Starting phenix.real_space_refine on Thu Jun 5 14:49:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ql0_14059/06_2025/7ql0_14059.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ql0_14059/06_2025/7ql0_14059.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.13 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ql0_14059/06_2025/7ql0_14059.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ql0_14059/06_2025/7ql0_14059.map" model { file = "/net/cci-nas-00/data/ceres_data/7ql0_14059/06_2025/7ql0_14059.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ql0_14059/06_2025/7ql0_14059.cif" } resolution = 3.13 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 1956 2.51 5 N 576 2.21 5 O 594 1.98 5 H 3258 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 22 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: 6390 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 1065 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 1065 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 3, 'TRANS': 65} Chain: "c" Number of atoms: 1065 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 1065 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 3, 'TRANS': 65} Chain: "A" Number of atoms: 1065 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 1065 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 3, 'TRANS': 65} Chain: "C" Number of atoms: 1065 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 1065 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 3, 'TRANS': 65} Chain: "D" Number of atoms: 1065 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 1065 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 3, 'TRANS': 65} Chain: "E" Number of atoms: 1065 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 1065 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 3, 'TRANS': 65} Time building chain proxies: 4.21, per 1000 atoms: 0.66 Number of scatterers: 6390 At special positions: 0 Unit cell: (93.936, 127.72, 34.608, 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 594 8.00 N 576 7.00 C 1956 6.00 H 3258 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: 1.69 Conformation dependent library (CDL) restraints added in 471.7 milliseconds 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 720 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 16 sheets defined 0.0% alpha, 39.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.61 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'c' and resid 313 through 314 removed outlier: 6.878A pdb=" N VAL B 313 " --> pdb=" O ASP A 314 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'c' and resid 317 through 318 removed outlier: 6.340A pdb=" N LYS B 317 " --> pdb=" O VAL A 318 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'c' and resid 325 through 330 removed outlier: 6.273A pdb=" N GLY B 326 " --> pdb=" O ASN c 327 " (cutoff:3.500A) removed outlier: 8.312A pdb=" N HIS c 329 " --> pdb=" O GLY B 326 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N ILE B 328 " --> pdb=" O HIS c 329 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N GLY A 326 " --> pdb=" O LEU B 325 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N ASN B 327 " --> pdb=" O GLY A 326 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'c' and resid 337 through 342 removed outlier: 6.649A pdb=" N VAL B 337 " --> pdb=" O GLU c 338 " (cutoff:3.500A) removed outlier: 7.866A pdb=" N LYS c 340 " --> pdb=" O VAL B 337 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N VAL B 339 " --> pdb=" O LYS c 340 " (cutoff:3.500A) removed outlier: 8.014A pdb=" N GLU c 342 " --> pdb=" O VAL B 339 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N SER B 341 " --> pdb=" O GLU c 342 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'c' and resid 345 through 346 removed outlier: 6.465A pdb=" N ASP B 345 " --> pdb=" O PHE A 346 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'c' and resid 350 through 357 removed outlier: 6.243A pdb=" N VAL B 350 " --> pdb=" O GLN c 351 " (cutoff:3.500A) removed outlier: 7.942A pdb=" N LYS c 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N SER B 352 " --> pdb=" O LYS c 353 " (cutoff:3.500A) removed outlier: 8.225A pdb=" N GLY c 355 " --> pdb=" O SER B 352 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N ILE B 354 " --> pdb=" O GLY c 355 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N LEU c 357 " --> pdb=" O ILE B 354 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N SER B 356 " --> pdb=" O LEU c 357 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'c' and resid 360 through 362 removed outlier: 6.432A pdb=" N THR B 361 " --> pdb=" O HIS c 362 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'c' and resid 369 through 375 removed outlier: 6.544A pdb=" N LYS B 369 " --> pdb=" O LYS A 370 " (cutoff:3.500A) removed outlier: 7.888A pdb=" N GLU A 372 " --> pdb=" O LYS B 369 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N ILE B 371 " --> pdb=" O GLU A 372 " (cutoff:3.500A) removed outlier: 8.318A pdb=" N HIS A 374 " --> pdb=" O ILE B 371 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N THR B 373 " --> pdb=" O HIS A 374 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 313 through 314 removed outlier: 6.794A pdb=" N VAL C 313 " --> pdb=" O ASP E 314 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 317 through 318 removed outlier: 6.522A pdb=" N LYS C 317 " --> pdb=" O VAL E 318 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 324 through 330 removed outlier: 9.443A pdb=" N SER C 324 " --> pdb=" O LEU D 325 " (cutoff:3.500A) removed outlier: 10.392A pdb=" N ASN D 327 " --> pdb=" O SER C 324 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N GLY C 326 " --> pdb=" O ASN D 327 " (cutoff:3.500A) removed outlier: 8.397A pdb=" N HIS D 329 " --> pdb=" O GLY C 326 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N ILE C 328 " --> pdb=" O HIS D 329 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N LEU C 325 " --> pdb=" O SER E 324 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N GLY E 326 " --> pdb=" O LEU C 325 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ASN C 327 " --> pdb=" O GLY E 326 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 337 through 342 Processing sheet with id=AB4, first strand: chain 'D' and resid 345 through 346 removed outlier: 6.495A pdb=" N ASP C 345 " --> pdb=" O PHE E 346 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 350 through 357 removed outlier: 6.215A pdb=" N VAL C 350 " --> pdb=" O GLN D 351 " (cutoff:3.500A) removed outlier: 7.921A pdb=" N LYS D 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N SER C 352 " --> pdb=" O LYS D 353 " (cutoff:3.500A) removed outlier: 8.200A pdb=" N GLY D 355 " --> pdb=" O SER C 352 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N ILE C 354 " --> pdb=" O GLY D 355 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N LEU D 357 " --> pdb=" O ILE C 354 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N SER C 356 " --> pdb=" O LEU D 357 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 360 through 362 removed outlier: 6.539A pdb=" N THR C 361 " --> pdb=" O HIS D 362 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 369 through 371 removed outlier: 6.388A pdb=" N LYS C 370 " --> pdb=" O ILE D 371 " (cutoff:3.500A) 56 hydrogen bonds defined for protein. 168 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.93 Time building geometry restraints manager: 2.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.94 - 1.11: 3252 1.11 - 1.29: 528 1.29 - 1.46: 885 1.46 - 1.64: 1767 1.64 - 1.82: 6 Bond restraints: 6438 Sorted by residual: bond pdb=" CE1 HIS B 330 " pdb=" HE1 HIS B 330 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.71e+01 bond pdb=" N LYS c 311 " pdb=" H LYS c 311 " 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 E 326 " pdb=" H GLY E 326 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.69e+01 bond pdb=" N ILE E 328 " pdb=" H ILE E 328 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.69e+01 bond pdb=" N SER A 356 " pdb=" H SER A 356 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.69e+01 ... (remaining 6433 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.42: 9668 2.42 - 4.85: 1591 4.85 - 7.27: 464 7.27 - 9.70: 24 9.70 - 12.12: 7 Bond angle restraints: 11754 Sorted by residual: angle pdb=" N GLY C 326 " pdb=" CA GLY C 326 " pdb=" C GLY C 326 " ideal model delta sigma weight residual 110.69 118.23 -7.54 1.33e+00 5.65e-01 3.21e+01 angle pdb=" N GLY B 326 " pdb=" CA GLY B 326 " pdb=" C GLY B 326 " ideal model delta sigma weight residual 110.74 117.48 -6.74 1.37e+00 5.33e-01 2.42e+01 angle pdb=" C ASP c 348 " pdb=" N ARG c 349 " pdb=" CA ARG c 349 " ideal model delta sigma weight residual 121.56 129.18 -7.62 1.56e+00 4.11e-01 2.39e+01 angle pdb=" C ASP D 348 " pdb=" N ARG D 349 " pdb=" CA ARG D 349 " ideal model delta sigma weight residual 121.31 128.35 -7.04 1.49e+00 4.50e-01 2.23e+01 angle pdb=" CB HIS A 374 " pdb=" CG HIS A 374 " pdb=" CD2 HIS A 374 " ideal model delta sigma weight residual 131.20 125.41 5.79 1.30e+00 5.92e-01 1.98e+01 ... (remaining 11749 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.08: 2623 16.08 - 32.16: 148 32.16 - 48.25: 69 48.25 - 64.33: 118 64.33 - 80.41: 6 Dihedral angle restraints: 2964 sinusoidal: 1704 harmonic: 1260 Sorted by residual: dihedral pdb=" CA GLN A 336 " pdb=" C GLN A 336 " pdb=" N VAL A 337 " pdb=" CA VAL A 337 " ideal model delta harmonic sigma weight residual 180.00 152.21 27.79 0 5.00e+00 4.00e-02 3.09e+01 dihedral pdb=" CA LYS E 375 " pdb=" C LYS E 375 " pdb=" N LEU E 376 " pdb=" CA LEU E 376 " ideal model delta harmonic sigma weight residual 180.00 153.45 26.55 0 5.00e+00 4.00e-02 2.82e+01 dihedral pdb=" CA VAL C 318 " pdb=" C VAL C 318 " pdb=" N THR C 319 " pdb=" CA THR C 319 " ideal model delta harmonic sigma weight residual 180.00 -154.58 -25.42 0 5.00e+00 4.00e-02 2.58e+01 ... (remaining 2961 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 282 0.070 - 0.139: 147 0.139 - 0.208: 36 0.208 - 0.278: 10 0.278 - 0.347: 5 Chirality restraints: 480 Sorted by residual: chirality pdb=" CA ASN D 327 " pdb=" N ASN D 327 " pdb=" C ASN D 327 " pdb=" CB ASN D 327 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.02e+00 chirality pdb=" CA LYS D 321 " pdb=" N LYS D 321 " pdb=" C LYS D 321 " pdb=" CB LYS D 321 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.87e+00 chirality pdb=" CA ASN C 327 " pdb=" N ASN C 327 " pdb=" C ASN C 327 " pdb=" CB ASN C 327 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.56e+00 ... (remaining 477 not shown) Planarity restraints: 930 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR c 310 " -0.149 2.00e-02 2.50e+03 6.00e-02 1.08e+02 pdb=" CG TYR c 310 " 0.026 2.00e-02 2.50e+03 pdb=" CD1 TYR c 310 " 0.054 2.00e-02 2.50e+03 pdb=" CD2 TYR c 310 " 0.041 2.00e-02 2.50e+03 pdb=" CE1 TYR c 310 " 0.011 2.00e-02 2.50e+03 pdb=" CE2 TYR c 310 " 0.035 2.00e-02 2.50e+03 pdb=" CZ TYR c 310 " -0.009 2.00e-02 2.50e+03 pdb=" OH TYR c 310 " -0.099 2.00e-02 2.50e+03 pdb=" HD1 TYR c 310 " 0.059 2.00e-02 2.50e+03 pdb=" HD2 TYR c 310 " 0.019 2.00e-02 2.50e+03 pdb=" HE1 TYR c 310 " -0.008 2.00e-02 2.50e+03 pdb=" HE2 TYR c 310 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR E 310 " 0.149 2.00e-02 2.50e+03 5.96e-02 1.07e+02 pdb=" CG TYR E 310 " -0.009 2.00e-02 2.50e+03 pdb=" CD1 TYR E 310 " -0.052 2.00e-02 2.50e+03 pdb=" CD2 TYR E 310 " -0.042 2.00e-02 2.50e+03 pdb=" CE1 TYR E 310 " -0.030 2.00e-02 2.50e+03 pdb=" CE2 TYR E 310 " -0.016 2.00e-02 2.50e+03 pdb=" CZ TYR E 310 " 0.020 2.00e-02 2.50e+03 pdb=" OH TYR E 310 " 0.095 2.00e-02 2.50e+03 pdb=" HD1 TYR E 310 " -0.033 2.00e-02 2.50e+03 pdb=" HD2 TYR E 310 " -0.064 2.00e-02 2.50e+03 pdb=" HE1 TYR E 310 " -0.015 2.00e-02 2.50e+03 pdb=" HE2 TYR E 310 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 310 " 0.139 2.00e-02 2.50e+03 5.47e-02 8.98e+01 pdb=" CG TYR C 310 " -0.025 2.00e-02 2.50e+03 pdb=" CD1 TYR C 310 " -0.045 2.00e-02 2.50e+03 pdb=" CD2 TYR C 310 " -0.050 2.00e-02 2.50e+03 pdb=" CE1 TYR C 310 " -0.031 2.00e-02 2.50e+03 pdb=" CE2 TYR C 310 " 0.001 2.00e-02 2.50e+03 pdb=" CZ TYR C 310 " 0.019 2.00e-02 2.50e+03 pdb=" OH TYR C 310 " 0.070 2.00e-02 2.50e+03 pdb=" HD1 TYR C 310 " -0.014 2.00e-02 2.50e+03 pdb=" HD2 TYR C 310 " -0.067 2.00e-02 2.50e+03 pdb=" HE1 TYR C 310 " -0.016 2.00e-02 2.50e+03 pdb=" HE2 TYR C 310 " 0.018 2.00e-02 2.50e+03 ... (remaining 927 not shown) Histogram of nonbonded interaction distances: 1.56 - 2.17: 424 2.17 - 2.77: 11012 2.77 - 3.38: 16927 3.38 - 3.99: 22645 3.99 - 4.60: 31452 Nonbonded interactions: 82460 Sorted by model distance: nonbonded pdb=" OD1 ASP E 314 " pdb=" HG SER E 316 " model vdw 1.557 2.450 nonbonded pdb=" OD1 ASP B 314 " pdb=" HG SER B 316 " model vdw 1.558 2.450 nonbonded pdb=" OD1 ASP C 314 " pdb=" HG SER C 316 " model vdw 1.558 2.450 nonbonded pdb=" OD1 ASP A 314 " pdb=" HG SER A 316 " model vdw 1.571 2.450 nonbonded pdb=" OD1 ASP D 314 " pdb=" HG SER D 316 " model vdw 1.596 2.450 ... (remaining 82455 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 'c' } 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: 3.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.120 Extract box with map and model: 0.270 Check model and map are aligned: 0.040 Set scattering table: 0.070 Process input model: 18.790 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7515 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 3180 Z= 0.700 Angle : 1.875 7.621 4254 Z= 1.238 Chirality : 0.093 0.347 480 Planarity : 0.011 0.068 540 Dihedral : 12.058 80.411 1224 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % 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: -2.04 (0.33), residues: 402 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.55 (0.25), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.019 0.005 HIS D 362 PHE 0.046 0.015 PHE A 346 TYR 0.128 0.046 TYR c 310 ARG 0.006 0.002 ARG D 349 Details of bonding type rmsd hydrogen bonds : bond 0.12782 ( 56) hydrogen bonds : angle 7.72118 ( 168) covalent geometry : bond 0.01096 ( 3180) covalent geometry : angle 1.87489 ( 4254) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 96 time to evaluate : 0.532 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 311 LYS cc_start: 0.7708 (mtmt) cc_final: 0.7232 (mttm) REVERT: B 345 ASP cc_start: 0.7855 (m-30) cc_final: 0.7438 (t0) REVERT: B 347 LYS cc_start: 0.8736 (mttt) cc_final: 0.8320 (mtpt) REVERT: c 311 LYS cc_start: 0.7811 (mtmt) cc_final: 0.7363 (mmtt) REVERT: A 310 TYR cc_start: 0.6480 (t80) cc_final: 0.6174 (t80) REVERT: A 311 LYS cc_start: 0.7317 (mtmt) cc_final: 0.7076 (mttp) REVERT: A 345 ASP cc_start: 0.8253 (m-30) cc_final: 0.8015 (t0) REVERT: A 347 LYS cc_start: 0.8685 (mttt) cc_final: 0.8282 (mtpt) REVERT: A 348 ASP cc_start: 0.8307 (t70) cc_final: 0.7492 (p0) REVERT: A 349 ARG cc_start: 0.7680 (mtm180) cc_final: 0.7304 (pmt-80) REVERT: A 375 LYS cc_start: 0.7516 (tttt) cc_final: 0.7044 (tttm) REVERT: D 311 LYS cc_start: 0.6375 (mtmt) cc_final: 0.5530 (mmtm) REVERT: D 349 ARG cc_start: 0.6886 (mtm180) cc_final: 0.6646 (mmp-170) REVERT: E 317 LYS cc_start: 0.7810 (mtmt) cc_final: 0.7387 (mttm) REVERT: E 343 LYS cc_start: 0.8872 (mttt) cc_final: 0.8639 (mttp) REVERT: E 349 ARG cc_start: 0.7244 (mtm180) cc_final: 0.6352 (pmt-80) outliers start: 0 outliers final: 0 residues processed: 96 average time/residue: 0.4944 time to fit residues: 53.8630 Evaluate side-chains 55 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 30 optimal weight: 5.9990 chunk 27 optimal weight: 5.9990 chunk 15 optimal weight: 2.9990 chunk 9 optimal weight: 3.9990 chunk 18 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 21 optimal weight: 5.9990 chunk 32 optimal weight: 0.9990 overall best weight: 1.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 362 HIS c 362 HIS A 362 HIS C 362 HIS D 362 HIS E 351 GLN E 362 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4494 r_free = 0.4494 target = 0.147553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.119473 restraints weight = 11422.604| |-----------------------------------------------------------------------------| r_work (start): 0.4206 rms_B_bonded: 2.23 r_work: 0.4098 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.4012 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.4012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.3271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3180 Z= 0.128 Angle : 0.656 5.714 4254 Z= 0.338 Chirality : 0.051 0.139 480 Planarity : 0.003 0.020 540 Dihedral : 7.513 20.691 420 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 1.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.25 % Favored : 99.75 % Rotamer: Outliers : 0.56 % Allowed : 8.89 % Favored : 90.56 % 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: -1.88 (0.32), residues: 402 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.42 (0.25), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS C 330 PHE 0.006 0.001 PHE c 346 TYR 0.012 0.002 TYR E 310 ARG 0.001 0.000 ARG A 349 Details of bonding type rmsd hydrogen bonds : bond 0.02606 ( 56) hydrogen bonds : angle 5.20075 ( 168) covalent geometry : bond 0.00289 ( 3180) covalent geometry : angle 0.65561 ( 4254) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 67 time to evaluate : 0.584 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 311 LYS cc_start: 0.8165 (mtmt) cc_final: 0.7882 (mttm) REVERT: B 345 ASP cc_start: 0.7700 (m-30) cc_final: 0.7432 (t0) REVERT: B 347 LYS cc_start: 0.8662 (mttt) cc_final: 0.8170 (mtpt) REVERT: B 372 GLU cc_start: 0.7263 (tt0) cc_final: 0.6719 (mt-10) REVERT: c 311 LYS cc_start: 0.8283 (mtmt) cc_final: 0.7854 (mmtt) REVERT: c 377 THR cc_start: 0.6430 (m) cc_final: 0.6143 (p) REVERT: A 310 TYR cc_start: 0.7999 (t80) cc_final: 0.7787 (t80) REVERT: A 321 LYS cc_start: 0.8186 (mttt) cc_final: 0.7356 (tmtt) REVERT: A 347 LYS cc_start: 0.8579 (mttt) cc_final: 0.8185 (mtpt) REVERT: A 348 ASP cc_start: 0.8397 (t70) cc_final: 0.7074 (p0) REVERT: A 349 ARG cc_start: 0.7255 (mtm180) cc_final: 0.6941 (pmt-80) REVERT: A 372 GLU cc_start: 0.7756 (tt0) cc_final: 0.7236 (mt-10) REVERT: A 375 LYS cc_start: 0.7903 (tttt) cc_final: 0.7666 (tttm) REVERT: D 311 LYS cc_start: 0.8433 (mtmt) cc_final: 0.7549 (mmtm) REVERT: E 343 LYS cc_start: 0.8871 (mttt) cc_final: 0.8572 (mttp) outliers start: 2 outliers final: 1 residues processed: 68 average time/residue: 0.5176 time to fit residues: 39.9033 Evaluate side-chains 53 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 52 time to evaluate : 0.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 315 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 22 optimal weight: 10.0000 chunk 20 optimal weight: 4.9990 chunk 31 optimal weight: 6.9990 chunk 10 optimal weight: 4.9990 chunk 13 optimal weight: 5.9990 chunk 30 optimal weight: 0.8980 chunk 32 optimal weight: 0.7980 chunk 28 optimal weight: 0.9980 chunk 33 optimal weight: 8.9990 chunk 19 optimal weight: 2.9990 chunk 6 optimal weight: 7.9990 overall best weight: 2.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 336 GLN A 336 GLN C 359 ASN D 359 ASN E 359 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4444 r_free = 0.4444 target = 0.142084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.115743 restraints weight = 12102.848| |-----------------------------------------------------------------------------| r_work (start): 0.4156 rms_B_bonded: 2.23 r_work: 0.4077 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3988 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.4251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 3180 Z= 0.126 Angle : 0.572 5.936 4254 Z= 0.294 Chirality : 0.051 0.136 480 Planarity : 0.002 0.021 540 Dihedral : 6.318 18.086 420 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 2.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.11 % Allowed : 9.72 % Favored : 89.17 % 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: -1.80 (0.34), residues: 402 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.36 (0.26), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 362 PHE 0.006 0.001 PHE A 346 TYR 0.017 0.003 TYR E 310 ARG 0.001 0.000 ARG E 349 Details of bonding type rmsd hydrogen bonds : bond 0.02233 ( 56) hydrogen bonds : angle 4.41480 ( 168) covalent geometry : bond 0.00272 ( 3180) covalent geometry : angle 0.57203 ( 4254) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 67 time to evaluate : 0.534 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 321 LYS cc_start: 0.7861 (mttt) cc_final: 0.7027 (tttm) REVERT: B 345 ASP cc_start: 0.7513 (m-30) cc_final: 0.7305 (t0) REVERT: B 347 LYS cc_start: 0.8583 (mttt) cc_final: 0.8097 (mtpt) REVERT: B 375 LYS cc_start: 0.7224 (tttt) cc_final: 0.6886 (tttm) REVERT: c 311 LYS cc_start: 0.8236 (mtmt) cc_final: 0.7871 (mmtm) REVERT: c 321 LYS cc_start: 0.8321 (mttt) cc_final: 0.7384 (tttm) REVERT: c 347 LYS cc_start: 0.8682 (mttt) cc_final: 0.8132 (mtpt) REVERT: c 375 LYS cc_start: 0.7998 (tttp) cc_final: 0.7469 (tptt) REVERT: c 377 THR cc_start: 0.6212 (m) cc_final: 0.5991 (p) REVERT: A 310 TYR cc_start: 0.8185 (t80) cc_final: 0.7946 (t80) REVERT: A 311 LYS cc_start: 0.8028 (mttp) cc_final: 0.7453 (ptpp) REVERT: A 321 LYS cc_start: 0.8185 (mttt) cc_final: 0.7351 (tttm) REVERT: A 347 LYS cc_start: 0.8567 (mttt) cc_final: 0.8116 (mtpt) REVERT: A 348 ASP cc_start: 0.8549 (OUTLIER) cc_final: 0.7262 (p0) REVERT: A 349 ARG cc_start: 0.7406 (mtm180) cc_final: 0.7004 (pmt-80) REVERT: A 372 GLU cc_start: 0.7911 (tt0) cc_final: 0.7447 (mt-10) REVERT: A 375 LYS cc_start: 0.8042 (tttt) cc_final: 0.7653 (tttm) REVERT: C 349 ARG cc_start: 0.6786 (mtm-85) cc_final: 0.5943 (mtt90) REVERT: E 343 LYS cc_start: 0.8914 (mttt) cc_final: 0.8608 (mttp) outliers start: 4 outliers final: 2 residues processed: 68 average time/residue: 0.5822 time to fit residues: 44.4364 Evaluate side-chains 59 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 56 time to evaluate : 0.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 315 LEU Chi-restraints excluded: chain A residue 348 ASP Chi-restraints excluded: chain D residue 345 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 22 optimal weight: 10.0000 chunk 1 optimal weight: 10.0000 chunk 14 optimal weight: 1.9990 chunk 19 optimal weight: 9.9990 chunk 5 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 32 optimal weight: 4.9990 chunk 3 optimal weight: 9.9990 chunk 25 optimal weight: 0.9980 chunk 8 optimal weight: 5.9990 chunk 13 optimal weight: 0.7980 overall best weight: 1.7586 ------------------------------------------------------------------------------- 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 = 0.4486 r_free = 0.4486 target = 0.145660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.119875 restraints weight = 12050.616| |-----------------------------------------------------------------------------| r_work (start): 0.4206 rms_B_bonded: 2.19 r_work: 0.4116 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.4033 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.4033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.4700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 3180 Z= 0.109 Angle : 0.534 5.600 4254 Z= 0.275 Chirality : 0.050 0.136 480 Planarity : 0.002 0.013 540 Dihedral : 5.847 16.980 420 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 2.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.25 % Favored : 99.75 % Rotamer: Outliers : 0.83 % Allowed : 10.56 % Favored : 88.61 % 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: -1.81 (0.33), residues: 402 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.37 (0.25), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS c 374 PHE 0.004 0.001 PHE A 346 TYR 0.011 0.002 TYR E 310 ARG 0.001 0.001 ARG C 349 Details of bonding type rmsd hydrogen bonds : bond 0.01945 ( 56) hydrogen bonds : angle 4.07148 ( 168) covalent geometry : bond 0.00235 ( 3180) covalent geometry : angle 0.53431 ( 4254) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 59 time to evaluate : 0.585 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 321 LYS cc_start: 0.7893 (mttt) cc_final: 0.7088 (tttm) REVERT: B 347 LYS cc_start: 0.8596 (mttt) cc_final: 0.8134 (mtpt) REVERT: B 375 LYS cc_start: 0.7281 (tttt) cc_final: 0.6928 (tttm) REVERT: c 311 LYS cc_start: 0.8159 (mtmt) cc_final: 0.7876 (mmtm) REVERT: c 321 LYS cc_start: 0.8296 (mttt) cc_final: 0.7387 (tttm) REVERT: c 347 LYS cc_start: 0.8719 (mttt) cc_final: 0.8180 (mtpt) REVERT: c 375 LYS cc_start: 0.7951 (tttp) cc_final: 0.7421 (tptt) REVERT: A 310 TYR cc_start: 0.8213 (t80) cc_final: 0.7836 (t80) REVERT: A 311 LYS cc_start: 0.7989 (mttp) cc_final: 0.7485 (ptpp) REVERT: A 321 LYS cc_start: 0.8180 (mttt) cc_final: 0.7347 (tttm) REVERT: A 347 LYS cc_start: 0.8543 (mttt) cc_final: 0.8088 (mtpt) REVERT: A 348 ASP cc_start: 0.8542 (t70) cc_final: 0.7362 (p0) REVERT: A 349 ARG cc_start: 0.7396 (mtm180) cc_final: 0.6974 (pmt-80) REVERT: A 372 GLU cc_start: 0.7979 (tt0) cc_final: 0.7536 (mt-10) REVERT: A 375 LYS cc_start: 0.8028 (tttt) cc_final: 0.7582 (tttm) REVERT: C 349 ARG cc_start: 0.6841 (mtm-85) cc_final: 0.5983 (mtt90) REVERT: E 343 LYS cc_start: 0.8935 (mttt) cc_final: 0.8654 (mttp) outliers start: 3 outliers final: 3 residues processed: 60 average time/residue: 0.5551 time to fit residues: 37.6023 Evaluate side-chains 59 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 56 time to evaluate : 0.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 377 THR Chi-restraints excluded: chain c residue 315 LEU Chi-restraints excluded: chain D residue 345 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 13 optimal weight: 7.9990 chunk 8 optimal weight: 0.0870 chunk 1 optimal weight: 5.9990 chunk 3 optimal weight: 8.9990 chunk 15 optimal weight: 0.8980 chunk 12 optimal weight: 1.9990 chunk 0 optimal weight: 9.9990 chunk 21 optimal weight: 10.0000 chunk 29 optimal weight: 0.2980 chunk 16 optimal weight: 0.7980 chunk 35 optimal weight: 4.9990 overall best weight: 0.8160 ------------------------------------------------------------------------------- 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 = 0.4504 r_free = 0.4504 target = 0.148079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.122500 restraints weight = 12048.158| |-----------------------------------------------------------------------------| r_work (start): 0.4236 rms_B_bonded: 2.19 r_work: 0.4153 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.4071 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.4071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.4996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 3180 Z= 0.071 Angle : 0.475 4.285 4254 Z= 0.245 Chirality : 0.050 0.133 480 Planarity : 0.002 0.012 540 Dihedral : 5.088 14.465 420 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 1.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.75 % Favored : 99.25 % Rotamer: Outliers : 0.83 % Allowed : 10.83 % Favored : 88.33 % 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: -1.67 (0.34), residues: 402 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.27 (0.26), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 330 PHE 0.002 0.000 PHE B 346 TYR 0.009 0.002 TYR c 310 ARG 0.001 0.000 ARG C 349 Details of bonding type rmsd hydrogen bonds : bond 0.01681 ( 56) hydrogen bonds : angle 3.84148 ( 168) covalent geometry : bond 0.00157 ( 3180) covalent geometry : angle 0.47546 ( 4254) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 69 time to evaluate : 0.592 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 321 LYS cc_start: 0.7934 (mttt) cc_final: 0.7113 (tttm) REVERT: B 347 LYS cc_start: 0.8555 (mttt) cc_final: 0.7999 (mtpt) REVERT: B 375 LYS cc_start: 0.7300 (tttt) cc_final: 0.6873 (tttm) REVERT: c 311 LYS cc_start: 0.8081 (mtmt) cc_final: 0.7827 (mmtm) REVERT: c 321 LYS cc_start: 0.8290 (mttt) cc_final: 0.7366 (tttm) REVERT: c 347 LYS cc_start: 0.8686 (mttt) cc_final: 0.8138 (mtpt) REVERT: c 375 LYS cc_start: 0.8012 (tttp) cc_final: 0.7528 (tptt) REVERT: A 310 TYR cc_start: 0.8169 (t80) cc_final: 0.7776 (t80) REVERT: A 311 LYS cc_start: 0.8040 (mttp) cc_final: 0.7485 (ptpp) REVERT: A 321 LYS cc_start: 0.8279 (mttt) cc_final: 0.7306 (tttm) REVERT: A 347 LYS cc_start: 0.8536 (mttt) cc_final: 0.8023 (mtpt) REVERT: A 348 ASP cc_start: 0.8566 (OUTLIER) cc_final: 0.7391 (p0) REVERT: A 349 ARG cc_start: 0.7374 (mtm180) cc_final: 0.6812 (pmt-80) REVERT: A 375 LYS cc_start: 0.8035 (tttt) cc_final: 0.7592 (tttm) REVERT: C 349 ARG cc_start: 0.6821 (mtm-85) cc_final: 0.5998 (mtt90) REVERT: E 343 LYS cc_start: 0.8918 (mttt) cc_final: 0.8499 (mttp) outliers start: 3 outliers final: 2 residues processed: 71 average time/residue: 0.5361 time to fit residues: 42.8775 Evaluate side-chains 58 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 55 time to evaluate : 0.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 376 LEU Chi-restraints excluded: chain c residue 377 THR Chi-restraints excluded: chain A residue 348 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 2 optimal weight: 7.9990 chunk 24 optimal weight: 3.9990 chunk 33 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 11 optimal weight: 4.9990 chunk 3 optimal weight: 4.9990 chunk 13 optimal weight: 7.9990 chunk 25 optimal weight: 7.9990 chunk 17 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 chunk 23 optimal weight: 5.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 330 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4453 r_free = 0.4453 target = 0.143019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.117482 restraints weight = 12342.727| |-----------------------------------------------------------------------------| r_work (start): 0.4176 rms_B_bonded: 2.16 r_work: 0.4094 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.4013 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.4013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.5187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 3180 Z= 0.121 Angle : 0.505 5.803 4254 Z= 0.259 Chirality : 0.050 0.145 480 Planarity : 0.002 0.013 540 Dihedral : 5.143 15.004 420 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.75 % Favored : 99.25 % Rotamer: Outliers : 1.11 % Allowed : 12.50 % Favored : 86.39 % 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: -1.68 (0.35), residues: 402 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.27 (0.27), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS c 374 PHE 0.004 0.001 PHE A 346 TYR 0.014 0.003 TYR C 310 ARG 0.002 0.000 ARG c 349 Details of bonding type rmsd hydrogen bonds : bond 0.01721 ( 56) hydrogen bonds : angle 3.62533 ( 168) covalent geometry : bond 0.00265 ( 3180) covalent geometry : angle 0.50541 ( 4254) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 57 time to evaluate : 0.596 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 321 LYS cc_start: 0.7936 (mttt) cc_final: 0.7149 (tttm) REVERT: B 347 LYS cc_start: 0.8626 (mttt) cc_final: 0.8069 (mtpt) REVERT: B 375 LYS cc_start: 0.7366 (tttt) cc_final: 0.6940 (tttm) REVERT: c 311 LYS cc_start: 0.8039 (mtmt) cc_final: 0.7830 (mmtm) REVERT: c 321 LYS cc_start: 0.8309 (mttt) cc_final: 0.7333 (tttm) REVERT: c 347 LYS cc_start: 0.8783 (mttt) cc_final: 0.8198 (mtpt) REVERT: c 375 LYS cc_start: 0.8010 (tttp) cc_final: 0.7506 (tptt) REVERT: A 310 TYR cc_start: 0.8249 (t80) cc_final: 0.7915 (t80) REVERT: A 311 LYS cc_start: 0.8030 (mttp) cc_final: 0.7484 (ptpp) REVERT: A 321 LYS cc_start: 0.8246 (mttt) cc_final: 0.7306 (tttm) REVERT: A 347 LYS cc_start: 0.8514 (mttt) cc_final: 0.8023 (mtpt) REVERT: A 348 ASP cc_start: 0.8556 (OUTLIER) cc_final: 0.7394 (p0) REVERT: A 349 ARG cc_start: 0.7497 (mtm180) cc_final: 0.7021 (pmt-80) REVERT: A 375 LYS cc_start: 0.8048 (tttt) cc_final: 0.7612 (tttm) REVERT: C 349 ARG cc_start: 0.6798 (mtm-85) cc_final: 0.5963 (mtt90) REVERT: D 349 ARG cc_start: 0.4965 (mmp-170) cc_final: 0.4746 (mmp-170) REVERT: E 343 LYS cc_start: 0.8917 (mttt) cc_final: 0.8493 (mttp) outliers start: 4 outliers final: 3 residues processed: 59 average time/residue: 0.5321 time to fit residues: 35.4302 Evaluate side-chains 58 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 54 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 376 LEU Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain A residue 348 ASP Chi-restraints excluded: chain D residue 345 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 29 optimal weight: 0.9980 chunk 18 optimal weight: 6.9990 chunk 31 optimal weight: 6.9990 chunk 21 optimal weight: 10.0000 chunk 5 optimal weight: 6.9990 chunk 20 optimal weight: 3.9990 chunk 7 optimal weight: 10.0000 chunk 23 optimal weight: 0.8980 chunk 24 optimal weight: 0.8980 chunk 32 optimal weight: 0.6980 chunk 10 optimal weight: 4.9990 overall best weight: 1.4982 ------------------------------------------------------------------------------- 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 = 0.4465 r_free = 0.4465 target = 0.144201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.118892 restraints weight = 12321.556| |-----------------------------------------------------------------------------| r_work (start): 0.4196 rms_B_bonded: 2.16 r_work: 0.4111 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.4029 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.4029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.5305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.014 3180 Z= 0.094 Angle : 0.482 4.986 4254 Z= 0.246 Chirality : 0.049 0.134 480 Planarity : 0.002 0.012 540 Dihedral : 4.923 14.689 420 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 2.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Rotamer: Outliers : 1.67 % Allowed : 12.50 % Favored : 85.83 % 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: -1.69 (0.35), residues: 402 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.28 (0.27), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS c 374 PHE 0.002 0.001 PHE A 346 TYR 0.010 0.002 TYR C 310 ARG 0.001 0.000 ARG C 349 Details of bonding type rmsd hydrogen bonds : bond 0.01544 ( 56) hydrogen bonds : angle 3.54486 ( 168) covalent geometry : bond 0.00205 ( 3180) covalent geometry : angle 0.48228 ( 4254) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 59 time to evaluate : 0.519 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 321 LYS cc_start: 0.7991 (mttt) cc_final: 0.7230 (tttm) REVERT: B 347 LYS cc_start: 0.8626 (mttt) cc_final: 0.8067 (mtpt) REVERT: B 375 LYS cc_start: 0.7415 (tttt) cc_final: 0.7011 (tttm) REVERT: c 311 LYS cc_start: 0.8016 (mtmt) cc_final: 0.7810 (mmtm) REVERT: c 321 LYS cc_start: 0.8386 (mttt) cc_final: 0.7440 (tttm) REVERT: c 327 ASN cc_start: 0.8503 (t0) cc_final: 0.8252 (t0) REVERT: c 347 LYS cc_start: 0.8766 (mttt) cc_final: 0.8192 (mtpt) REVERT: c 375 LYS cc_start: 0.8054 (tttp) cc_final: 0.7522 (tptt) REVERT: A 310 TYR cc_start: 0.8227 (t80) cc_final: 0.7823 (t80) REVERT: A 311 LYS cc_start: 0.8030 (mttp) cc_final: 0.7464 (ptpp) REVERT: A 321 LYS cc_start: 0.8277 (mttt) cc_final: 0.7309 (tttm) REVERT: A 347 LYS cc_start: 0.8499 (mttt) cc_final: 0.8019 (mtpt) REVERT: A 348 ASP cc_start: 0.8544 (OUTLIER) cc_final: 0.7371 (p0) REVERT: A 349 ARG cc_start: 0.7531 (mtm180) cc_final: 0.6987 (pmt-80) REVERT: A 375 LYS cc_start: 0.8010 (tttt) cc_final: 0.7572 (tttm) REVERT: C 349 ARG cc_start: 0.6813 (mtm-85) cc_final: 0.5995 (mtt90) REVERT: E 343 LYS cc_start: 0.8901 (mttt) cc_final: 0.8497 (mttp) outliers start: 6 outliers final: 5 residues processed: 63 average time/residue: 0.5025 time to fit residues: 35.9733 Evaluate side-chains 62 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 56 time to evaluate : 0.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 376 LEU Chi-restraints excluded: chain c residue 377 THR Chi-restraints excluded: chain A residue 348 ASP Chi-restraints excluded: chain C residue 324 SER Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain D residue 345 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 10 optimal weight: 0.5980 chunk 29 optimal weight: 0.0970 chunk 22 optimal weight: 0.7980 chunk 21 optimal weight: 0.9980 chunk 30 optimal weight: 0.9990 chunk 18 optimal weight: 2.9990 chunk 31 optimal weight: 7.9990 chunk 3 optimal weight: 7.9990 chunk 17 optimal weight: 0.3980 chunk 2 optimal weight: 3.9990 chunk 4 optimal weight: 0.8980 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 368 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4501 r_free = 0.4501 target = 0.147386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.122177 restraints weight = 12169.919| |-----------------------------------------------------------------------------| r_work (start): 0.4239 rms_B_bonded: 2.17 r_work: 0.4156 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.4073 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.4073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.5460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 3180 Z= 0.066 Angle : 0.462 4.407 4254 Z= 0.237 Chirality : 0.050 0.132 480 Planarity : 0.002 0.012 540 Dihedral : 4.659 13.252 420 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 2.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.75 % Favored : 99.25 % Rotamer: Outliers : 1.39 % Allowed : 13.06 % Favored : 85.56 % 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: -1.69 (0.35), residues: 402 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.28 (0.27), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS C 330 PHE 0.001 0.000 PHE C 346 TYR 0.008 0.002 TYR c 310 ARG 0.001 0.000 ARG C 349 Details of bonding type rmsd hydrogen bonds : bond 0.01375 ( 56) hydrogen bonds : angle 3.51844 ( 168) covalent geometry : bond 0.00151 ( 3180) covalent geometry : angle 0.46236 ( 4254) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 59 time to evaluate : 0.520 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 321 LYS cc_start: 0.7979 (mttt) cc_final: 0.7210 (tttm) REVERT: B 347 LYS cc_start: 0.8604 (mttt) cc_final: 0.8034 (mtpt) REVERT: B 375 LYS cc_start: 0.7381 (tttt) cc_final: 0.6971 (tttm) REVERT: c 311 LYS cc_start: 0.7996 (mtmt) cc_final: 0.7787 (mmtm) REVERT: c 321 LYS cc_start: 0.8389 (mttt) cc_final: 0.7449 (tttm) REVERT: c 327 ASN cc_start: 0.8469 (t0) cc_final: 0.8249 (t0) REVERT: c 347 LYS cc_start: 0.8744 (mttt) cc_final: 0.8165 (mtpt) REVERT: c 375 LYS cc_start: 0.8018 (tttp) cc_final: 0.7489 (tptt) REVERT: A 310 TYR cc_start: 0.8168 (t80) cc_final: 0.7870 (t80) REVERT: A 311 LYS cc_start: 0.8071 (mttp) cc_final: 0.7486 (ptpp) REVERT: A 321 LYS cc_start: 0.8279 (mttt) cc_final: 0.7306 (tttm) REVERT: A 347 LYS cc_start: 0.8496 (mttt) cc_final: 0.8021 (mtpt) REVERT: A 348 ASP cc_start: 0.8510 (OUTLIER) cc_final: 0.7333 (p0) REVERT: A 349 ARG cc_start: 0.7476 (mtm180) cc_final: 0.6917 (pmt-80) REVERT: A 375 LYS cc_start: 0.7973 (tttt) cc_final: 0.7517 (tttm) REVERT: C 349 ARG cc_start: 0.6682 (mtm-85) cc_final: 0.5935 (mtt90) REVERT: D 349 ARG cc_start: 0.4833 (mmp-170) cc_final: 0.4111 (mmp-170) REVERT: E 343 LYS cc_start: 0.8880 (mttt) cc_final: 0.8506 (mttp) outliers start: 5 outliers final: 4 residues processed: 62 average time/residue: 0.6581 time to fit residues: 47.3221 Evaluate side-chains 62 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 57 time to evaluate : 0.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 376 LEU Chi-restraints excluded: chain c residue 377 THR Chi-restraints excluded: chain A residue 348 ASP Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain D residue 345 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 35 optimal weight: 3.9990 chunk 7 optimal weight: 10.0000 chunk 20 optimal weight: 3.9990 chunk 17 optimal weight: 0.9990 chunk 16 optimal weight: 4.9990 chunk 34 optimal weight: 2.9990 chunk 5 optimal weight: 0.7980 chunk 19 optimal weight: 7.9990 chunk 1 optimal weight: 2.9990 chunk 11 optimal weight: 0.9990 chunk 23 optimal weight: 0.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 368 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4474 r_free = 0.4474 target = 0.145151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.119943 restraints weight = 12398.864| |-----------------------------------------------------------------------------| r_work (start): 0.4212 rms_B_bonded: 2.16 r_work: 0.4121 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.4039 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.4039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.5477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.012 3180 Z= 0.086 Angle : 0.465 4.209 4254 Z= 0.238 Chirality : 0.049 0.132 480 Planarity : 0.002 0.012 540 Dihedral : 4.652 13.288 420 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Rotamer: Outliers : 1.94 % Allowed : 12.50 % Favored : 85.56 % 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: -1.66 (0.36), residues: 402 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.26 (0.28), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS c 374 PHE 0.002 0.001 PHE A 346 TYR 0.010 0.002 TYR C 310 ARG 0.002 0.000 ARG C 349 Details of bonding type rmsd hydrogen bonds : bond 0.01422 ( 56) hydrogen bonds : angle 3.43831 ( 168) covalent geometry : bond 0.00189 ( 3180) covalent geometry : angle 0.46486 ( 4254) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 54 time to evaluate : 0.673 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 321 LYS cc_start: 0.7995 (mttt) cc_final: 0.7227 (tttm) REVERT: B 347 LYS cc_start: 0.8608 (mttt) cc_final: 0.8048 (mtpt) REVERT: B 375 LYS cc_start: 0.7404 (tttt) cc_final: 0.7001 (tttm) REVERT: c 311 LYS cc_start: 0.7997 (mtmt) cc_final: 0.7786 (mmtm) REVERT: c 321 LYS cc_start: 0.8387 (mttt) cc_final: 0.7443 (tttm) REVERT: c 327 ASN cc_start: 0.8489 (t0) cc_final: 0.8267 (t0) REVERT: c 347 LYS cc_start: 0.8770 (mttt) cc_final: 0.8193 (mtpt) REVERT: c 375 LYS cc_start: 0.8042 (tttp) cc_final: 0.7490 (tptt) REVERT: A 310 TYR cc_start: 0.8187 (t80) cc_final: 0.7818 (t80) REVERT: A 311 LYS cc_start: 0.8036 (mttp) cc_final: 0.7442 (ptpp) REVERT: A 347 LYS cc_start: 0.8497 (mttt) cc_final: 0.8011 (mtpt) REVERT: A 348 ASP cc_start: 0.8514 (OUTLIER) cc_final: 0.7316 (p0) REVERT: A 349 ARG cc_start: 0.7553 (mtm180) cc_final: 0.7028 (pmt-80) REVERT: A 375 LYS cc_start: 0.7973 (tttt) cc_final: 0.7571 (tttm) REVERT: C 349 ARG cc_start: 0.6686 (mtm-85) cc_final: 0.5932 (mtt90) REVERT: E 343 LYS cc_start: 0.8885 (mttt) cc_final: 0.8513 (mttp) outliers start: 7 outliers final: 6 residues processed: 59 average time/residue: 0.7910 time to fit residues: 54.6680 Evaluate side-chains 61 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 54 time to evaluate : 0.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 376 LEU Chi-restraints excluded: chain c residue 377 THR Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain A residue 348 ASP Chi-restraints excluded: chain C residue 324 SER Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain D residue 345 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 33 optimal weight: 4.9990 chunk 1 optimal weight: 10.0000 chunk 18 optimal weight: 6.9990 chunk 17 optimal weight: 2.9990 chunk 15 optimal weight: 0.9980 chunk 24 optimal weight: 0.8980 chunk 21 optimal weight: 2.9990 chunk 9 optimal weight: 5.9990 chunk 31 optimal weight: 6.9990 chunk 7 optimal weight: 0.8980 chunk 20 optimal weight: 3.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 368 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4456 r_free = 0.4456 target = 0.143382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.118054 restraints weight = 12551.559| |-----------------------------------------------------------------------------| r_work (start): 0.4187 rms_B_bonded: 2.17 r_work: 0.4100 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.4015 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.4015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.5514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.013 3180 Z= 0.104 Angle : 0.473 4.284 4254 Z= 0.244 Chirality : 0.049 0.133 480 Planarity : 0.002 0.012 540 Dihedral : 4.724 13.589 420 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 1.67 % Allowed : 13.06 % Favored : 85.28 % 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: -1.68 (0.36), residues: 402 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.27 (0.28), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS c 374 PHE 0.002 0.001 PHE A 346 TYR 0.012 0.002 TYR C 310 ARG 0.002 0.000 ARG c 349 Details of bonding type rmsd hydrogen bonds : bond 0.01453 ( 56) hydrogen bonds : angle 3.41267 ( 168) covalent geometry : bond 0.00226 ( 3180) covalent geometry : angle 0.47304 ( 4254) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 55 time to evaluate : 0.984 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 321 LYS cc_start: 0.7992 (mttt) cc_final: 0.7208 (tttm) REVERT: B 347 LYS cc_start: 0.8626 (mttt) cc_final: 0.8061 (mtpt) REVERT: B 375 LYS cc_start: 0.7451 (tttt) cc_final: 0.7035 (tttm) REVERT: c 311 LYS cc_start: 0.8005 (mtmt) cc_final: 0.7786 (mmtm) REVERT: c 321 LYS cc_start: 0.8380 (mttt) cc_final: 0.7426 (tttm) REVERT: c 327 ASN cc_start: 0.8529 (t0) cc_final: 0.8277 (t0) REVERT: c 347 LYS cc_start: 0.8786 (mttt) cc_final: 0.8185 (mtpt) REVERT: c 375 LYS cc_start: 0.8023 (tttp) cc_final: 0.7478 (tptt) REVERT: A 310 TYR cc_start: 0.8153 (t80) cc_final: 0.7760 (t80) REVERT: A 311 LYS cc_start: 0.8018 (mttp) cc_final: 0.7421 (ptpp) REVERT: A 321 LYS cc_start: 0.8300 (mttt) cc_final: 0.7327 (tttm) REVERT: A 347 LYS cc_start: 0.8503 (mttt) cc_final: 0.8002 (mtpt) REVERT: A 348 ASP cc_start: 0.8509 (OUTLIER) cc_final: 0.7320 (p0) REVERT: A 349 ARG cc_start: 0.7593 (mtm180) cc_final: 0.7054 (pmt-80) REVERT: A 375 LYS cc_start: 0.7983 (tttt) cc_final: 0.7572 (tttm) REVERT: C 349 ARG cc_start: 0.6668 (mtm-85) cc_final: 0.5912 (mtt90) REVERT: D 349 ARG cc_start: 0.4967 (mmp-170) cc_final: 0.4192 (mmp-170) REVERT: E 343 LYS cc_start: 0.8875 (mttt) cc_final: 0.8481 (mttp) outliers start: 6 outliers final: 5 residues processed: 59 average time/residue: 0.6908 time to fit residues: 47.1433 Evaluate side-chains 61 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 55 time to evaluate : 0.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 376 LEU Chi-restraints excluded: chain c residue 377 THR Chi-restraints excluded: chain A residue 348 ASP Chi-restraints excluded: chain C residue 324 SER Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain D residue 345 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 19 optimal weight: 9.9990 chunk 28 optimal weight: 1.9990 chunk 6 optimal weight: 0.0970 chunk 30 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 chunk 13 optimal weight: 0.0570 chunk 26 optimal weight: 0.7980 chunk 17 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 8 optimal weight: 5.9990 chunk 16 optimal weight: 4.9990 overall best weight: 0.7698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 368 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4493 r_free = 0.4493 target = 0.146599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4229 r_free = 0.4229 target = 0.121217 restraints weight = 12543.967| |-----------------------------------------------------------------------------| r_work (start): 0.4232 rms_B_bonded: 2.21 r_work: 0.4144 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.4059 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.4059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.5609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.001 0.012 3180 Z= 0.066 Angle : 0.462 6.277 4254 Z= 0.233 Chirality : 0.049 0.131 480 Planarity : 0.002 0.012 540 Dihedral : 4.498 13.194 420 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.75 % Favored : 99.25 % Rotamer: Outliers : 1.67 % Allowed : 12.78 % Favored : 85.56 % 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: -1.68 (0.36), residues: 402 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.27 (0.28), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 330 PHE 0.002 0.001 PHE C 346 TYR 0.009 0.002 TYR c 310 ARG 0.001 0.000 ARG C 349 Details of bonding type rmsd hydrogen bonds : bond 0.01295 ( 56) hydrogen bonds : angle 3.37063 ( 168) covalent geometry : bond 0.00147 ( 3180) covalent geometry : angle 0.46227 ( 4254) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5266.15 seconds wall clock time: 94 minutes 58.38 seconds (5698.38 seconds total)