Starting phenix.real_space_refine on Tue Feb 11 00:21:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7qjz_14027/02_2025/7qjz_14027.cif Found real_map, /net/cci-nas-00/data/ceres_data/7qjz_14027/02_2025/7qjz_14027.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7qjz_14027/02_2025/7qjz_14027.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7qjz_14027/02_2025/7qjz_14027.map" model { file = "/net/cci-nas-00/data/ceres_data/7qjz_14027/02_2025/7qjz_14027.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7qjz_14027/02_2025/7qjz_14027.cif" } resolution = 3.4 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= 0.003 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: 4 Type Number sf(0) Gaussians S 6 5.16 5 C 2124 2.51 5 N 612 2.21 5 O 636 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 3378 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 563 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 3, 'TRANS': 70} Chain: "B" Number of atoms: 563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 563 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 3, 'TRANS': 70} Chain: "C" Number of atoms: 563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 563 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 3, 'TRANS': 70} Chain: "D" Number of atoms: 563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 563 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 3, 'TRANS': 70} Chain: "E" Number of atoms: 563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 563 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 3, 'TRANS': 70} Chain: "F" Number of atoms: 563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 563 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 3, 'TRANS': 70} Time building chain proxies: 2.83, per 1000 atoms: 0.84 Number of scatterers: 3378 At special positions: 0 Unit cell: (122.08, 116.63, 39.24, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 6 16.00 O 636 8.00 N 612 7.00 C 2124 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.70 Conformation dependent library (CDL) restraints added in 387.7 milliseconds 864 Ramachandran restraints generated. 432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 780 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 14 sheets defined 0.0% alpha, 40.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.44 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'B' and resid 306 through 310 removed outlier: 7.040A pdb=" N VAL A 306 " --> pdb=" O GLN C 307 " (cutoff:3.500A) removed outlier: 8.432A pdb=" N VAL C 309 " --> pdb=" O VAL A 306 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N ILE A 308 " --> pdb=" O VAL C 309 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 313 through 314 removed outlier: 6.816A pdb=" N VAL A 313 " --> pdb=" O ASP B 314 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 326 through 330 removed outlier: 7.938A pdb=" N HIS C 330 " --> pdb=" O ASN A 327 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N HIS A 329 " --> pdb=" O HIS C 330 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 341 through 342 Processing sheet with id=AA5, first strand: chain 'B' and resid 354 through 362 removed outlier: 9.046A pdb=" N ILE A 354 " --> pdb=" O GLY B 355 " (cutoff:3.500A) removed outlier: 9.888A pdb=" N LEU B 357 " --> pdb=" O ILE A 354 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N SER A 356 " --> pdb=" O LEU B 357 " (cutoff:3.500A) removed outlier: 7.882A pdb=" N ASN B 359 " --> pdb=" O SER A 356 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N ASP A 358 " --> pdb=" O ASN B 359 " (cutoff:3.500A) removed outlier: 8.027A pdb=" N THR B 361 " --> pdb=" O ASP A 358 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N ILE A 360 " --> pdb=" O THR B 361 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N GLY A 355 " --> pdb=" O ILE C 354 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N SER C 356 " --> pdb=" O GLY A 355 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 370 through 371 removed outlier: 6.479A pdb=" N LYS A 370 " --> pdb=" O ILE C 371 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 306 through 310 removed outlier: 6.461A pdb=" N GLN D 307 " --> pdb=" O ILE E 308 " (cutoff:3.500A) removed outlier: 8.097A pdb=" N TYR E 310 " --> pdb=" O GLN D 307 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N VAL D 309 " --> pdb=" O TYR E 310 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 313 through 316 removed outlier: 7.341A pdb=" N SER E 320 " --> pdb=" O LYS D 317 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N THR D 319 " --> pdb=" O SER E 320 " (cutoff:3.500A) removed outlier: 8.219A pdb=" N CYS E 322 " --> pdb=" O THR D 319 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N LYS D 321 " --> pdb=" O CYS E 322 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 313 through 316 Processing sheet with id=AB1, first strand: chain 'E' and resid 327 through 330 removed outlier: 6.377A pdb=" N ASN D 327 " --> pdb=" O ILE F 328 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N HIS F 330 " --> pdb=" O ASN D 327 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N HIS D 329 " --> pdb=" O HIS F 330 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 337 through 340 removed outlier: 6.984A pdb=" N GLU D 338 " --> pdb=" O VAL E 339 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N VAL D 337 " --> pdb=" O GLU F 338 " (cutoff:3.500A) removed outlier: 8.217A pdb=" N LYS F 340 " --> pdb=" O VAL D 337 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N VAL D 339 " --> pdb=" O LYS F 340 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'E' and resid 350 through 362 removed outlier: 8.960A pdb=" N VAL D 350 " --> pdb=" O GLN E 351 " (cutoff:3.500A) removed outlier: 10.333A pdb=" N LYS E 353 " --> pdb=" O VAL D 350 " (cutoff:3.500A) removed outlier: 8.901A pdb=" N SER D 352 " --> pdb=" O LYS E 353 " (cutoff:3.500A) removed outlier: 10.417A pdb=" N GLY E 355 " --> pdb=" O SER D 352 " (cutoff:3.500A) removed outlier: 9.014A pdb=" N ILE D 354 " --> pdb=" O GLY E 355 " (cutoff:3.500A) removed outlier: 9.975A pdb=" N LEU E 357 " --> pdb=" O ILE D 354 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N SER D 356 " --> pdb=" O LEU E 357 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N ASN E 359 " --> pdb=" O SER D 356 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N ASP D 358 " --> pdb=" O ASN E 359 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N THR E 361 " --> pdb=" O ASP D 358 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N ILE D 360 " --> pdb=" O THR E 361 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 350 through 362 removed outlier: 8.960A pdb=" N VAL D 350 " --> pdb=" O GLN E 351 " (cutoff:3.500A) removed outlier: 10.333A pdb=" N LYS E 353 " --> pdb=" O VAL D 350 " (cutoff:3.500A) removed outlier: 8.901A pdb=" N SER D 352 " --> pdb=" O LYS E 353 " (cutoff:3.500A) removed outlier: 10.417A pdb=" N GLY E 355 " --> pdb=" O SER D 352 " (cutoff:3.500A) removed outlier: 9.014A pdb=" N ILE D 354 " --> pdb=" O GLY E 355 " (cutoff:3.500A) removed outlier: 9.975A pdb=" N LEU E 357 " --> pdb=" O ILE D 354 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N SER D 356 " --> pdb=" O LEU E 357 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N ASN E 359 " --> pdb=" O SER D 356 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N ASP D 358 " --> pdb=" O ASN E 359 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N THR E 361 " --> pdb=" O ASP D 358 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N ILE D 360 " --> pdb=" O THR E 361 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N ILE F 354 " --> pdb=" O LYS D 353 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N GLY D 355 " --> pdb=" O ILE F 354 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N SER F 356 " --> pdb=" O GLY D 355 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 369 through 371 removed outlier: 6.438A pdb=" N LYS D 370 " --> pdb=" O ILE F 371 " (cutoff:3.500A) 51 hydrogen bonds defined for protein. 153 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: 0.71 Time building geometry restraints manager: 0.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 881 1.33 - 1.45: 493 1.45 - 1.57: 2052 1.57 - 1.69: 0 1.69 - 1.81: 6 Bond restraints: 3432 Sorted by residual: bond pdb=" CZ ARG F 349 " pdb=" NH2 ARG F 349 " ideal model delta sigma weight residual 1.330 1.293 0.037 1.30e-02 5.92e+03 8.03e+00 bond pdb=" CA LYS D 311 " pdb=" CB LYS D 311 " ideal model delta sigma weight residual 1.526 1.553 -0.026 9.30e-03 1.16e+04 8.02e+00 bond pdb=" CZ ARG D 349 " pdb=" NH2 ARG D 349 " ideal model delta sigma weight residual 1.330 1.296 0.034 1.30e-02 5.92e+03 6.69e+00 bond pdb=" CZ ARG B 349 " pdb=" NH2 ARG B 349 " ideal model delta sigma weight residual 1.330 1.297 0.033 1.30e-02 5.92e+03 6.45e+00 bond pdb=" CZ ARG E 349 " pdb=" NH2 ARG E 349 " ideal model delta sigma weight residual 1.330 1.297 0.033 1.30e-02 5.92e+03 6.31e+00 ... (remaining 3427 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.01: 3140 2.01 - 4.03: 1170 4.03 - 6.04: 261 6.04 - 8.05: 21 8.05 - 10.06: 4 Bond angle restraints: 4596 Sorted by residual: angle pdb=" CA ASN C 327 " pdb=" CB ASN C 327 " pdb=" CG ASN C 327 " ideal model delta sigma weight residual 112.60 119.73 -7.13 1.00e+00 1.00e+00 5.09e+01 angle pdb=" CA LYS C 331 " pdb=" C LYS C 331 " pdb=" N PRO C 332 " ideal model delta sigma weight residual 118.16 122.99 -4.83 7.00e-01 2.04e+00 4.75e+01 angle pdb=" CA ASN A 327 " pdb=" CB ASN A 327 " pdb=" CG ASN A 327 " ideal model delta sigma weight residual 112.60 119.09 -6.49 1.00e+00 1.00e+00 4.22e+01 angle pdb=" CA LYS B 331 " pdb=" C LYS B 331 " pdb=" N PRO B 332 " ideal model delta sigma weight residual 118.16 122.34 -4.18 7.00e-01 2.04e+00 3.56e+01 angle pdb=" CA ASN B 327 " pdb=" CB ASN B 327 " pdb=" CG ASN B 327 " ideal model delta sigma weight residual 112.60 118.20 -5.60 1.00e+00 1.00e+00 3.13e+01 ... (remaining 4591 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.24: 1888 16.24 - 32.48: 156 32.48 - 48.72: 29 48.72 - 64.96: 5 64.96 - 81.19: 10 Dihedral angle restraints: 2088 sinusoidal: 864 harmonic: 1224 Sorted by residual: dihedral pdb=" CA THR A 319 " pdb=" C THR A 319 " pdb=" N SER A 320 " pdb=" CA SER A 320 " ideal model delta harmonic sigma weight residual 180.00 152.94 27.06 0 5.00e+00 4.00e-02 2.93e+01 dihedral pdb=" CA GLY F 365 " pdb=" C GLY F 365 " pdb=" N GLY F 366 " pdb=" CA GLY F 366 " ideal model delta harmonic sigma weight residual 180.00 -153.00 -27.00 0 5.00e+00 4.00e-02 2.92e+01 dihedral pdb=" CA ASP E 314 " pdb=" C ASP E 314 " pdb=" N LEU E 315 " pdb=" CA LEU E 315 " ideal model delta harmonic sigma weight residual 180.00 153.52 26.48 0 5.00e+00 4.00e-02 2.80e+01 ... (remaining 2085 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 258 0.062 - 0.124: 161 0.124 - 0.185: 73 0.185 - 0.247: 23 0.247 - 0.309: 7 Chirality restraints: 522 Sorted by residual: chirality pdb=" CA LYS C 343 " pdb=" N LYS C 343 " pdb=" C LYS C 343 " pdb=" CB LYS C 343 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.38e+00 chirality pdb=" CA SER A 324 " pdb=" N SER A 324 " pdb=" C SER A 324 " pdb=" CB SER A 324 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.29e+00 chirality pdb=" CA ASP D 345 " pdb=" N ASP D 345 " pdb=" C ASP D 345 " pdb=" CB ASP D 345 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.93e+00 ... (remaining 519 not shown) Planarity restraints: 582 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR E 310 " 0.075 2.00e-02 2.50e+03 5.14e-02 5.29e+01 pdb=" CG TYR E 310 " -0.004 2.00e-02 2.50e+03 pdb=" CD1 TYR E 310 " -0.024 2.00e-02 2.50e+03 pdb=" CD2 TYR E 310 " -0.033 2.00e-02 2.50e+03 pdb=" CE1 TYR E 310 " -0.046 2.00e-02 2.50e+03 pdb=" CE2 TYR E 310 " -0.044 2.00e-02 2.50e+03 pdb=" CZ TYR E 310 " -0.022 2.00e-02 2.50e+03 pdb=" OH TYR E 310 " 0.097 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR D 310 " 0.084 2.00e-02 2.50e+03 5.11e-02 5.22e+01 pdb=" CG TYR D 310 " -0.015 2.00e-02 2.50e+03 pdb=" CD1 TYR D 310 " -0.027 2.00e-02 2.50e+03 pdb=" CD2 TYR D 310 " -0.042 2.00e-02 2.50e+03 pdb=" CE1 TYR D 310 " -0.041 2.00e-02 2.50e+03 pdb=" CE2 TYR D 310 " -0.037 2.00e-02 2.50e+03 pdb=" CZ TYR D 310 " -0.010 2.00e-02 2.50e+03 pdb=" OH TYR D 310 " 0.089 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS F 329 " -0.076 2.00e-02 2.50e+03 5.66e-02 4.81e+01 pdb=" CG HIS F 329 " 0.077 2.00e-02 2.50e+03 pdb=" ND1 HIS F 329 " 0.037 2.00e-02 2.50e+03 pdb=" CD2 HIS F 329 " 0.049 2.00e-02 2.50e+03 pdb=" CE1 HIS F 329 " -0.036 2.00e-02 2.50e+03 pdb=" NE2 HIS F 329 " -0.050 2.00e-02 2.50e+03 ... (remaining 579 not shown) Histogram of nonbonded interaction distances: 2.49 - 2.97: 1511 2.97 - 3.45: 2933 3.45 - 3.94: 5105 3.94 - 4.42: 5246 4.42 - 4.90: 10498 Nonbonded interactions: 25293 Sorted by model distance: nonbonded pdb=" OD1 ASP D 314 " pdb=" OG SER D 316 " model vdw 2.490 3.040 nonbonded pdb=" OD1 ASP E 314 " pdb=" OG SER E 316 " model vdw 2.509 3.040 nonbonded pdb=" OD1 ASP F 314 " pdb=" OG SER F 316 " model vdw 2.539 3.040 nonbonded pdb=" N GLY A 366 " pdb=" O GLY A 366 " model vdw 2.640 2.496 nonbonded pdb=" OD2 ASP A 314 " pdb=" NZ LYS A 370 " model vdw 2.643 3.120 ... (remaining 25288 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: 0.730 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: 0.010 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 12.400 Find NCS groups from input model: 0.110 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:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7173 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 0.037 3432 Z= 0.762 Angle : 2.094 10.065 4596 Z= 1.374 Chirality : 0.097 0.309 522 Planarity : 0.013 0.062 582 Dihedral : 13.722 81.195 1308 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 0.44 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.32 % Favored : 94.44 % Rotamer: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % 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: -3.28 (0.30), residues: 432 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.49 (0.23), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.013 0.004 HIS B 362 PHE 0.072 0.018 PHE E 346 TYR 0.097 0.028 TYR E 310 ARG 0.004 0.001 ARG B 349 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 864 Ramachandran restraints generated. 432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 864 Ramachandran restraints generated. 432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 92 time to evaluate : 0.368 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 341 SER cc_start: 0.7637 (p) cc_final: 0.7416 (t) REVERT: A 347 LYS cc_start: 0.8093 (mttt) cc_final: 0.7784 (tptm) REVERT: B 341 SER cc_start: 0.7599 (p) cc_final: 0.7306 (t) REVERT: C 341 SER cc_start: 0.8039 (p) cc_final: 0.7824 (t) REVERT: C 345 ASP cc_start: 0.8747 (t0) cc_final: 0.8365 (t0) REVERT: C 347 LYS cc_start: 0.8144 (mttt) cc_final: 0.7858 (tttt) REVERT: C 353 LYS cc_start: 0.8249 (tttm) cc_final: 0.7741 (mtpt) REVERT: E 321 LYS cc_start: 0.8154 (ttpt) cc_final: 0.7755 (tptp) REVERT: E 347 LYS cc_start: 0.7176 (mmtm) cc_final: 0.5849 (mtmm) REVERT: F 343 LYS cc_start: 0.8540 (mtmt) cc_final: 0.6804 (tptt) REVERT: F 349 ARG cc_start: 0.8927 (ttp80) cc_final: 0.7725 (tpm170) outliers start: 0 outliers final: 0 residues processed: 92 average time/residue: 0.2265 time to fit residues: 23.8370 Evaluate side-chains 57 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 57 time to evaluate : 0.405 ------------------------------------------------------------------------------- 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: 5.9990 chunk 31 optimal weight: 8.9990 chunk 17 optimal weight: 4.9990 chunk 10 optimal weight: 10.0000 chunk 21 optimal weight: 8.9990 chunk 32 optimal weight: 10.0000 chunk 12 optimal weight: 5.9990 chunk 20 optimal weight: 5.9990 chunk 24 optimal weight: 6.9990 chunk 38 optimal weight: 6.9990 chunk 11 optimal weight: 6.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 327 ASN A 362 HIS C 327 ASN D 307 GLN D 336 GLN D 362 HIS E 307 GLN E 336 GLN E 362 HIS F 307 GLN F 336 GLN F 362 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.126901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.109277 restraints weight = 5227.454| |-----------------------------------------------------------------------------| r_work (start): 0.3899 rms_B_bonded: 2.41 r_work: 0.3805 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3709 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7390 moved from start: 0.2624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 3432 Z= 0.411 Angle : 0.896 6.196 4596 Z= 0.467 Chirality : 0.056 0.161 522 Planarity : 0.005 0.031 582 Dihedral : 8.305 20.338 450 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 1.03 % Allowed : 11.03 % Favored : 87.95 % 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: -3.17 (0.30), residues: 432 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.41 (0.23), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.010 0.003 HIS C 362 PHE 0.008 0.002 PHE D 346 TYR 0.018 0.004 TYR E 310 ARG 0.001 0.000 ARG F 349 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 864 Ramachandran restraints generated. 432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 864 Ramachandran restraints generated. 432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 63 time to evaluate : 0.398 Fit side-chains REVERT: A 347 LYS cc_start: 0.7824 (mttt) cc_final: 0.7531 (tptm) REVERT: A 353 LYS cc_start: 0.8288 (tttm) cc_final: 0.7462 (mtpt) REVERT: A 375 LYS cc_start: 0.8439 (ttpt) cc_final: 0.8041 (tttp) REVERT: C 345 ASP cc_start: 0.8487 (t0) cc_final: 0.7753 (t0) REVERT: C 347 LYS cc_start: 0.7729 (mttt) cc_final: 0.7344 (tttt) REVERT: C 353 LYS cc_start: 0.8305 (tttm) cc_final: 0.7390 (mtpt) REVERT: F 349 ARG cc_start: 0.8686 (ttp80) cc_final: 0.7346 (mmp80) outliers start: 4 outliers final: 3 residues processed: 66 average time/residue: 0.1926 time to fit residues: 15.0846 Evaluate side-chains 52 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 49 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain E residue 305 SER Chi-restraints excluded: chain F residue 305 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 39 optimal weight: 0.1980 chunk 14 optimal weight: 0.8980 chunk 15 optimal weight: 10.0000 chunk 12 optimal weight: 9.9990 chunk 10 optimal weight: 3.9990 chunk 41 optimal weight: 9.9990 chunk 34 optimal weight: 0.9990 chunk 36 optimal weight: 10.0000 chunk 1 optimal weight: 7.9990 chunk 40 optimal weight: 0.8980 chunk 38 optimal weight: 7.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- 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 = 0.4214 r_free = 0.4214 target = 0.132732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.114975 restraints weight = 4994.431| |-----------------------------------------------------------------------------| r_work (start): 0.3974 rms_B_bonded: 2.40 r_work: 0.3885 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3792 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7275 moved from start: 0.3289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 3432 Z= 0.164 Angle : 0.711 7.601 4596 Z= 0.357 Chirality : 0.052 0.135 522 Planarity : 0.003 0.024 582 Dihedral : 6.796 18.587 450 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 1.54 % Allowed : 12.56 % Favored : 85.90 % 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: -2.80 (0.32), residues: 432 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.12 (0.25), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.001 HIS C 362 PHE 0.007 0.002 PHE A 346 TYR 0.012 0.002 TYR A 310 ARG 0.006 0.001 ARG F 349 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 864 Ramachandran restraints generated. 432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 864 Ramachandran restraints generated. 432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 63 time to evaluate : 0.439 Fit side-chains REVERT: A 342 GLU cc_start: 0.5761 (tt0) cc_final: 0.5535 (tt0) REVERT: A 347 LYS cc_start: 0.7785 (mttt) cc_final: 0.7477 (tptm) REVERT: A 353 LYS cc_start: 0.8168 (tttm) cc_final: 0.7473 (mtpt) REVERT: A 363 VAL cc_start: 0.8994 (t) cc_final: 0.8780 (t) REVERT: A 375 LYS cc_start: 0.8327 (ttpt) cc_final: 0.7912 (tttp) REVERT: B 307 GLN cc_start: 0.7049 (tm-30) cc_final: 0.6649 (mp-120) REVERT: B 372 GLU cc_start: 0.6851 (mp0) cc_final: 0.6632 (mp0) REVERT: C 345 ASP cc_start: 0.8478 (t0) cc_final: 0.7813 (t0) REVERT: C 347 LYS cc_start: 0.7709 (mttt) cc_final: 0.7323 (tttt) REVERT: C 353 LYS cc_start: 0.8189 (tttm) cc_final: 0.7323 (mtpt) REVERT: C 369 LYS cc_start: 0.8579 (ttpt) cc_final: 0.8297 (tttp) REVERT: C 375 LYS cc_start: 0.8431 (tttp) cc_final: 0.8052 (tttp) REVERT: D 338 GLU cc_start: 0.7939 (tm-30) cc_final: 0.7506 (tm-30) REVERT: E 338 GLU cc_start: 0.7891 (tm-30) cc_final: 0.7675 (tm-30) REVERT: F 338 GLU cc_start: 0.8140 (tm-30) cc_final: 0.7777 (tm-30) REVERT: F 349 ARG cc_start: 0.8630 (ttp80) cc_final: 0.7563 (mmp80) outliers start: 6 outliers final: 4 residues processed: 66 average time/residue: 0.1958 time to fit residues: 15.3405 Evaluate side-chains 63 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 59 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 320 SER Chi-restraints excluded: chain C residue 371 ILE Chi-restraints excluded: chain D residue 371 ILE Chi-restraints excluded: chain E residue 305 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 25 optimal weight: 9.9990 chunk 22 optimal weight: 20.0000 chunk 4 optimal weight: 6.9990 chunk 41 optimal weight: 10.0000 chunk 35 optimal weight: 9.9990 chunk 7 optimal weight: 20.0000 chunk 17 optimal weight: 9.9990 chunk 33 optimal weight: 9.9990 chunk 37 optimal weight: 10.0000 chunk 12 optimal weight: 0.6980 chunk 34 optimal weight: 4.9990 overall best weight: 6.5388 ------------------------------------------------------------------------------- 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 = 0.4113 r_free = 0.4113 target = 0.124839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.106924 restraints weight = 5286.287| |-----------------------------------------------------------------------------| r_work (start): 0.3857 rms_B_bonded: 2.38 r_work: 0.3766 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3672 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7444 moved from start: 0.3709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 3432 Z= 0.441 Angle : 0.822 5.821 4596 Z= 0.426 Chirality : 0.053 0.139 522 Planarity : 0.005 0.033 582 Dihedral : 7.068 18.937 450 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.18 % Favored : 92.82 % Rotamer: Outliers : 2.82 % Allowed : 13.59 % Favored : 83.59 % 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: -3.15 (0.31), residues: 432 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.39 (0.24), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.003 HIS E 374 PHE 0.010 0.002 PHE D 346 TYR 0.010 0.002 TYR E 310 ARG 0.003 0.001 ARG D 349 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 864 Ramachandran restraints generated. 432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 864 Ramachandran restraints generated. 432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 61 time to evaluate : 0.394 Fit side-chains REVERT: A 338 GLU cc_start: 0.7153 (tt0) cc_final: 0.6453 (tm-30) REVERT: A 342 GLU cc_start: 0.5955 (tt0) cc_final: 0.5695 (tt0) REVERT: A 347 LYS cc_start: 0.7911 (mttt) cc_final: 0.7480 (tptm) REVERT: A 353 LYS cc_start: 0.8337 (tttm) cc_final: 0.7441 (mtpt) REVERT: A 375 LYS cc_start: 0.8239 (ttpt) cc_final: 0.7786 (tttp) REVERT: B 347 LYS cc_start: 0.8136 (mttt) cc_final: 0.7336 (pttm) REVERT: B 372 GLU cc_start: 0.7123 (mp0) cc_final: 0.6857 (mp0) REVERT: C 307 GLN cc_start: 0.7926 (tm-30) cc_final: 0.7310 (tm-30) REVERT: C 347 LYS cc_start: 0.7669 (mttt) cc_final: 0.7321 (tttt) REVERT: C 353 LYS cc_start: 0.8260 (tttm) cc_final: 0.7363 (mtpt) REVERT: C 369 LYS cc_start: 0.8614 (ttpt) cc_final: 0.8344 (tttp) REVERT: C 375 LYS cc_start: 0.8382 (tttp) cc_final: 0.8097 (tttp) REVERT: D 338 GLU cc_start: 0.8077 (tm-30) cc_final: 0.7853 (tm-30) REVERT: E 338 GLU cc_start: 0.8122 (tm-30) cc_final: 0.7911 (tm-30) REVERT: F 338 GLU cc_start: 0.8208 (tm-30) cc_final: 0.7373 (tm-30) REVERT: F 349 ARG cc_start: 0.8737 (ttp80) cc_final: 0.7656 (mmp80) outliers start: 11 outliers final: 8 residues processed: 69 average time/residue: 0.1949 time to fit residues: 15.8733 Evaluate side-chains 68 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 60 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 341 SER Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain C residue 371 ILE Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 371 ILE Chi-restraints excluded: chain E residue 305 SER Chi-restraints excluded: chain F residue 376 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 15 optimal weight: 6.9990 chunk 23 optimal weight: 6.9990 chunk 34 optimal weight: 0.0470 chunk 26 optimal weight: 0.9990 chunk 31 optimal weight: 10.0000 chunk 30 optimal weight: 5.9990 chunk 24 optimal weight: 4.9990 chunk 6 optimal weight: 1.9990 chunk 2 optimal weight: 9.9990 chunk 0 optimal weight: 20.0000 chunk 29 optimal weight: 3.9990 overall best weight: 2.4086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4241 r_free = 0.4241 target = 0.134405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.117471 restraints weight = 4971.620| |-----------------------------------------------------------------------------| r_work (start): 0.3985 rms_B_bonded: 2.24 r_work: 0.3901 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3809 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7388 moved from start: 0.4004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3432 Z= 0.199 Angle : 0.673 5.877 4596 Z= 0.339 Chirality : 0.050 0.131 522 Planarity : 0.003 0.032 582 Dihedral : 6.207 17.110 450 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 1.54 % Allowed : 15.13 % Favored : 83.33 % 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: -2.85 (0.33), residues: 432 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.16 (0.25), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS C 362 PHE 0.016 0.002 PHE B 378 TYR 0.007 0.001 TYR A 310 ARG 0.002 0.000 ARG F 349 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 864 Ramachandran restraints generated. 432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 864 Ramachandran restraints generated. 432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 62 time to evaluate : 0.383 Fit side-chains REVERT: A 347 LYS cc_start: 0.7927 (mttt) cc_final: 0.7545 (tptm) REVERT: A 353 LYS cc_start: 0.8354 (tttm) cc_final: 0.7522 (mtpt) REVERT: A 363 VAL cc_start: 0.9069 (t) cc_final: 0.8859 (t) REVERT: A 375 LYS cc_start: 0.8310 (ttpt) cc_final: 0.7891 (tttp) REVERT: B 307 GLN cc_start: 0.7277 (tm-30) cc_final: 0.6630 (mp-120) REVERT: B 347 LYS cc_start: 0.8117 (mttt) cc_final: 0.7359 (pttm) REVERT: C 347 LYS cc_start: 0.7770 (mttt) cc_final: 0.7461 (tttt) REVERT: C 353 LYS cc_start: 0.8176 (tttm) cc_final: 0.7352 (mtpt) REVERT: C 369 LYS cc_start: 0.8694 (ttpt) cc_final: 0.8079 (mttt) REVERT: C 375 LYS cc_start: 0.8517 (tttp) cc_final: 0.8255 (tttp) REVERT: D 338 GLU cc_start: 0.8013 (tm-30) cc_final: 0.7589 (tm-30) REVERT: D 349 ARG cc_start: 0.8826 (ttm110) cc_final: 0.8602 (ttm-80) REVERT: E 338 GLU cc_start: 0.8031 (tm-30) cc_final: 0.7770 (tm-30) REVERT: F 338 GLU cc_start: 0.8094 (tm-30) cc_final: 0.7397 (tm-30) REVERT: F 349 ARG cc_start: 0.8590 (ttp80) cc_final: 0.7649 (mmp80) outliers start: 6 outliers final: 5 residues processed: 65 average time/residue: 0.2049 time to fit residues: 15.7113 Evaluate side-chains 66 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 61 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 341 SER Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 371 ILE Chi-restraints excluded: chain E residue 305 SER Chi-restraints excluded: chain F residue 305 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 28 optimal weight: 8.9990 chunk 2 optimal weight: 20.0000 chunk 26 optimal weight: 7.9990 chunk 6 optimal weight: 5.9990 chunk 27 optimal weight: 5.9990 chunk 1 optimal weight: 9.9990 chunk 24 optimal weight: 9.9990 chunk 36 optimal weight: 8.9990 chunk 9 optimal weight: 7.9990 chunk 35 optimal weight: 9.9990 chunk 10 optimal weight: 6.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.127950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.111394 restraints weight = 5353.528| |-----------------------------------------------------------------------------| r_work (start): 0.3905 rms_B_bonded: 2.18 r_work: 0.3807 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3707 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7481 moved from start: 0.4243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.045 3432 Z= 0.472 Angle : 0.827 7.189 4596 Z= 0.428 Chirality : 0.053 0.163 522 Planarity : 0.005 0.031 582 Dihedral : 6.702 18.125 450 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.26 % Favored : 90.74 % Rotamer: Outliers : 3.08 % Allowed : 14.10 % Favored : 82.82 % 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: -3.27 (0.32), residues: 432 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.48 (0.24), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS A 362 PHE 0.016 0.002 PHE B 378 TYR 0.010 0.003 TYR E 310 ARG 0.003 0.001 ARG F 349 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 864 Ramachandran restraints generated. 432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 864 Ramachandran restraints generated. 432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 62 time to evaluate : 0.374 Fit side-chains REVERT: A 321 LYS cc_start: 0.8260 (mttp) cc_final: 0.7729 (mptt) REVERT: A 338 GLU cc_start: 0.7206 (tt0) cc_final: 0.6480 (tm-30) REVERT: A 342 GLU cc_start: 0.6146 (tt0) cc_final: 0.5889 (tt0) REVERT: A 347 LYS cc_start: 0.7926 (mttt) cc_final: 0.7600 (tttt) REVERT: A 353 LYS cc_start: 0.8369 (tttm) cc_final: 0.7469 (mtpt) REVERT: A 375 LYS cc_start: 0.8283 (ttpt) cc_final: 0.7824 (tttp) REVERT: A 378 PHE cc_start: 0.6230 (m-80) cc_final: 0.5974 (t80) REVERT: B 307 GLN cc_start: 0.7278 (tm-30) cc_final: 0.6590 (mp10) REVERT: B 347 LYS cc_start: 0.8339 (mttt) cc_final: 0.7483 (pttm) REVERT: B 369 LYS cc_start: 0.8852 (tttm) cc_final: 0.8647 (tmtt) REVERT: C 307 GLN cc_start: 0.7685 (tm-30) cc_final: 0.7122 (tm-30) REVERT: C 347 LYS cc_start: 0.7885 (mttt) cc_final: 0.7552 (tttt) REVERT: C 353 LYS cc_start: 0.8194 (tttm) cc_final: 0.7276 (mtpt) REVERT: C 369 LYS cc_start: 0.8359 (ttpt) cc_final: 0.7630 (mttt) REVERT: C 375 LYS cc_start: 0.8460 (tttp) cc_final: 0.8223 (tttp) REVERT: D 338 GLU cc_start: 0.8050 (tm-30) cc_final: 0.7609 (tm-30) REVERT: D 349 ARG cc_start: 0.8902 (ttm110) cc_final: 0.8639 (ttm-80) REVERT: E 338 GLU cc_start: 0.8149 (tm-30) cc_final: 0.7888 (tm-30) REVERT: F 338 GLU cc_start: 0.8179 (tm-30) cc_final: 0.7396 (tm-30) REVERT: F 349 ARG cc_start: 0.8844 (ttp80) cc_final: 0.7729 (mmp80) outliers start: 12 outliers final: 11 residues processed: 72 average time/residue: 0.1983 time to fit residues: 16.7967 Evaluate side-chains 71 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 60 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 341 SER Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain D residue 305 SER Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 371 ILE Chi-restraints excluded: chain E residue 305 SER Chi-restraints excluded: chain E residue 320 SER Chi-restraints excluded: chain F residue 305 SER Chi-restraints excluded: chain F residue 320 SER Chi-restraints excluded: chain F residue 376 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 11 optimal weight: 10.0000 chunk 13 optimal weight: 6.9990 chunk 22 optimal weight: 20.0000 chunk 27 optimal weight: 7.9990 chunk 8 optimal weight: 7.9990 chunk 5 optimal weight: 7.9990 chunk 19 optimal weight: 0.9980 chunk 15 optimal weight: 0.0570 chunk 20 optimal weight: 0.9980 chunk 17 optimal weight: 5.9990 chunk 21 optimal weight: 9.9990 overall best weight: 3.0102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.132333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.115544 restraints weight = 4992.611| |-----------------------------------------------------------------------------| r_work (start): 0.3977 rms_B_bonded: 2.21 r_work: 0.3876 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3778 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7427 moved from start: 0.4415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 3432 Z= 0.238 Angle : 0.710 8.154 4596 Z= 0.354 Chirality : 0.051 0.151 522 Planarity : 0.003 0.032 582 Dihedral : 6.115 16.377 450 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.48 % Favored : 93.52 % Rotamer: Outliers : 1.79 % Allowed : 14.87 % Favored : 83.33 % 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: -2.96 (0.34), residues: 432 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.24 (0.26), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS B 362 PHE 0.013 0.002 PHE B 378 TYR 0.005 0.001 TYR B 310 ARG 0.002 0.000 ARG F 349 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 864 Ramachandran restraints generated. 432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 864 Ramachandran restraints generated. 432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 60 time to evaluate : 0.416 Fit side-chains REVERT: A 347 LYS cc_start: 0.7887 (mttt) cc_final: 0.7590 (tttt) REVERT: A 353 LYS cc_start: 0.8265 (tttm) cc_final: 0.7432 (mtpt) REVERT: A 375 LYS cc_start: 0.8287 (ttpt) cc_final: 0.7829 (tttp) REVERT: A 378 PHE cc_start: 0.6195 (m-80) cc_final: 0.5968 (t80) REVERT: B 307 GLN cc_start: 0.7309 (tm-30) cc_final: 0.6865 (mp10) REVERT: B 347 LYS cc_start: 0.8287 (mttt) cc_final: 0.7479 (pttm) REVERT: B 369 LYS cc_start: 0.8717 (tttm) cc_final: 0.7598 (mttt) REVERT: C 347 LYS cc_start: 0.7871 (mttt) cc_final: 0.7576 (tttt) REVERT: C 353 LYS cc_start: 0.8196 (tttm) cc_final: 0.7345 (mtpt) REVERT: C 369 LYS cc_start: 0.8493 (ttpt) cc_final: 0.7774 (mttt) REVERT: C 372 GLU cc_start: 0.7533 (mp0) cc_final: 0.7305 (mp0) REVERT: D 338 GLU cc_start: 0.8016 (tm-30) cc_final: 0.7569 (tm-30) REVERT: E 338 GLU cc_start: 0.8042 (tm-30) cc_final: 0.7765 (tm-30) REVERT: F 338 GLU cc_start: 0.8142 (tm-30) cc_final: 0.7414 (tm-30) REVERT: F 349 ARG cc_start: 0.8806 (ttp80) cc_final: 0.7686 (mmp80) outliers start: 7 outliers final: 6 residues processed: 65 average time/residue: 0.1974 time to fit residues: 15.2765 Evaluate side-chains 63 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 57 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 341 SER Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 371 ILE Chi-restraints excluded: chain E residue 305 SER Chi-restraints excluded: chain F residue 305 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 10 optimal weight: 0.0770 chunk 7 optimal weight: 9.9990 chunk 25 optimal weight: 10.0000 chunk 33 optimal weight: 7.9990 chunk 28 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 22 optimal weight: 10.0000 chunk 26 optimal weight: 0.8980 chunk 0 optimal weight: 6.9990 chunk 9 optimal weight: 9.9990 chunk 27 optimal weight: 5.9990 overall best weight: 2.5944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4250 r_free = 0.4250 target = 0.134744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.117813 restraints weight = 4987.005| |-----------------------------------------------------------------------------| r_work (start): 0.3982 rms_B_bonded: 2.24 r_work: 0.3895 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3799 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7395 moved from start: 0.4608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3432 Z= 0.209 Angle : 0.675 8.516 4596 Z= 0.336 Chirality : 0.051 0.173 522 Planarity : 0.003 0.031 582 Dihedral : 5.810 15.782 450 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.48 % Favored : 93.52 % Rotamer: Outliers : 1.79 % Allowed : 14.87 % Favored : 83.33 % 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: -2.89 (0.34), residues: 432 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.20 (0.26), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS B 362 PHE 0.006 0.001 PHE D 346 TYR 0.004 0.001 TYR B 310 ARG 0.001 0.000 ARG F 349 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 864 Ramachandran restraints generated. 432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 864 Ramachandran restraints generated. 432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 58 time to evaluate : 0.420 Fit side-chains REVERT: A 347 LYS cc_start: 0.7796 (mttt) cc_final: 0.7588 (tttt) REVERT: A 353 LYS cc_start: 0.8231 (tttm) cc_final: 0.7374 (mtpt) REVERT: A 375 LYS cc_start: 0.8275 (ttpt) cc_final: 0.7834 (tttp) REVERT: B 307 GLN cc_start: 0.7309 (tm-30) cc_final: 0.6894 (mp-120) REVERT: B 308 ILE cc_start: 0.7715 (tt) cc_final: 0.7509 (tt) REVERT: B 347 LYS cc_start: 0.8246 (mttt) cc_final: 0.7444 (pttm) REVERT: B 369 LYS cc_start: 0.8721 (tttm) cc_final: 0.7619 (mttt) REVERT: C 307 GLN cc_start: 0.7717 (tm-30) cc_final: 0.7353 (tm-30) REVERT: C 347 LYS cc_start: 0.8042 (mttt) cc_final: 0.7797 (tttt) REVERT: C 353 LYS cc_start: 0.8148 (tttm) cc_final: 0.7296 (mtpt) REVERT: C 369 LYS cc_start: 0.8482 (ttpt) cc_final: 0.7765 (mttt) REVERT: D 338 GLU cc_start: 0.7988 (tm-30) cc_final: 0.7536 (tm-30) REVERT: F 338 GLU cc_start: 0.8114 (tm-30) cc_final: 0.7328 (tm-30) REVERT: F 349 ARG cc_start: 0.8774 (ttp80) cc_final: 0.7682 (mmp80) outliers start: 7 outliers final: 6 residues processed: 64 average time/residue: 0.1913 time to fit residues: 14.5230 Evaluate side-chains 61 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 55 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 371 ILE Chi-restraints excluded: chain E residue 305 SER Chi-restraints excluded: chain F residue 371 ILE Chi-restraints excluded: chain F residue 376 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 5 optimal weight: 20.0000 chunk 6 optimal weight: 3.9990 chunk 38 optimal weight: 9.9990 chunk 4 optimal weight: 8.9990 chunk 8 optimal weight: 0.1980 chunk 39 optimal weight: 0.3980 chunk 9 optimal weight: 2.9990 chunk 14 optimal weight: 10.0000 chunk 17 optimal weight: 0.9990 chunk 28 optimal weight: 30.0000 chunk 21 optimal weight: 5.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4284 r_free = 0.4284 target = 0.137303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.120315 restraints weight = 4843.289| |-----------------------------------------------------------------------------| r_work (start): 0.4026 rms_B_bonded: 2.23 r_work: 0.3938 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3847 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7349 moved from start: 0.4778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 3432 Z= 0.164 Angle : 0.662 8.400 4596 Z= 0.326 Chirality : 0.050 0.134 522 Planarity : 0.003 0.032 582 Dihedral : 5.511 14.108 450 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 1.03 % Allowed : 15.64 % Favored : 83.33 % 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: -2.77 (0.34), residues: 432 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.10 (0.26), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS B 362 PHE 0.015 0.001 PHE B 346 TYR 0.005 0.001 TYR B 310 ARG 0.000 0.000 ARG D 349 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 864 Ramachandran restraints generated. 432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 864 Ramachandran restraints generated. 432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 58 time to evaluate : 0.439 Fit side-chains REVERT: A 342 GLU cc_start: 0.6077 (tt0) cc_final: 0.5488 (mm-30) REVERT: A 353 LYS cc_start: 0.8189 (tttm) cc_final: 0.7347 (mtpt) REVERT: A 375 LYS cc_start: 0.8286 (ttpt) cc_final: 0.8076 (tttp) REVERT: B 307 GLN cc_start: 0.7204 (tm-30) cc_final: 0.6936 (mp-120) REVERT: B 347 LYS cc_start: 0.8131 (mttt) cc_final: 0.7322 (pttm) REVERT: B 375 LYS cc_start: 0.4682 (pttm) cc_final: 0.3523 (tptm) REVERT: C 307 GLN cc_start: 0.7691 (tm-30) cc_final: 0.7391 (tm-30) REVERT: C 321 LYS cc_start: 0.7809 (mttt) cc_final: 0.7298 (mttp) REVERT: C 347 LYS cc_start: 0.8062 (mttt) cc_final: 0.7812 (tttt) REVERT: C 353 LYS cc_start: 0.8128 (tttm) cc_final: 0.7274 (mtpt) REVERT: C 369 LYS cc_start: 0.8479 (ttpt) cc_final: 0.7776 (mttt) REVERT: D 338 GLU cc_start: 0.7926 (tm-30) cc_final: 0.7495 (tm-30) REVERT: F 338 GLU cc_start: 0.8017 (tm-30) cc_final: 0.7687 (tm-30) REVERT: F 349 ARG cc_start: 0.8693 (ttp80) cc_final: 0.7560 (mmp80) outliers start: 4 outliers final: 4 residues processed: 61 average time/residue: 0.2236 time to fit residues: 16.0263 Evaluate side-chains 61 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 57 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 371 ILE Chi-restraints excluded: chain F residue 371 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 15 optimal weight: 3.9990 chunk 41 optimal weight: 8.9990 chunk 7 optimal weight: 0.7980 chunk 0 optimal weight: 5.9990 chunk 10 optimal weight: 8.9990 chunk 36 optimal weight: 8.9990 chunk 2 optimal weight: 9.9990 chunk 11 optimal weight: 8.9990 chunk 39 optimal weight: 7.9990 chunk 17 optimal weight: 9.9990 chunk 19 optimal weight: 1.9990 overall best weight: 4.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.132631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.115602 restraints weight = 5008.632| |-----------------------------------------------------------------------------| r_work (start): 0.3965 rms_B_bonded: 2.20 r_work: 0.3879 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3785 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7440 moved from start: 0.4869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 3432 Z= 0.293 Angle : 0.728 7.661 4596 Z= 0.365 Chirality : 0.050 0.135 522 Planarity : 0.004 0.041 582 Dihedral : 5.759 14.782 450 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.10 % Favored : 91.90 % Rotamer: Outliers : 1.54 % Allowed : 15.90 % Favored : 82.56 % 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: -2.95 (0.34), residues: 432 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.24 (0.26), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS B 362 PHE 0.014 0.002 PHE B 346 TYR 0.005 0.002 TYR F 310 ARG 0.001 0.000 ARG B 349 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 864 Ramachandran restraints generated. 432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 864 Ramachandran restraints generated. 432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 59 time to evaluate : 0.360 Fit side-chains REVERT: A 342 GLU cc_start: 0.6225 (tt0) cc_final: 0.5562 (mm-30) REVERT: A 347 LYS cc_start: 0.8297 (tttt) cc_final: 0.7982 (tptm) REVERT: A 353 LYS cc_start: 0.8238 (tttm) cc_final: 0.7395 (mtpt) REVERT: B 307 GLN cc_start: 0.7425 (tm-30) cc_final: 0.7074 (mp10) REVERT: B 347 LYS cc_start: 0.8238 (mttt) cc_final: 0.7451 (pttm) REVERT: B 375 LYS cc_start: 0.4848 (pttm) cc_final: 0.3583 (tptm) REVERT: C 307 GLN cc_start: 0.7704 (tm-30) cc_final: 0.7405 (tm-30) REVERT: C 321 LYS cc_start: 0.7852 (mttt) cc_final: 0.7348 (mttp) REVERT: C 347 LYS cc_start: 0.8061 (mttt) cc_final: 0.7855 (tttt) REVERT: C 353 LYS cc_start: 0.8072 (tttm) cc_final: 0.7287 (mtpt) REVERT: C 369 LYS cc_start: 0.8545 (ttpt) cc_final: 0.7924 (mttt) REVERT: D 338 GLU cc_start: 0.8028 (tm-30) cc_final: 0.7578 (tm-30) REVERT: F 338 GLU cc_start: 0.8109 (tm-30) cc_final: 0.7287 (tm-30) REVERT: F 349 ARG cc_start: 0.8821 (ttp80) cc_final: 0.7523 (mmp80) outliers start: 6 outliers final: 5 residues processed: 63 average time/residue: 0.2347 time to fit residues: 17.2056 Evaluate side-chains 63 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 58 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 341 SER Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 371 ILE Chi-restraints excluded: chain E residue 305 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 12 optimal weight: 10.0000 chunk 20 optimal weight: 4.9990 chunk 40 optimal weight: 9.9990 chunk 25 optimal weight: 10.0000 chunk 8 optimal weight: 10.0000 chunk 16 optimal weight: 4.9990 chunk 35 optimal weight: 9.9990 chunk 6 optimal weight: 8.9990 chunk 9 optimal weight: 0.7980 chunk 41 optimal weight: 0.1980 chunk 33 optimal weight: 7.9990 overall best weight: 3.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.132100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.115055 restraints weight = 5053.046| |-----------------------------------------------------------------------------| r_work (start): 0.4001 rms_B_bonded: 2.22 r_work: 0.3917 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3826 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7467 moved from start: 0.4932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 3432 Z= 0.274 Angle : 0.727 7.588 4596 Z= 0.365 Chirality : 0.050 0.136 522 Planarity : 0.004 0.039 582 Dihedral : 5.818 14.930 450 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.80 % Favored : 91.20 % Rotamer: Outliers : 1.54 % Allowed : 15.90 % Favored : 82.56 % 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: -2.97 (0.34), residues: 432 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.26 (0.26), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS B 362 PHE 0.016 0.002 PHE B 346 TYR 0.005 0.002 TYR E 310 ARG 0.002 0.000 ARG E 349 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2033.58 seconds wall clock time: 37 minutes 12.07 seconds (2232.07 seconds total)