Starting phenix.real_space_refine on Fri Aug 22 13:42:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8q7p_18228/08_2025/8q7p_18228.cif Found real_map, /net/cci-nas-00/data/ceres_data/8q7p_18228/08_2025/8q7p_18228.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.28 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8q7p_18228/08_2025/8q7p_18228.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8q7p_18228/08_2025/8q7p_18228.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8q7p_18228/08_2025/8q7p_18228.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8q7p_18228/08_2025/8q7p_18228.map" } resolution = 3.28 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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 2136 2.51 5 N 618 2.21 5 O 642 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 3402 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 567 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "D" Number of atoms: 567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 567 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "F" Number of atoms: 567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 567 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "A" Number of atoms: 567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 567 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "C" Number of atoms: 567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 567 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "E" Number of atoms: 567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 567 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Time building chain proxies: 1.42, per 1000 atoms: 0.42 Number of scatterers: 3402 At special positions: 0 Unit cell: (122.136, 102.507, 38.531, 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 642 8.00 N 618 7.00 C 2136 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: 0.28 Conformation dependent library (CDL) restraints added in 143.3 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 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 22 sheets defined 0.0% alpha, 50.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.19 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'D' and resid 306 through 310 Processing sheet with id=AA2, first strand: chain 'D' and resid 313 through 314 removed outlier: 6.845A pdb=" N VAL B 313 " --> pdb=" O ASP D 314 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 317 through 325 Processing sheet with id=AA4, first strand: chain 'D' and resid 328 through 330 removed outlier: 6.738A pdb=" N ILE B 328 " --> pdb=" O HIS D 329 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 333 through 334 removed outlier: 6.877A pdb=" N GLY B 333 " --> pdb=" O GLY D 334 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 337 through 342 removed outlier: 6.572A pdb=" N VAL B 337 " --> pdb=" O GLU F 338 " (cutoff:3.500A) removed outlier: 8.186A pdb=" N LYS F 340 " --> pdb=" O VAL B 337 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N VAL B 339 " --> pdb=" O LYS F 340 " (cutoff:3.500A) removed outlier: 8.177A pdb=" N GLU F 342 " --> pdb=" O VAL B 339 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N SER B 341 " --> pdb=" O GLU F 342 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 345 through 346 removed outlier: 6.626A pdb=" N ASP B 345 " --> pdb=" O PHE D 346 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 350 through 354 removed outlier: 6.626A pdb=" N GLN B 351 " --> pdb=" O SER D 352 " (cutoff:3.500A) removed outlier: 8.397A pdb=" N ILE D 354 " --> pdb=" O GLN B 351 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N LYS B 353 " --> pdb=" O ILE D 354 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 357 through 358 removed outlier: 7.115A pdb=" N LEU B 357 " --> pdb=" O ASP F 358 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 361 through 362 removed outlier: 6.404A pdb=" N THR B 361 " --> pdb=" O HIS F 362 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 368 through 377 removed outlier: 6.458A pdb=" N LYS B 369 " --> pdb=" O LYS D 370 " (cutoff:3.500A) removed outlier: 7.929A pdb=" N GLU D 372 " --> pdb=" O LYS B 369 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N ILE B 371 " --> pdb=" O GLU D 372 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N HIS D 374 " --> pdb=" O ILE B 371 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N THR B 373 " --> pdb=" O HIS D 374 " (cutoff:3.500A) removed outlier: 7.954A pdb=" N LEU D 376 " --> pdb=" O THR B 373 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N LYS B 375 " --> pdb=" O LEU D 376 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 306 through 310 Processing sheet with id=AB4, first strand: chain 'C' and resid 313 through 314 removed outlier: 6.857A pdb=" N VAL A 313 " --> pdb=" O ASP C 314 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 317 through 325 removed outlier: 6.279A pdb=" N VAL A 318 " --> pdb=" O THR E 319 " (cutoff:3.500A) removed outlier: 7.928A pdb=" N LYS E 321 " --> pdb=" O VAL A 318 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N SER A 320 " --> pdb=" O LYS E 321 " (cutoff:3.500A) removed outlier: 7.873A pdb=" N GLY E 323 " --> pdb=" O SER A 320 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N CYS A 322 " --> pdb=" O GLY E 323 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N LEU E 325 " --> pdb=" O CYS A 322 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N SER A 324 " --> pdb=" O LEU E 325 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 328 through 330 removed outlier: 6.459A pdb=" N ILE A 328 " --> pdb=" O HIS C 329 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 333 through 334 removed outlier: 6.830A pdb=" N GLY A 333 " --> pdb=" O GLY C 334 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 337 through 342 removed outlier: 6.535A pdb=" N VAL A 337 " --> pdb=" O GLU E 338 " (cutoff:3.500A) removed outlier: 8.131A pdb=" N LYS E 340 " --> pdb=" O VAL A 337 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N VAL A 339 " --> pdb=" O LYS E 340 " (cutoff:3.500A) removed outlier: 8.202A pdb=" N GLU E 342 " --> pdb=" O VAL A 339 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N SER A 341 " --> pdb=" O GLU E 342 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 345 through 346 removed outlier: 6.626A pdb=" N ASP A 345 " --> pdb=" O PHE C 346 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 350 through 354 removed outlier: 6.626A pdb=" N GLN A 351 " --> pdb=" O SER C 352 " (cutoff:3.500A) removed outlier: 8.421A pdb=" N ILE C 354 " --> pdb=" O GLN A 351 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N LYS A 353 " --> pdb=" O ILE C 354 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 357 through 358 removed outlier: 7.093A pdb=" N LEU A 357 " --> pdb=" O ASP E 358 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.367A pdb=" N THR A 361 " --> pdb=" O HIS E 362 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 368 through 377 removed outlier: 6.459A pdb=" N LYS A 369 " --> pdb=" O LYS C 370 " (cutoff:3.500A) removed outlier: 7.948A pdb=" N GLU C 372 " --> pdb=" O LYS A 369 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N ILE A 371 " --> pdb=" O GLU C 372 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N HIS C 374 " --> pdb=" O ILE A 371 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N THR A 373 " --> pdb=" O HIS C 374 " (cutoff:3.500A) removed outlier: 7.954A pdb=" N LEU C 376 " --> pdb=" O THR A 373 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N LYS A 375 " --> pdb=" O LEU C 376 " (cutoff:3.500A) 94 hydrogen bonds defined for protein. 276 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: 0.51 Time building geometry restraints manager: 0.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1042 1.34 - 1.46: 387 1.46 - 1.58: 2021 1.58 - 1.69: 0 1.69 - 1.81: 6 Bond restraints: 3456 Sorted by residual: bond pdb=" CZ ARG B 349 " pdb=" NH2 ARG B 349 " ideal model delta sigma weight residual 1.330 1.294 0.036 1.30e-02 5.92e+03 7.51e+00 bond pdb=" CZ ARG D 349 " pdb=" NH2 ARG D 349 " ideal model delta sigma weight residual 1.330 1.295 0.035 1.30e-02 5.92e+03 7.44e+00 bond pdb=" CZ ARG F 349 " pdb=" NH2 ARG F 349 " ideal model delta sigma weight residual 1.330 1.295 0.035 1.30e-02 5.92e+03 7.27e+00 bond pdb=" CZ ARG C 349 " pdb=" NH2 ARG C 349 " ideal model delta sigma weight residual 1.330 1.295 0.035 1.30e-02 5.92e+03 7.26e+00 bond pdb=" CZ ARG A 349 " pdb=" NH2 ARG A 349 " ideal model delta sigma weight residual 1.330 1.295 0.035 1.30e-02 5.92e+03 7.19e+00 ... (remaining 3451 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.35: 2549 1.35 - 2.70: 1430 2.70 - 4.04: 527 4.04 - 5.39: 98 5.39 - 6.74: 22 Bond angle restraints: 4626 Sorted by residual: angle pdb=" OE1 GLN E 336 " pdb=" CD GLN E 336 " pdb=" NE2 GLN E 336 " ideal model delta sigma weight residual 122.60 117.65 4.95 1.00e+00 1.00e+00 2.45e+01 angle pdb=" OE1 GLN C 336 " pdb=" CD GLN C 336 " pdb=" NE2 GLN C 336 " ideal model delta sigma weight residual 122.60 117.66 4.94 1.00e+00 1.00e+00 2.44e+01 angle pdb=" CA LYS D 331 " pdb=" C LYS D 331 " pdb=" N PRO D 332 " ideal model delta sigma weight residual 118.16 121.60 -3.44 7.00e-01 2.04e+00 2.41e+01 angle pdb=" OE1 GLN A 336 " pdb=" CD GLN A 336 " pdb=" NE2 GLN A 336 " ideal model delta sigma weight residual 122.60 117.75 4.85 1.00e+00 1.00e+00 2.35e+01 angle pdb=" N SER E 356 " pdb=" CA SER E 356 " pdb=" C SER E 356 " ideal model delta sigma weight residual 111.36 116.63 -5.27 1.09e+00 8.42e-01 2.34e+01 ... (remaining 4621 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.57: 1959 14.57 - 29.14: 97 29.14 - 43.71: 22 43.71 - 58.28: 6 58.28 - 72.85: 10 Dihedral angle restraints: 2094 sinusoidal: 864 harmonic: 1230 Sorted by residual: dihedral pdb=" CA ASN B 327 " pdb=" C ASN B 327 " pdb=" N ILE B 328 " pdb=" CA ILE B 328 " ideal model delta harmonic sigma weight residual 180.00 161.52 18.48 0 5.00e+00 4.00e-02 1.37e+01 dihedral pdb=" CA ILE B 371 " pdb=" C ILE B 371 " pdb=" N GLU B 372 " pdb=" CA GLU B 372 " ideal model delta harmonic sigma weight residual 180.00 162.23 17.77 0 5.00e+00 4.00e-02 1.26e+01 dihedral pdb=" C LYS E 347 " pdb=" N LYS E 347 " pdb=" CA LYS E 347 " pdb=" CB LYS E 347 " ideal model delta harmonic sigma weight residual -122.60 -131.46 8.86 0 2.50e+00 1.60e-01 1.26e+01 ... (remaining 2091 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 279 0.062 - 0.123: 164 0.123 - 0.185: 53 0.185 - 0.247: 15 0.247 - 0.308: 11 Chirality restraints: 522 Sorted by residual: chirality pdb=" CA GLU B 342 " pdb=" N GLU B 342 " pdb=" C GLU B 342 " pdb=" CB GLU B 342 " 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 GLU A 342 " pdb=" N GLU A 342 " pdb=" C GLU A 342 " pdb=" CB GLU A 342 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.37e+00 chirality pdb=" CA LYS E 347 " pdb=" N LYS E 347 " pdb=" C LYS E 347 " pdb=" CB LYS E 347 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.19e+00 ... (remaining 519 not shown) Planarity restraints: 588 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR F 310 " -0.066 2.00e-02 2.50e+03 3.37e-02 2.27e+01 pdb=" CG TYR F 310 " 0.035 2.00e-02 2.50e+03 pdb=" CD1 TYR F 310 " 0.028 2.00e-02 2.50e+03 pdb=" CD2 TYR F 310 " 0.029 2.00e-02 2.50e+03 pdb=" CE1 TYR F 310 " 0.007 2.00e-02 2.50e+03 pdb=" CE2 TYR F 310 " 0.008 2.00e-02 2.50e+03 pdb=" CZ TYR F 310 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR F 310 " -0.042 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR E 310 " 0.066 2.00e-02 2.50e+03 3.35e-02 2.24e+01 pdb=" CG TYR E 310 " -0.035 2.00e-02 2.50e+03 pdb=" CD1 TYR E 310 " -0.027 2.00e-02 2.50e+03 pdb=" CD2 TYR E 310 " -0.029 2.00e-02 2.50e+03 pdb=" CE1 TYR E 310 " -0.008 2.00e-02 2.50e+03 pdb=" CE2 TYR E 310 " -0.008 2.00e-02 2.50e+03 pdb=" CZ TYR E 310 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR E 310 " 0.042 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS D 362 " 0.044 2.00e-02 2.50e+03 3.31e-02 1.64e+01 pdb=" CG HIS D 362 " -0.056 2.00e-02 2.50e+03 pdb=" ND1 HIS D 362 " -0.015 2.00e-02 2.50e+03 pdb=" CD2 HIS D 362 " -0.018 2.00e-02 2.50e+03 pdb=" CE1 HIS D 362 " 0.019 2.00e-02 2.50e+03 pdb=" NE2 HIS D 362 " 0.026 2.00e-02 2.50e+03 ... (remaining 585 not shown) Histogram of nonbonded interaction distances: 2.48 - 2.96: 1408 2.96 - 3.45: 2645 3.45 - 3.93: 5364 3.93 - 4.42: 5382 4.42 - 4.90: 10371 Nonbonded interactions: 25170 Sorted by model distance: nonbonded pdb=" OD1 ASP F 314 " pdb=" OG SER F 316 " model vdw 2.479 3.040 nonbonded pdb=" OD1 ASP E 314 " pdb=" OG SER E 316 " model vdw 2.488 3.040 nonbonded pdb=" OD1 ASP B 314 " pdb=" OG SER B 316 " model vdw 2.502 3.040 nonbonded pdb=" OD1 ASP A 314 " pdb=" OG SER A 316 " model vdw 2.508 3.040 nonbonded pdb=" OD1 ASP D 314 " pdb=" OG SER D 316 " model vdw 2.546 3.040 ... (remaining 25165 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.020 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: 0.000 Extract box with map and model: 0.100 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 6.050 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.000 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:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7454 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 0.036 3456 Z= 0.677 Angle : 1.825 6.739 4626 Z= 1.232 Chirality : 0.091 0.308 522 Planarity : 0.009 0.035 588 Dihedral : 11.615 72.854 1314 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 0.00 % Allowed : 0.26 % Favored : 99.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.91 (0.32), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.45 (0.25), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 349 TYR 0.066 0.020 TYR F 310 PHE 0.047 0.017 PHE A 346 HIS 0.007 0.002 HIS F 362 Details of bonding type rmsd covalent geometry : bond 0.01063 ( 3456) covalent geometry : angle 1.82468 ( 4626) hydrogen bonds : bond 0.06548 ( 94) hydrogen bonds : angle 7.06959 ( 276) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 142 time to evaluate : 0.186 Fit side-chains REVERT: B 321 LYS cc_start: 0.7598 (mttt) cc_final: 0.7247 (mttp) REVERT: B 347 LYS cc_start: 0.8280 (mttt) cc_final: 0.7554 (ptmt) REVERT: D 311 LYS cc_start: 0.7899 (mttt) cc_final: 0.7647 (mttm) REVERT: D 321 LYS cc_start: 0.8051 (mttt) cc_final: 0.7814 (mttp) REVERT: D 342 GLU cc_start: 0.7732 (pt0) cc_final: 0.7529 (pt0) REVERT: D 343 LYS cc_start: 0.8955 (mttt) cc_final: 0.7715 (pptt) REVERT: D 347 LYS cc_start: 0.8265 (mttt) cc_final: 0.7758 (pttm) REVERT: D 359 ASN cc_start: 0.8983 (t0) cc_final: 0.8613 (t0) REVERT: D 369 LYS cc_start: 0.8578 (tttt) cc_final: 0.8306 (tttp) REVERT: F 317 LYS cc_start: 0.8215 (mttt) cc_final: 0.7790 (mttm) REVERT: F 347 LYS cc_start: 0.8269 (mttt) cc_final: 0.7857 (ptmt) REVERT: A 317 LYS cc_start: 0.8125 (mttt) cc_final: 0.7534 (mtmt) REVERT: A 369 LYS cc_start: 0.8438 (tttt) cc_final: 0.8224 (tttm) REVERT: C 311 LYS cc_start: 0.8065 (mttt) cc_final: 0.7442 (mtmt) REVERT: C 317 LYS cc_start: 0.8596 (mttt) cc_final: 0.8179 (mtmt) REVERT: C 331 LYS cc_start: 0.8460 (mttt) cc_final: 0.8198 (mttt) REVERT: C 342 GLU cc_start: 0.8199 (pt0) cc_final: 0.7995 (pt0) REVERT: C 343 LYS cc_start: 0.8564 (mttt) cc_final: 0.8053 (pptt) REVERT: C 359 ASN cc_start: 0.8415 (t0) cc_final: 0.8139 (t0) REVERT: C 369 LYS cc_start: 0.8885 (tttt) cc_final: 0.8475 (mtpp) REVERT: E 317 LYS cc_start: 0.8210 (mttt) cc_final: 0.7876 (mtmt) REVERT: E 360 ILE cc_start: 0.8422 (mt) cc_final: 0.8213 (mp) REVERT: E 369 LYS cc_start: 0.8249 (tttt) cc_final: 0.8005 (tttm) REVERT: E 371 ILE cc_start: 0.8497 (mt) cc_final: 0.8186 (mt) outliers start: 0 outliers final: 0 residues processed: 142 average time/residue: 0.1190 time to fit residues: 19.1136 Evaluate side-chains 89 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 89 time to evaluate : 0.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 24 optimal weight: 0.9990 chunk 26 optimal weight: 5.9990 chunk 2 optimal weight: 0.6980 chunk 16 optimal weight: 0.8980 chunk 32 optimal weight: 3.9990 chunk 31 optimal weight: 7.9990 chunk 25 optimal weight: 1.9990 chunk 19 optimal weight: 5.9990 chunk 30 optimal weight: 5.9990 chunk 22 optimal weight: 5.9990 chunk 37 optimal weight: 0.7980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 327 ASN ** E 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.142025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.128761 restraints weight = 5315.856| |-----------------------------------------------------------------------------| r_work (start): 0.3957 rms_B_bonded: 2.42 r_work: 0.3850 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3749 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.2232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3456 Z= 0.115 Angle : 0.585 4.685 4626 Z= 0.305 Chirality : 0.052 0.158 522 Planarity : 0.003 0.029 588 Dihedral : 5.608 14.645 456 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 1.28 % Allowed : 8.72 % Favored : 90.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.45 (0.35), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.10 (0.27), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG C 349 TYR 0.014 0.004 TYR A 310 PHE 0.009 0.001 PHE A 346 HIS 0.002 0.000 HIS B 329 Details of bonding type rmsd covalent geometry : bond 0.00260 ( 3456) covalent geometry : angle 0.58487 ( 4626) hydrogen bonds : bond 0.02006 ( 94) hydrogen bonds : angle 5.49932 ( 276) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 96 time to evaluate : 0.170 Fit side-chains REVERT: D 347 LYS cc_start: 0.8157 (mttt) cc_final: 0.7769 (pttp) REVERT: D 368 ASN cc_start: 0.8623 (m-40) cc_final: 0.8395 (m-40) REVERT: F 342 GLU cc_start: 0.8048 (pt0) cc_final: 0.6544 (mm-30) REVERT: A 317 LYS cc_start: 0.8642 (mttt) cc_final: 0.8225 (mtmt) REVERT: C 317 LYS cc_start: 0.8621 (mttt) cc_final: 0.8276 (mtmt) REVERT: C 347 LYS cc_start: 0.8582 (mttt) cc_final: 0.8126 (mptt) REVERT: E 317 LYS cc_start: 0.8822 (mttt) cc_final: 0.8541 (mtmt) REVERT: E 353 LYS cc_start: 0.7867 (tttm) cc_final: 0.7647 (ttmt) REVERT: E 371 ILE cc_start: 0.8940 (mt) cc_final: 0.8582 (mt) outliers start: 5 outliers final: 3 residues processed: 98 average time/residue: 0.0810 time to fit residues: 9.4497 Evaluate side-chains 80 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 77 time to evaluate : 0.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain C residue 306 VAL Chi-restraints excluded: chain E residue 306 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 14 optimal weight: 0.9990 chunk 8 optimal weight: 7.9990 chunk 16 optimal weight: 4.9990 chunk 31 optimal weight: 0.2980 chunk 19 optimal weight: 0.0970 chunk 9 optimal weight: 3.9990 chunk 39 optimal weight: 0.9990 chunk 17 optimal weight: 7.9990 chunk 13 optimal weight: 8.9990 chunk 5 optimal weight: 4.9990 chunk 26 optimal weight: 9.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 329 HIS C 330 HIS E 336 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.141634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.128279 restraints weight = 5294.772| |-----------------------------------------------------------------------------| r_work (start): 0.3946 rms_B_bonded: 2.33 r_work: 0.3846 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3749 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.2766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 3456 Z= 0.101 Angle : 0.555 6.964 4626 Z= 0.275 Chirality : 0.051 0.131 522 Planarity : 0.003 0.025 588 Dihedral : 5.124 15.140 456 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.46 % Favored : 99.54 % Rotamer: Outliers : 2.56 % Allowed : 12.56 % Favored : 84.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.44 (0.36), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.09 (0.27), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG C 349 TYR 0.010 0.003 TYR A 310 PHE 0.007 0.001 PHE F 346 HIS 0.002 0.000 HIS A 329 Details of bonding type rmsd covalent geometry : bond 0.00228 ( 3456) covalent geometry : angle 0.55535 ( 4626) hydrogen bonds : bond 0.01750 ( 94) hydrogen bonds : angle 5.10986 ( 276) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 79 time to evaluate : 0.176 Fit side-chains REVERT: B 348 ASP cc_start: 0.8371 (OUTLIER) cc_final: 0.8096 (m-30) REVERT: D 347 LYS cc_start: 0.8136 (mttt) cc_final: 0.7654 (pttm) REVERT: F 342 GLU cc_start: 0.7994 (pt0) cc_final: 0.6653 (tp30) REVERT: C 317 LYS cc_start: 0.8620 (mttt) cc_final: 0.8317 (mtmt) REVERT: C 343 LYS cc_start: 0.9124 (mmtp) cc_final: 0.7972 (pttp) REVERT: C 347 LYS cc_start: 0.8631 (mttt) cc_final: 0.8082 (mmtm) outliers start: 10 outliers final: 7 residues processed: 85 average time/residue: 0.0643 time to fit residues: 6.8410 Evaluate side-chains 85 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 77 time to evaluate : 0.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 348 ASP Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain D residue 352 SER Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain C residue 306 VAL Chi-restraints excluded: chain C residue 307 GLN Chi-restraints excluded: chain C residue 352 SER Chi-restraints excluded: chain E residue 306 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 41 optimal weight: 0.8980 chunk 9 optimal weight: 0.6980 chunk 30 optimal weight: 9.9990 chunk 23 optimal weight: 2.9990 chunk 4 optimal weight: 9.9990 chunk 16 optimal weight: 0.7980 chunk 36 optimal weight: 9.9990 chunk 13 optimal weight: 4.9990 chunk 37 optimal weight: 0.0040 chunk 8 optimal weight: 7.9990 chunk 33 optimal weight: 0.5980 overall best weight: 0.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 368 ASN E 336 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.144188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.131018 restraints weight = 5138.676| |-----------------------------------------------------------------------------| r_work (start): 0.3987 rms_B_bonded: 2.26 r_work: 0.3890 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3796 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.3034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.014 3456 Z= 0.076 Angle : 0.495 5.274 4626 Z= 0.248 Chirality : 0.050 0.163 522 Planarity : 0.002 0.022 588 Dihedral : 4.667 14.378 456 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.46 % Favored : 99.54 % Rotamer: Outliers : 1.54 % Allowed : 12.05 % Favored : 86.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.43 (0.36), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.08 (0.28), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 349 TYR 0.010 0.002 TYR A 310 PHE 0.006 0.001 PHE E 346 HIS 0.002 0.000 HIS A 329 Details of bonding type rmsd covalent geometry : bond 0.00171 ( 3456) covalent geometry : angle 0.49465 ( 4626) hydrogen bonds : bond 0.01738 ( 94) hydrogen bonds : angle 4.87096 ( 276) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 78 time to evaluate : 0.185 Fit side-chains REVERT: B 348 ASP cc_start: 0.8330 (OUTLIER) cc_final: 0.8090 (m-30) REVERT: D 347 LYS cc_start: 0.8089 (mttt) cc_final: 0.7630 (pttm) REVERT: D 368 ASN cc_start: 0.8595 (m-40) cc_final: 0.8368 (m-40) REVERT: F 342 GLU cc_start: 0.7918 (pt0) cc_final: 0.6612 (tp30) REVERT: C 317 LYS cc_start: 0.8603 (mttt) cc_final: 0.8296 (mtmt) REVERT: C 343 LYS cc_start: 0.9096 (mmtp) cc_final: 0.7984 (pttp) REVERT: C 347 LYS cc_start: 0.8625 (mttt) cc_final: 0.8177 (mptt) outliers start: 6 outliers final: 4 residues processed: 82 average time/residue: 0.0663 time to fit residues: 6.7339 Evaluate side-chains 80 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 75 time to evaluate : 0.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 348 ASP Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain C residue 306 VAL Chi-restraints excluded: chain E residue 306 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 24 optimal weight: 8.9990 chunk 21 optimal weight: 10.0000 chunk 22 optimal weight: 9.9990 chunk 38 optimal weight: 0.6980 chunk 8 optimal weight: 7.9990 chunk 19 optimal weight: 8.9990 chunk 36 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 chunk 9 optimal weight: 0.0010 chunk 33 optimal weight: 4.9990 chunk 13 optimal weight: 8.9990 overall best weight: 2.3392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 368 ASN E 336 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.140432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.126645 restraints weight = 5343.243| |-----------------------------------------------------------------------------| r_work (start): 0.3930 rms_B_bonded: 2.38 r_work: 0.3829 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3734 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.3200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3456 Z= 0.152 Angle : 0.536 5.045 4626 Z= 0.269 Chirality : 0.051 0.171 522 Planarity : 0.002 0.018 588 Dihedral : 4.779 13.429 456 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % Rotamer: Outliers : 2.56 % Allowed : 13.33 % Favored : 84.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.53 (0.36), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.16 (0.27), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 349 TYR 0.012 0.003 TYR A 310 PHE 0.007 0.002 PHE E 346 HIS 0.002 0.000 HIS C 374 Details of bonding type rmsd covalent geometry : bond 0.00343 ( 3456) covalent geometry : angle 0.53617 ( 4626) hydrogen bonds : bond 0.01691 ( 94) hydrogen bonds : angle 4.49817 ( 276) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 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: 10 poor density : 82 time to evaluate : 0.148 Fit side-chains REVERT: B 348 ASP cc_start: 0.8357 (OUTLIER) cc_final: 0.8099 (m-30) REVERT: D 315 LEU cc_start: 0.8901 (OUTLIER) cc_final: 0.8698 (mp) REVERT: D 347 LYS cc_start: 0.8189 (mttt) cc_final: 0.7684 (pttm) REVERT: F 342 GLU cc_start: 0.8038 (pt0) cc_final: 0.6719 (tp30) REVERT: C 343 LYS cc_start: 0.9131 (mmtp) cc_final: 0.8028 (pttp) REVERT: C 347 LYS cc_start: 0.8739 (mttt) cc_final: 0.8287 (mptt) outliers start: 10 outliers final: 7 residues processed: 89 average time/residue: 0.0646 time to fit residues: 7.1555 Evaluate side-chains 86 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 77 time to evaluate : 0.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 348 ASP Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain D residue 352 SER Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain C residue 306 VAL Chi-restraints excluded: chain C residue 352 SER Chi-restraints excluded: chain E residue 306 VAL Chi-restraints excluded: chain E residue 325 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 41 optimal weight: 0.6980 chunk 8 optimal weight: 6.9990 chunk 7 optimal weight: 10.0000 chunk 21 optimal weight: 10.0000 chunk 23 optimal weight: 4.9990 chunk 27 optimal weight: 5.9990 chunk 12 optimal weight: 10.0000 chunk 5 optimal weight: 0.9980 chunk 17 optimal weight: 7.9990 chunk 10 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 336 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.138477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.125262 restraints weight = 5297.425| |-----------------------------------------------------------------------------| r_work (start): 0.3898 rms_B_bonded: 2.26 r_work: 0.3801 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3709 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.3414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 3456 Z= 0.155 Angle : 0.555 6.764 4626 Z= 0.275 Chirality : 0.050 0.139 522 Planarity : 0.002 0.017 588 Dihedral : 4.864 13.214 456 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 2.56 % Allowed : 14.62 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.64 (0.35), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.24 (0.27), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 349 TYR 0.011 0.003 TYR A 310 PHE 0.007 0.002 PHE E 346 HIS 0.002 0.000 HIS B 329 Details of bonding type rmsd covalent geometry : bond 0.00350 ( 3456) covalent geometry : angle 0.55513 ( 4626) hydrogen bonds : bond 0.01659 ( 94) hydrogen bonds : angle 4.34294 ( 276) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 78 time to evaluate : 0.195 Fit side-chains REVERT: B 348 ASP cc_start: 0.8368 (OUTLIER) cc_final: 0.8104 (m-30) REVERT: D 343 LYS cc_start: 0.9124 (mttt) cc_final: 0.7782 (pptt) REVERT: D 347 LYS cc_start: 0.8213 (mttt) cc_final: 0.7704 (pttm) REVERT: F 342 GLU cc_start: 0.8069 (pt0) cc_final: 0.6741 (tp30) REVERT: C 343 LYS cc_start: 0.9115 (mmtp) cc_final: 0.8057 (pttp) REVERT: C 347 LYS cc_start: 0.8688 (mttt) cc_final: 0.8280 (mptt) outliers start: 10 outliers final: 6 residues processed: 82 average time/residue: 0.0604 time to fit residues: 6.2911 Evaluate side-chains 82 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 75 time to evaluate : 0.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 348 ASP Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain D residue 352 SER Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain C residue 352 SER Chi-restraints excluded: chain E residue 306 VAL Chi-restraints excluded: chain E residue 325 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 23 optimal weight: 9.9990 chunk 8 optimal weight: 6.9990 chunk 18 optimal weight: 10.0000 chunk 15 optimal weight: 1.9990 chunk 32 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 41 optimal weight: 2.9990 chunk 30 optimal weight: 0.6980 chunk 13 optimal weight: 0.5980 chunk 11 optimal weight: 9.9990 chunk 39 optimal weight: 9.9990 overall best weight: 2.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 329 HIS C 336 GLN E 336 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.136683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.123568 restraints weight = 5376.552| |-----------------------------------------------------------------------------| r_work (start): 0.3870 rms_B_bonded: 2.27 r_work: 0.3775 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3679 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.3600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 3456 Z= 0.164 Angle : 0.574 8.389 4626 Z= 0.282 Chirality : 0.051 0.158 522 Planarity : 0.002 0.015 588 Dihedral : 4.906 14.225 456 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % Rotamer: Outliers : 2.05 % Allowed : 15.64 % Favored : 82.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.70 (0.36), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.29 (0.27), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 349 TYR 0.011 0.003 TYR A 310 PHE 0.007 0.001 PHE F 346 HIS 0.001 0.000 HIS C 374 Details of bonding type rmsd covalent geometry : bond 0.00368 ( 3456) covalent geometry : angle 0.57436 ( 4626) hydrogen bonds : bond 0.01808 ( 94) hydrogen bonds : angle 4.26978 ( 276) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 73 time to evaluate : 0.168 Fit side-chains REVERT: B 348 ASP cc_start: 0.8371 (OUTLIER) cc_final: 0.8107 (m-30) REVERT: D 347 LYS cc_start: 0.8217 (mttt) cc_final: 0.7718 (pttm) REVERT: F 342 GLU cc_start: 0.8151 (pt0) cc_final: 0.6780 (tp30) REVERT: C 347 LYS cc_start: 0.8721 (mttt) cc_final: 0.8315 (mptt) outliers start: 8 outliers final: 6 residues processed: 77 average time/residue: 0.0405 time to fit residues: 4.3424 Evaluate side-chains 80 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 73 time to evaluate : 0.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 348 ASP Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain D residue 352 SER Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain C residue 352 SER Chi-restraints excluded: chain E residue 306 VAL Chi-restraints excluded: chain E residue 325 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 19 optimal weight: 0.0000 chunk 25 optimal weight: 9.9990 chunk 24 optimal weight: 6.9990 chunk 41 optimal weight: 0.9980 chunk 28 optimal weight: 6.9990 chunk 5 optimal weight: 8.9990 chunk 3 optimal weight: 7.9990 chunk 38 optimal weight: 9.9990 chunk 16 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 37 optimal weight: 4.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 336 GLN E 336 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.135344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.121474 restraints weight = 5475.866| |-----------------------------------------------------------------------------| r_work (start): 0.3844 rms_B_bonded: 2.42 r_work: 0.3751 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3656 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.3741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 3456 Z= 0.225 Angle : 0.622 7.181 4626 Z= 0.308 Chirality : 0.051 0.146 522 Planarity : 0.002 0.014 588 Dihedral : 5.208 16.310 456 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Rotamer: Outliers : 2.56 % Allowed : 15.64 % Favored : 81.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.89 (0.35), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.43 (0.26), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 349 TYR 0.013 0.003 TYR C 310 PHE 0.008 0.002 PHE E 346 HIS 0.002 0.001 HIS C 362 Details of bonding type rmsd covalent geometry : bond 0.00513 ( 3456) covalent geometry : angle 0.62188 ( 4626) hydrogen bonds : bond 0.01801 ( 94) hydrogen bonds : angle 4.18899 ( 276) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 75 time to evaluate : 0.157 Fit side-chains REVERT: B 348 ASP cc_start: 0.8422 (OUTLIER) cc_final: 0.8150 (m-30) REVERT: D 347 LYS cc_start: 0.8248 (mttt) cc_final: 0.7680 (pttm) REVERT: C 347 LYS cc_start: 0.8745 (mttt) cc_final: 0.8319 (mptt) outliers start: 10 outliers final: 9 residues processed: 78 average time/residue: 0.0397 time to fit residues: 4.3194 Evaluate side-chains 84 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 74 time to evaluate : 0.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain B residue 348 ASP Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain D residue 352 SER Chi-restraints excluded: chain F residue 352 SER Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain C residue 306 VAL Chi-restraints excluded: chain C residue 352 SER Chi-restraints excluded: chain E residue 306 VAL Chi-restraints excluded: chain E residue 325 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 0 optimal weight: 10.0000 chunk 5 optimal weight: 9.9990 chunk 11 optimal weight: 1.9990 chunk 31 optimal weight: 0.1980 chunk 20 optimal weight: 1.9990 chunk 36 optimal weight: 6.9990 chunk 13 optimal weight: 1.9990 chunk 22 optimal weight: 6.9990 chunk 7 optimal weight: 4.9990 chunk 2 optimal weight: 0.6980 chunk 29 optimal weight: 5.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 336 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.140313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.126580 restraints weight = 5278.699| |-----------------------------------------------------------------------------| r_work (start): 0.3921 rms_B_bonded: 2.38 r_work: 0.3829 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3731 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.3890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 3456 Z= 0.106 Angle : 0.553 8.280 4626 Z= 0.269 Chirality : 0.051 0.179 522 Planarity : 0.002 0.012 588 Dihedral : 4.789 14.355 456 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % Rotamer: Outliers : 2.31 % Allowed : 17.18 % Favored : 80.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.97 (0.35), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.49 (0.27), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 349 TYR 0.009 0.002 TYR A 310 PHE 0.005 0.001 PHE C 346 HIS 0.003 0.001 HIS D 330 Details of bonding type rmsd covalent geometry : bond 0.00235 ( 3456) covalent geometry : angle 0.55341 ( 4626) hydrogen bonds : bond 0.01621 ( 94) hydrogen bonds : angle 4.12208 ( 276) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 73 time to evaluate : 0.131 Fit side-chains REVERT: B 348 ASP cc_start: 0.8386 (OUTLIER) cc_final: 0.8151 (m-30) REVERT: D 347 LYS cc_start: 0.8223 (mttt) cc_final: 0.7692 (pttm) REVERT: F 342 GLU cc_start: 0.8145 (pt0) cc_final: 0.6705 (tp30) REVERT: C 347 LYS cc_start: 0.8745 (mttt) cc_final: 0.8314 (mptt) outliers start: 9 outliers final: 8 residues processed: 75 average time/residue: 0.0421 time to fit residues: 4.4098 Evaluate side-chains 81 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 72 time to evaluate : 0.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain B residue 348 ASP Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain D residue 352 SER Chi-restraints excluded: chain F residue 328 ILE Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain C residue 306 VAL Chi-restraints excluded: chain E residue 306 VAL Chi-restraints excluded: chain E residue 325 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 40 optimal weight: 0.3980 chunk 0 optimal weight: 10.0000 chunk 30 optimal weight: 7.9990 chunk 13 optimal weight: 1.9990 chunk 9 optimal weight: 0.6980 chunk 24 optimal weight: 9.9990 chunk 3 optimal weight: 9.9990 chunk 27 optimal weight: 7.9990 chunk 19 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 12 optimal weight: 4.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 359 ASN E 336 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.139655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.125941 restraints weight = 5331.779| |-----------------------------------------------------------------------------| r_work (start): 0.3915 rms_B_bonded: 2.38 r_work: 0.3820 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3722 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.3968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3456 Z= 0.133 Angle : 0.557 7.548 4626 Z= 0.271 Chirality : 0.051 0.160 522 Planarity : 0.002 0.013 588 Dihedral : 4.737 14.538 456 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % Rotamer: Outliers : 2.31 % Allowed : 17.44 % Favored : 80.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.02 (0.35), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.53 (0.27), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG E 349 TYR 0.009 0.002 TYR A 310 PHE 0.007 0.001 PHE E 346 HIS 0.002 0.000 HIS B 329 Details of bonding type rmsd covalent geometry : bond 0.00298 ( 3456) covalent geometry : angle 0.55748 ( 4626) hydrogen bonds : bond 0.01615 ( 94) hydrogen bonds : angle 4.07200 ( 276) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 70 time to evaluate : 0.195 Fit side-chains REVERT: B 348 ASP cc_start: 0.8396 (OUTLIER) cc_final: 0.8161 (m-30) REVERT: D 347 LYS cc_start: 0.8242 (mttt) cc_final: 0.7704 (pttm) REVERT: F 342 GLU cc_start: 0.8216 (pt0) cc_final: 0.6794 (tp30) REVERT: C 347 LYS cc_start: 0.8757 (mttt) cc_final: 0.8349 (mptt) outliers start: 9 outliers final: 7 residues processed: 73 average time/residue: 0.0431 time to fit residues: 4.3267 Evaluate side-chains 78 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 70 time to evaluate : 0.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain B residue 348 ASP Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain D residue 352 SER Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain C residue 306 VAL Chi-restraints excluded: chain E residue 306 VAL Chi-restraints excluded: chain E residue 325 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 9 optimal weight: 0.0070 chunk 14 optimal weight: 0.9990 chunk 22 optimal weight: 10.0000 chunk 23 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 40 optimal weight: 8.9990 chunk 18 optimal weight: 0.0970 chunk 29 optimal weight: 5.9990 chunk 17 optimal weight: 10.0000 chunk 1 optimal weight: 8.9990 chunk 5 optimal weight: 10.0000 overall best weight: 1.2202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 336 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.137900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.125145 restraints weight = 5383.304| |-----------------------------------------------------------------------------| r_work (start): 0.3914 rms_B_bonded: 2.34 r_work: 0.3823 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3726 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.4084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 3456 Z= 0.099 Angle : 0.546 7.888 4626 Z= 0.265 Chirality : 0.050 0.154 522 Planarity : 0.002 0.013 588 Dihedral : 4.537 12.974 456 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 2.05 % Allowed : 18.21 % Favored : 79.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.02 (0.35), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.53 (0.27), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG C 349 TYR 0.008 0.002 TYR A 310 PHE 0.005 0.001 PHE E 346 HIS 0.001 0.000 HIS F 329 Details of bonding type rmsd covalent geometry : bond 0.00221 ( 3456) covalent geometry : angle 0.54583 ( 4626) hydrogen bonds : bond 0.01575 ( 94) hydrogen bonds : angle 4.05497 ( 276) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1118.19 seconds wall clock time: 20 minutes 2.45 seconds (1202.45 seconds total)