0.598 Fit side-chains REVERT: F 349 ARG cc_start: 0.7983 (OUTLIER) cc_final: 0.7716 (mtt180) REVERT: A 338 GLU cc_start: 0.7992 (OUTLIER) cc_final: 0.7586 (mp0) REVERT: A 349 ARG cc_start: 0.7919 (mtt180) cc_final: 0.7601 (mtt180) REVERT: B 349 ARG cc_start: 0.8277 (mtt180) cc_final: 0.6684 (mmp-170) REVERT: C 338 GLU cc_start: 0.8040 (OUTLIER) cc_final: 0.7537 (mp0) REVERT: C 349 ARG cc_start: 0.8241 (mtt180) cc_final: 0.6604 (mmp-170) REVERT: D 338 GLU cc_start: 0.7983 (OUTLIER) cc_final: 0.7755 (mp0) REVERT: D 348 ASP cc_start: 0.8445 (t70) cc_final: 0.8226 (t0) REVERT: D 349 ARG cc_start: 0.7768 (mtt180) cc_final: 0.6523 (pmt-80) REVERT: E 338 GLU cc_start: 0.7974 (OUTLIER) cc_final: 0.7250 (mp0) REVERT: E 348 ASP cc_start: 0.8475 (t70) cc_final: 0.8239 (t0) REVERT: E 349 ARG cc_start: 0.7652 (mtt180) cc_final: 0.6451 (pmt-80) outliers start: 13 outliers final: 3 residues processed: 70 average time/residue: 2.7190 time to fit residues: 195.6272 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 : 0.647 ------------------------------------------------------------------------------- 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: 0.6980 chunk 11 optimal weight: 7.9990 chunk 20 optimal weight: 1.9990 chunk 40 optimal weight: 5.9990 chunk 10 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 chunk 14 optimal weight: 3.9990 chunk 28 optimal weight: 0.0970 overall best weight: 1.1584 ------------------------------------------------------------------------------- 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 = 0.3995 r_free = 0.3995 target = 0.128540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.118324 restraints weight = 12462.189| |-----------------------------------------------------------------------------| r_work (start): 0.3867 rms_B_bonded: 1.58 r_work: 0.3793 rms_B_bonded: 1.61 restraints_weight: 0.5000 r_work: 0.3705 rms_B_bonded: 2.86 restraints_weight: 0.2500 r_work (final): 0.3705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8756 moved from start: 0.5374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 3522 Z= 0.094 Angle : 0.458 3.452 4710 Z= 0.228 Chirality : 0.051 0.128 528 Planarity : 0.002 0.014 600 Dihedral : 4.498 15.440 468 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 0.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 3.03 % Allowed : 16.41 % Favored : 80.56 % 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 0.001 0.000 HIS E 374 PHE 0.008 0.001 PHE B 378 TYR 0.006 0.001 TYR D 310 ARG 0.002 0.000 ARG A 349 Details of bonding type rmsd hydrogen bonds : bond 0.01657 ( 74) hydrogen bonds : angle 4.48142 ( 222) covalent geometry : bond 0.00226 ( 3522) covalent geometry : angle 0.45840 ( 4710) *********************** 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 82 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 70 time to evaluate : 0.597 Fit side-chains REVERT: F 348 ASP cc_start: 0.8477 (t70) cc_final: 0.8210 (t0) REVERT: A 338 GLU cc_start: 0.8026 (OUTLIER) cc_final: 0.7663 (mp0) REVERT: A 349 ARG cc_start: 0.7931 (mtt180) cc_final: 0.7587 (mtt180) REVERT: B 349 ARG cc_start: 0.8330 (mtt180) cc_final: 0.6719 (mmp-170) REVERT: C 338 GLU cc_start: 0.8072 (OUTLIER) cc_final: 0.7711 (mp0) REVERT: C 349 ARG cc_start: 0.8247 (mtt180) cc_final: 0.6586 (mmp-170) REVERT: D 348 ASP cc_start: 0.8409 (t70) cc_final: 0.8201 (t0) REVERT: D 349 ARG cc_start: 0.7773 (mtt180) cc_final: 0.6514 (pmt-80) REVERT: E 311 LYS cc_start: 0.9029 (OUTLIER) cc_final: 0.8682 (ptmt) REVERT: E 314 ASP cc_start: 0.8952 (t0) cc_final: 0.8735 (t0) REVERT: E 348 ASP cc_start: 0.8420 (t70) cc_final: 0.8194 (t0) REVERT: E 349 ARG cc_start: 0.7711 (mtt180) cc_final: 0.6427 (pmt-80) outliers start: 12 outliers final: 1 residues processed: 75 average time/residue: 2.6157 time to fit residues: 201.5988 Evaluate side-chains 67 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 63 time to evaluate : 0.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain C 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: 3.9990 chunk 13 optimal weight: 7.9990 chunk 30 optimal weight: 0.9980 chunk 25 optimal weight: 5.9990 chunk 26 optimal weight: 6.9990 chunk 22 optimal weight: 3.9990 chunk 21 optimal weight: 0.5980 chunk 20 optimal weight: 5.9990 chunk 5 optimal weight: 6.9990 chunk 3 optimal weight: 5.9990 chunk 15 optimal weight: 4.9990 overall best weight: 2.9186 ------------------------------------------------------------------------------- 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 = 0.3935 r_free = 0.3935 target = 0.123708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.113433 restraints weight = 12724.078| |-----------------------------------------------------------------------------| r_work (start): 0.3803 rms_B_bonded: 1.58 r_work: 0.3726 rms_B_bonded: 1.60 restraints_weight: 0.5000 r_work: 0.3635 rms_B_bonded: 2.84 restraints_weight: 0.2500 r_work (final): 0.3635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8796 moved from start: 0.5508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 3522 Z= 0.189 Angle : 0.509 3.640 4710 Z= 0.254 Chirality : 0.051 0.142 528 Planarity : 0.002 0.013 600 Dihedral : 4.596 15.674 468 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 0.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 2.27 % Allowed : 17.68 % 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: -1.38 (0.36), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.04 (0.28), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 329 PHE 0.008 0.001 PHE D 378 TYR 0.005 0.001 TYR A 310 ARG 0.002 0.000 ARG E 349 Details of bonding type rmsd hydrogen bonds : bond 0.02152 ( 74) hydrogen bonds : angle 4.50473 ( 222) covalent geometry : bond 0.00432 ( 3522) covalent geometry : angle 0.50866 ( 4710) *********************** 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 70 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 61 time to evaluate : 0.651 Fit side-chains REVERT: F 345 ASP cc_start: 0.8497 (m-30) cc_final: 0.8292 (m-30) REVERT: F 348 ASP cc_start: 0.8456 (OUTLIER) cc_final: 0.8164 (t0) REVERT: B 349 ARG cc_start: 0.8382 (mtt180) cc_final: 0.6700 (mmp-170) REVERT: C 349 ARG cc_start: 0.8263 (mtt180) cc_final: 0.6707 (mmp80) REVERT: D 348 ASP cc_start: 0.8459 (t70) cc_final: 0.8212 (t0) REVERT: D 349 ARG cc_start: 0.7893 (mtt180) cc_final: 0.6448 (pmt-80) REVERT: E 311 LYS cc_start: 0.9030 (OUTLIER) cc_final: 0.8690 (ptmt) REVERT: E 349 ARG cc_start: 0.7868 (mtt180) cc_final: 0.6436 (pmt-80) outliers start: 9 outliers final: 3 residues processed: 67 average time/residue: 2.7277 time to fit residues: 187.6576 Evaluate side-chains 63 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 58 time to evaluate : 0.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 311 LYS Chi-restraints excluded: chain F residue 348 ASP Chi-restraints excluded: chain B residue 341 SER 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: 3.9990 chunk 30 optimal weight: 6.9990 chunk 36 optimal weight: 0.2980 chunk 4 optimal weight: 2.9990 chunk 24 optimal weight: 5.9990 chunk 37 optimal weight: 2.9990 chunk 7 optimal weight: 5.9990 chunk 20 optimal weight: 0.9990 chunk 32 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 overall best weight: 2.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 351 GLN A 351 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.124612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.114446 restraints weight = 12610.863| |-----------------------------------------------------------------------------| r_work (start): 0.3814 rms_B_bonded: 1.58 r_work: 0.3737 rms_B_bonded: 1.59 restraints_weight: 0.5000 r_work: 0.3646 rms_B_bonded: 2.83 restraints_weight: 0.2500 r_work (final): 0.3646 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8790 moved from start: 0.5629 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= 0.134 Angle : 0.479 3.568 4710 Z= 0.237 Chirality : 0.050 0.133 528 Planarity : 0.002 0.013 600 Dihedral : 4.382 14.328 468 Min Nonbonded Distance : 2.631 Molprobity Statistics. All-atom Clashscore : 0.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 2.27 % Allowed : 16.92 % 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: -1.43 (0.37), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.08 (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 0.002 0.000 ARG B 379 Details of bonding type rmsd hydrogen bonds : bond 0.01837 ( 74) hydrogen bonds : angle 4.25342 ( 222) covalent geometry : bond 0.00303 ( 3522) covalent geometry : angle 0.47874 ( 4710) *********************** 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: 9 poor density : 58 time to evaluate : 0.640 Fit side-chains REVERT: F 345 ASP cc_start: 0.8473 (m-30) cc_final: 0.8264 (m-30) REVERT: F 348 ASP cc_start: 0.8457 (OUTLIER) cc_final: 0.8163 (t0) REVERT: A 338 GLU cc_start: 0.8015 (OUTLIER) cc_final: 0.7624 (mp0) REVERT: B 349 ARG cc_start: 0.8391 (mtt180) cc_final: 0.6712 (mmp-170) REVERT: C 349 ARG cc_start: 0.8282 (mtt180) cc_final: 0.6666 (mmp-170) REVERT: D 348 ASP cc_start: 0.8452 (t70) cc_final: 0.8104 (t0) REVERT: D 349 ARG cc_start: 0.7958 (mtt180) cc_final: 0.6390 (pmt-80) REVERT: E 311 LYS cc_start: 0.9012 (OUTLIER) cc_final: 0.8639 (ptmt) REVERT: E 349 ARG cc_start: 0.7997 (mtt180) cc_final: 0.6454 (pmt-80) outliers start: 9 outliers final: 4 residues processed: 61 average time/residue: 2.6048 time to fit residues: 163.5320 Evaluate side-chains 65 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 58 time to evaluate : 0.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 311 LYS Chi-restraints excluded: chain F residue 348 ASP 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 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: 0.4980 chunk 4 optimal weight: 7.9990 chunk 27 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 39 optimal weight: 5.9990 chunk 22 optimal weight: 0.6980 chunk 11 optimal weight: 4.9990 chunk 13 optimal weight: 0.7980 chunk 15 optimal weight: 0.2980 chunk 2 optimal weight: 3.9990 chunk 23 optimal weight: 4.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- 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 = 0.4004 r_free = 0.4004 target = 0.128789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.118750 restraints weight = 12352.720| |-----------------------------------------------------------------------------| r_work (start): 0.3878 rms_B_bonded: 1.56 r_work: 0.3801 rms_B_bonded: 1.60 restraints_weight: 0.5000 r_work: 0.3715 rms_B_bonded: 2.84 restraints_weight: 0.2500 r_work (final): 0.3715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8758 moved from start: 0.5740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 3522 Z= 0.076 Angle : 0.443 3.395 4710 Z= 0.219 Chirality : 0.051 0.126 528 Planarity : 0.002 0.013 600 Dihedral : 4.023 13.280 468 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 0.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 1.52 % Allowed : 17.42 % 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: -1.39 (0.37), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.05 (0.28), 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 0.002 0.000 ARG B 379 Details of bonding type rmsd hydrogen bonds : bond 0.01340 ( 74) hydrogen bonds : angle 3.86358 ( 222) covalent geometry : bond 0.00185 ( 3522) covalent geometry : angle 0.44275 ( 4710) *********************** 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 65 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 59 time to evaluate : 0.595 Fit side-chains REVERT: F 345 ASP cc_start: 0.8466 (m-30) cc_final: 0.8260 (m-30) REVERT: F 348 ASP cc_start: 0.8404 (OUTLIER) cc_final: 0.8135 (t0) REVERT: B 338 GLU cc_start: 0.7417 (mp0) cc_final: 0.7095 (mt-10) REVERT: B 349 ARG cc_start: 0.8336 (mtt180) cc_final: 0.6750 (mmp-170) REVERT: C 349 ARG cc_start: 0.8245 (mtt180) cc_final: 0.6610 (mmp-170) REVERT: D 348 ASP cc_start: 0.8468 (t70) cc_final: 0.8216 (t0) REVERT: D 349 ARG cc_start: 0.7952 (mtt180) cc_final: 0.6481 (pmt-80) REVERT: E 338 GLU cc_start: 0.7989 (OUTLIER) cc_final: 0.7291 (mp0) REVERT: E 348 ASP cc_start: 0.8342 (t70) cc_final: 0.8034 (t0) REVERT: E 349 ARG cc_start: 0.7997 (mtt180) cc_final: 0.6455 (pmt-80) outliers start: 6 outliers final: 3 residues processed: 62 average time/residue: 2.7037 time to fit residues: 172.3202 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 : 0.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 311 LYS Chi-restraints excluded: chain F residue 348 ASP Chi-restraints excluded: chain B residue 341 SER Chi-restraints excluded: chain D 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: 2.9990 chunk 33 optimal weight: 0.1980 chunk 4 optimal weight: 7.9990 chunk 15 optimal weight: 3.9990 chunk 30 optimal weight: 0.7980 chunk 11 optimal weight: 7.9990 chunk 2 optimal weight: 0.8980 chunk 1 optimal weight: 0.9990 chunk 29 optimal weight: 2.9990 chunk 3 optimal weight: 0.9990 chunk 13 optimal weight: 6.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- 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 = 0.4010 r_free = 0.4010 target = 0.129173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.119154 restraints weight = 12302.038| |-----------------------------------------------------------------------------| r_work (start): 0.3884 rms_B_bonded: 1.55 r_work: 0.3808 rms_B_bonded: 1.60 restraints_weight: 0.5000 r_work: 0.3723 rms_B_bonded: 2.83 restraints_weight: 0.2500 r_work (final): 0.3723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8753 moved from start: 0.5812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 3522 Z= 0.079 Angle : 0.433 3.337 4710 Z= 0.212 Chirality : 0.050 0.125 528 Planarity : 0.002 0.015 600 Dihedral : 3.863 12.444 468 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 0.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 1.01 % Allowed : 17.93 % 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 (0.29), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS E 329 PHE 0.005 0.001 PHE D 378 TYR 0.004 0.001 TYR A 310 ARG 0.001 0.000 ARG F 379 Details of bonding type rmsd hydrogen bonds : bond 0.01362 ( 74) hydrogen bonds : angle 3.72658 ( 222) covalent geometry : bond 0.00193 ( 3522) covalent geometry : angle 0.43342 ( 4710) *********************** 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 66 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 62 time to evaluate : 0.614 Fit side-chains REVERT: F 348 ASP cc_start: 0.8382 (OUTLIER) cc_final: 0.8116 (t0) REVERT: B 338 GLU cc_start: 0.7402 (mp0) cc_final: 0.7077 (mt-10) REVERT: B 349 ARG cc_start: 0.8316 (mtt180) cc_final: 0.6735 (mmp-170) REVERT: B 372 GLU cc_start: 0.8155 (tt0) cc_final: 0.7934 (tt0) REVERT: C 349 ARG cc_start: 0.8207 (mtt180) cc_final: 0.6575 (mmp-170) REVERT: D 348 ASP cc_start: 0.8463 (t70) cc_final: 0.8158 (t0) REVERT: D 349 ARG cc_start: 0.8011 (mtt180) cc_final: 0.6437 (pmt-80) REVERT: E 349 ARG cc_start: 0.8030 (mtt180) cc_final: 0.6485 (pmt-80) REVERT: E 351 GLN cc_start: 0.8567 (tt0) cc_final: 0.8343 (tt0) outliers start: 4 outliers final: 3 residues processed: 64 average time/residue: 2.8546 time to fit residues: 189.1642 Evaluate side-chains 63 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 59 time to evaluate : 0.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 311 LYS Chi-restraints excluded: chain F residue 348 ASP Chi-restraints excluded: chain B residue 341 SER Chi-restraints excluded: chain E 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: 6.9990 chunk 19 optimal weight: 0.3980 chunk 31 optimal weight: 0.1980 chunk 9 optimal weight: 5.9990 chunk 18 optimal weight: 6.9990 chunk 2 optimal weight: 3.9990 chunk 12 optimal weight: 0.8980 chunk 27 optimal weight: 1.9990 chunk 28 optimal weight: 0.5980 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 = 0.4011 r_free = 0.4011 target = 0.129081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.119033 restraints weight = 12584.501| |-----------------------------------------------------------------------------| r_work (start): 0.3881 rms_B_bonded: 1.56 r_work: 0.3806 rms_B_bonded: 1.61 restraints_weight: 0.5000 r_work: 0.3720 rms_B_bonded: 2.85 restraints_weight: 0.2500 r_work (final): 0.3720 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8752 moved from start: 0.5848 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= 0.077 Angle : 0.433 3.330 4710 Z= 0.212 Chirality : 0.050 0.124 528 Planarity : 0.002 0.014 600 Dihedral : 3.766 12.012 468 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 0.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Rotamer: Outliers : 0.76 % Allowed : 17.93 % Favored : 81.31 % 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: -1.38 (0.37), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.04 (0.29), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS E 329 PHE 0.005 0.001 PHE D 378 TYR 0.005 0.001 TYR A 310 ARG 0.001 0.000 ARG B 379 Details of bonding type rmsd hydrogen bonds : bond 0.01320 ( 74) hydrogen bonds : angle 3.67584 ( 222) covalent geometry : bond 0.00190 ( 3522) covalent geometry : angle 0.43334 ( 4710) *********************** 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 65 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 62 time to evaluate : 0.963 Fit side-chains REVERT: F 348 ASP cc_start: 0.8360 (OUTLIER) cc_final: 0.8096 (t0) REVERT: B 338 GLU cc_start: 0.7418 (mp0) cc_final: 0.7077 (mt-10) REVERT: B 349 ARG cc_start: 0.8296 (mtt180) cc_final: 0.6721 (mmp-170) REVERT: C 349 ARG cc_start: 0.8194 (mtt180) cc_final: 0.6569 (mmp-170) REVERT: D 348 ASP cc_start: 0.8436 (t70) cc_final: 0.8126 (t0) REVERT: D 349 ARG cc_start: 0.8028 (mtt180) cc_final: 0.6444 (pmt-80) REVERT: E 349 ARG cc_start: 0.8073 (mtt180) cc_final: 0.6507 (pmt-80) REVERT: E 351 GLN cc_start: 0.8567 (tt0) cc_final: 0.8335 (tt0) outliers start: 3 outliers final: 2 residues processed: 64 average time/residue: 3.0616 time to fit residues: 202.2672 Evaluate side-chains 63 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 60 time to evaluate : 0.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 311 LYS Chi-restraints excluded: chain F residue 348 ASP Chi-restraints excluded: chain B residue 341 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 18 optimal weight: 6.9990 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: 0.5980 chunk 11 optimal weight: 5.9990 chunk 16 optimal weight: 0.0270 chunk 39 optimal weight: 2.9990 chunk 8 optimal weight: 5.9990 overall best weight: 2.7244 ------------------------------------------------------------------------------- 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 = 0.3936 r_free = 0.3936 target = 0.123770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.113529 restraints weight = 12941.534| |-----------------------------------------------------------------------------| r_work (start): 0.3798 rms_B_bonded: 1.59 r_work: 0.3720 rms_B_bonded: 1.62 restraints_weight: 0.5000 r_work: 0.3628 rms_B_bonded: 2.87 restraints_weight: 0.2500 r_work (final): 0.3628 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8798 moved from start: 0.5788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 3522 Z= 0.171 Angle : 0.487 3.486 4710 Z= 0.242 Chirality : 0.050 0.140 528 Planarity : 0.002 0.013 600 Dihedral : 4.181 13.138 468 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 1.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 1.01 % Allowed : 17.17 % 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: -1.40 (0.37), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.05 (0.28), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS E 329 PHE 0.008 0.001 PHE D 378 TYR 0.005 0.001 TYR A 310 ARG 0.002 0.000 ARG C 349 Details of bonding type rmsd hydrogen bonds : bond 0.01973 ( 74) hydrogen bonds : angle 4.02718 ( 222) covalent geometry : bond 0.00383 ( 3522) covalent geometry : angle 0.48683 ( 4710) ********************** 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 63 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 59 time to evaluate : 0.722 Fit side-chains REVERT: B 338 GLU cc_start: 0.7460 (mp0) cc_final: 0.7135 (mt-10) REVERT: B 349 ARG cc_start: 0.8420 (mtt180) cc_final: 0.6803 (mmp-170) REVERT: C 349 ARG cc_start: 0.8256 (mtt180) cc_final: 0.6730 (mmp-170) REVERT: D 348 ASP cc_start: 0.8427 (t70) cc_final: 0.8069 (t0) REVERT: D 349 ARG cc_start: 0.8126 (mtt180) cc_final: 0.6461 (pmt-80) REVERT: E 348 ASP cc_start: 0.8541 (t0) cc_final: 0.8278 (t70) REVERT: E 349 ARG cc_start: 0.8169 (mtt180) cc_final: 0.6411 (pmt-80) outliers start: 4 outliers final: 2 residues processed: 62 average time/residue: 2.9089 time to fit residues: 185.4817 Evaluate side-chains 59 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 57 time to evaluate : 0.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 311 LYS Chi-restraints excluded: chain B residue 341 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 18 optimal weight: 3.9990 chunk 11 optimal weight: 6.9990 chunk 24 optimal weight: 5.9990 chunk 20 optimal weight: 3.9990 chunk 1 optimal weight: 6.9990 chunk 16 optimal weight: 4.9990 chunk 41 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 0 optimal weight: 4.9990 chunk 4 optimal weight: 0.8980 chunk 19 optimal weight: 2.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 351 GLN C 351 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.124520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.114413 restraints weight = 12725.570| |-----------------------------------------------------------------------------| r_work (start): 0.3811 rms_B_bonded: 1.57 r_work: 0.3732 rms_B_bonded: 1.62 restraints_weight: 0.5000 r_work: 0.3643 rms_B_bonded: 2.84 restraints_weight: 0.2500 r_work (final): 0.3643 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8793 moved from start: 0.5831 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= 0.139 Angle : 0.470 3.530 4710 Z= 0.233 Chirality : 0.050 0.132 528 Planarity : 0.002 0.011 600 Dihedral : 4.123 12.909 468 Min Nonbonded Distance : 2.632 Molprobity Statistics. All-atom Clashscore : 0.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 1.01 % Allowed : 17.17 % 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: -1.44 (0.37), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.09 (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 0.002 0.000 ARG B 379 Details of bonding type rmsd hydrogen bonds : bond 0.01792 ( 74) hydrogen bonds : angle 3.97392 ( 222) covalent geometry : bond 0.00311 ( 3522) covalent geometry : angle 0.46987 ( 4710) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6800.26 seconds wall clock time: 117 minutes 52.54 seconds (7072.54 seconds total)