Starting phenix.real_space_refine on Wed Mar 5 20:09:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8q7p_18228/03_2025/8q7p_18228.cif Found real_map, /net/cci-nas-00/data/ceres_data/8q7p_18228/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8q7p_18228/03_2025/8q7p_18228.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8q7p_18228/03_2025/8q7p_18228.map" model { file = "/net/cci-nas-00/data/ceres_data/8q7p_18228/03_2025/8q7p_18228.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8q7p_18228/03_2025/8q7p_18228.cif" } resolution = 3.28 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 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): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: 3.89, per 1000 atoms: 1.14 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: 0.74 Conformation dependent library (CDL) restraints added in 493.0 milliseconds 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: 0.50 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: 0.77 Time building geometry restraints manager: 0.89 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: 0.01 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: 2.570 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.190 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 15.580 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.010 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:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.240 ------------------------------------------------------------------------------- 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= 0.723 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.91 (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 HIS 0.007 0.002 HIS F 362 PHE 0.047 0.017 PHE A 346 TYR 0.066 0.020 TYR F 310 ARG 0.005 0.001 ARG E 349 *********************** 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 : 0.638 Fit side-chains REVERT: B 321 LYS cc_start: 0.7598 (mttt) cc_final: 0.7248 (mttp) REVERT: B 347 LYS cc_start: 0.8280 (mttt) cc_final: 0.7555 (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: 0.7815 (mttp) REVERT: D 347 LYS cc_start: 0.8265 (mttt) cc_final: 0.7759 (pttm) REVERT: D 359 ASN cc_start: 0.8983 (t0) cc_final: 0.8612 (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: 0.7856 (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: 0.8180 (mtmt) REVERT: C 331 LYS cc_start: 0.8460 (mttt) cc_final: 0.8198 (mttt) 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: 0.8474 (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: 0.2542 time to fit residues: 40.7270 Evaluate side-chains 88 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 88 time to evaluate : 0.522 ------------------------------------------------------------------------------- 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: 3.9990 chunk 31 optimal weight: 5.9990 chunk 17 optimal weight: 3.9990 chunk 10 optimal weight: 10.0000 chunk 21 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 12 optimal weight: 5.9990 chunk 20 optimal weight: 0.3980 chunk 24 optimal weight: 5.9990 chunk 38 optimal weight: 5.9990 chunk 11 optimal weight: 3.9990 overall best weight: 2.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 327 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.139370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.126469 restraints weight = 5364.378| |-----------------------------------------------------------------------------| r_work (start): 0.3920 rms_B_bonded: 2.26 r_work: 0.3818 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3720 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3720 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.2254 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= 0.249 Angle : 0.614 4.780 4626 Z= 0.321 Chirality : 0.052 0.160 522 Planarity : 0.003 0.029 588 Dihedral : 5.765 14.698 456 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 1.54 % Allowed : 8.46 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.46 (0.35), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.10 (0.26), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 329 PHE 0.010 0.002 PHE A 346 TYR 0.014 0.004 TYR A 310 ARG 0.002 0.001 ARG C 349 *********************** 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 95 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 89 time to evaluate : 0.478 Fit side-chains REVERT: D 347 LYS cc_start: 0.8137 (mttt) cc_final: 0.7787 (pttp) REVERT: D 368 ASN cc_start: 0.8627 (m-40) cc_final: 0.8414 (m-40) REVERT: F 342 GLU cc_start: 0.8113 (pt0) cc_final: 0.6730 (tp30) REVERT: A 317 LYS cc_start: 0.8672 (mttt) cc_final: 0.8292 (mtmt) REVERT: E 317 LYS cc_start: 0.8830 (mttt) cc_final: 0.8551 (mtmt) REVERT: E 353 LYS cc_start: 0.7896 (tttm) cc_final: 0.7622 (ttmt) REVERT: E 371 ILE cc_start: 0.8910 (mt) cc_final: 0.8564 (mt) outliers start: 6 outliers final: 4 residues processed: 92 average time/residue: 0.1543 time to fit residues: 17.4047 Evaluate side-chains 78 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 74 time to evaluate : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 6 optimal weight: 9.9990 chunk 25 optimal weight: 10.0000 chunk 36 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 10 optimal weight: 9.9990 chunk 22 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 2 optimal weight: 0.4980 chunk 7 optimal weight: 0.5980 chunk 27 optimal weight: 0.7980 overall best weight: 1.1784 ------------------------------------------------------------------------------- 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 = 0.4101 r_free = 0.4101 target = 0.142004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.128490 restraints weight = 5162.512| |-----------------------------------------------------------------------------| r_work (start): 0.3955 rms_B_bonded: 2.41 r_work: 0.3849 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3751 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.2817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 3456 Z= 0.158 Angle : 0.542 5.886 4626 Z= 0.273 Chirality : 0.052 0.161 522 Planarity : 0.003 0.023 588 Dihedral : 5.092 15.083 456 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % Rotamer: Outliers : 1.54 % Allowed : 13.59 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (0.36), residues: 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 HIS 0.002 0.000 HIS A 329 PHE 0.006 0.001 PHE D 378 TYR 0.011 0.002 TYR A 310 ARG 0.000 0.000 ARG E 349 *********************** 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 85 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 79 time to evaluate : 0.424 Fit side-chains REVERT: D 347 LYS cc_start: 0.8130 (mttt) cc_final: 0.7672 (pttm) REVERT: F 342 GLU cc_start: 0.8047 (pt0) cc_final: 0.6657 (tp30) REVERT: C 317 LYS cc_start: 0.8667 (mttt) cc_final: 0.8358 (mtmt) REVERT: C 347 LYS cc_start: 0.8653 (mttt) cc_final: 0.8180 (mptt) outliers start: 6 outliers final: 4 residues processed: 84 average time/residue: 0.1258 time to fit residues: 13.4420 Evaluate side-chains 79 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 75 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 21 optimal weight: 10.0000 chunk 6 optimal weight: 9.9990 chunk 19 optimal weight: 10.0000 chunk 35 optimal weight: 1.9990 chunk 10 optimal weight: 8.9990 chunk 15 optimal weight: 7.9990 chunk 12 optimal weight: 5.9990 chunk 16 optimal weight: 0.9990 chunk 25 optimal weight: 10.0000 chunk 40 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 329 HIS A 329 HIS A 336 GLN C 336 GLN C 368 ASN E 336 GLN E 368 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.132509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.119106 restraints weight = 5411.433| |-----------------------------------------------------------------------------| r_work (start): 0.3812 rms_B_bonded: 2.36 r_work: 0.3710 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3611 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.3241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.048 3456 Z= 0.446 Angle : 0.674 6.290 4626 Z= 0.345 Chirality : 0.054 0.175 522 Planarity : 0.003 0.022 588 Dihedral : 5.761 17.675 456 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 3.90 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.74 (0.34), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.32 (0.26), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 362 PHE 0.011 0.002 PHE E 346 TYR 0.017 0.004 TYR C 310 ARG 0.002 0.001 ARG C 349 *********************** 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 97 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 87 time to evaluate : 0.447 Fit side-chains REVERT: B 348 ASP cc_start: 0.8446 (OUTLIER) cc_final: 0.8120 (m-30) REVERT: D 347 LYS cc_start: 0.8297 (mttt) cc_final: 0.7714 (pttm) REVERT: D 368 ASN cc_start: 0.8692 (m-40) cc_final: 0.8463 (m-40) REVERT: A 317 LYS cc_start: 0.8755 (mttt) cc_final: 0.8415 (mtmt) REVERT: C 347 LYS cc_start: 0.8799 (mttt) cc_final: 0.8289 (mmtm) outliers start: 10 outliers final: 6 residues processed: 90 average time/residue: 0.1192 time to fit residues: 13.8222 Evaluate side-chains 85 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 78 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 348 ASP 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 5 optimal weight: 7.9990 chunk 10 optimal weight: 10.0000 chunk 37 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 15 optimal weight: 8.9990 chunk 0 optimal weight: 9.9990 chunk 9 optimal weight: 0.9990 chunk 18 optimal weight: 3.9990 chunk 19 optimal weight: 4.9990 chunk 28 optimal weight: 10.0000 chunk 16 optimal weight: 0.5980 overall best weight: 2.3188 ------------------------------------------------------------------------------- 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 = 0.4031 r_free = 0.4031 target = 0.136033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.122699 restraints weight = 5335.018| |-----------------------------------------------------------------------------| r_work (start): 0.3866 rms_B_bonded: 2.37 r_work: 0.3762 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3664 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 moved from start: 0.3480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3456 Z= 0.225 Angle : 0.577 7.944 4626 Z= 0.287 Chirality : 0.051 0.168 522 Planarity : 0.002 0.020 588 Dihedral : 5.236 15.505 456 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.46 % Favored : 99.54 % Rotamer: Outliers : 2.05 % Allowed : 16.15 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.81 (0.35), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.37 (0.26), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS C 330 PHE 0.006 0.001 PHE B 346 TYR 0.023 0.003 TYR E 310 ARG 0.001 0.000 ARG E 349 *********************** 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 87 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 79 time to evaluate : 0.405 Fit side-chains REVERT: B 348 ASP cc_start: 0.8411 (OUTLIER) cc_final: 0.8132 (m-30) REVERT: D 347 LYS cc_start: 0.8214 (mttt) cc_final: 0.7705 (pttm) REVERT: D 368 ASN cc_start: 0.8647 (m-40) cc_final: 0.8406 (m-40) REVERT: F 342 GLU cc_start: 0.8157 (pt0) cc_final: 0.6709 (tp30) REVERT: C 347 LYS cc_start: 0.8745 (mttt) cc_final: 0.8316 (mptt) outliers start: 8 outliers final: 7 residues processed: 81 average time/residue: 0.0977 time to fit residues: 10.8210 Evaluate side-chains 86 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 78 time to evaluate : 0.453 ------------------------------------------------------------------------------- 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 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 5 optimal weight: 10.0000 chunk 29 optimal weight: 7.9990 chunk 33 optimal weight: 10.0000 chunk 26 optimal weight: 10.0000 chunk 39 optimal weight: 10.0000 chunk 32 optimal weight: 9.9990 chunk 13 optimal weight: 9.9990 chunk 30 optimal weight: 6.9990 chunk 14 optimal weight: 10.0000 chunk 40 optimal weight: 0.1980 chunk 3 optimal weight: 7.9990 overall best weight: 6.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 336 GLN C 329 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 = 0.3960 r_free = 0.3960 target = 0.130804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.117045 restraints weight = 5528.382| |-----------------------------------------------------------------------------| r_work (start): 0.3775 rms_B_bonded: 2.41 r_work: 0.3681 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3585 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3585 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.3817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.059 3456 Z= 0.566 Angle : 0.744 6.190 4626 Z= 0.380 Chirality : 0.054 0.177 522 Planarity : 0.003 0.017 588 Dihedral : 5.985 20.893 456 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 2.31 % Allowed : 15.90 % 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 (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: -2.17 (0.33), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.64 (0.25), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS C 362 PHE 0.011 0.003 PHE E 346 TYR 0.018 0.004 TYR E 310 ARG 0.003 0.000 ARG E 349 *********************** 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: 9 poor density : 79 time to evaluate : 0.454 Fit side-chains REVERT: D 347 LYS cc_start: 0.8185 (mttt) cc_final: 0.7644 (pttm) REVERT: C 347 LYS cc_start: 0.8783 (mttt) cc_final: 0.8336 (mptt) outliers start: 9 outliers final: 8 residues processed: 82 average time/residue: 0.0955 time to fit residues: 10.7440 Evaluate side-chains 87 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 79 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 9 optimal weight: 0.2980 chunk 15 optimal weight: 8.9990 chunk 1 optimal weight: 4.9990 chunk 7 optimal weight: 9.9990 chunk 0 optimal weight: 9.9990 chunk 40 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 3 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 11 optimal weight: 6.9990 overall best weight: 2.4588 ------------------------------------------------------------------------------- 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 = 0.4023 r_free = 0.4023 target = 0.135164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.121673 restraints weight = 5383.231| |-----------------------------------------------------------------------------| r_work (start): 0.3845 rms_B_bonded: 2.37 r_work: 0.3753 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3657 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3657 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.3829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3456 Z= 0.235 Angle : 0.579 6.451 4626 Z= 0.290 Chirality : 0.050 0.160 522 Planarity : 0.002 0.015 588 Dihedral : 5.261 17.122 456 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 2.05 % Allowed : 17.18 % Favored : 80.77 % 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: -2.16 (0.34), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.64 (0.26), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS D 362 PHE 0.006 0.001 PHE C 346 TYR 0.019 0.003 TYR E 310 ARG 0.002 0.000 ARG E 349 *********************** 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 90 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 82 time to evaluate : 0.406 Fit side-chains REVERT: D 347 LYS cc_start: 0.8104 (mttt) cc_final: 0.7603 (pttm) REVERT: D 368 ASN cc_start: 0.8673 (m-40) cc_final: 0.8461 (m-40) REVERT: F 342 GLU cc_start: 0.8222 (pt0) cc_final: 0.6724 (tp30) outliers start: 8 outliers final: 7 residues processed: 85 average time/residue: 0.0857 time to fit residues: 10.2085 Evaluate side-chains 87 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 80 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 8 optimal weight: 6.9990 chunk 36 optimal weight: 5.9990 chunk 23 optimal weight: 5.9990 chunk 27 optimal weight: 8.9990 chunk 26 optimal weight: 0.7980 chunk 5 optimal weight: 9.9990 chunk 31 optimal weight: 9.9990 chunk 10 optimal weight: 9.9990 chunk 18 optimal weight: 5.9990 chunk 15 optimal weight: 10.0000 chunk 37 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 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 = 0.3990 r_free = 0.3990 target = 0.132889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.119293 restraints weight = 5426.200| |-----------------------------------------------------------------------------| r_work (start): 0.3811 rms_B_bonded: 2.38 r_work: 0.3714 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3616 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.3987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 3456 Z= 0.367 Angle : 0.643 6.304 4626 Z= 0.322 Chirality : 0.051 0.142 522 Planarity : 0.003 0.016 588 Dihedral : 5.430 18.357 456 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 2.82 % Allowed : 16.41 % Favored : 80.77 % 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: -2.30 (0.33), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.75 (0.25), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 362 PHE 0.007 0.002 PHE E 346 TYR 0.013 0.003 TYR E 310 ARG 0.001 0.000 ARG E 349 *********************** 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 86 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 75 time to evaluate : 0.428 Fit side-chains REVERT: D 347 LYS cc_start: 0.8093 (mttt) cc_final: 0.7588 (pttm) REVERT: E 374 HIS cc_start: 0.8442 (m-70) cc_final: 0.8112 (m-70) outliers start: 11 outliers final: 11 residues processed: 78 average time/residue: 0.0871 time to fit residues: 9.5147 Evaluate side-chains 84 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 73 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 328 ILE 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 A residue 328 ILE Chi-restraints excluded: chain C residue 306 VAL Chi-restraints excluded: chain C residue 307 GLN Chi-restraints excluded: chain C residue 342 GLU 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 28 optimal weight: 10.0000 chunk 8 optimal weight: 0.8980 chunk 23 optimal weight: 0.9980 chunk 24 optimal weight: 10.0000 chunk 38 optimal weight: 20.0000 chunk 1 optimal weight: 5.9990 chunk 6 optimal weight: 3.9990 chunk 22 optimal weight: 10.0000 chunk 35 optimal weight: 0.0870 chunk 12 optimal weight: 4.9990 chunk 30 optimal weight: 4.9990 overall best weight: 2.1962 ------------------------------------------------------------------------------- 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 = 0.4031 r_free = 0.4031 target = 0.135655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.122307 restraints weight = 5322.137| |-----------------------------------------------------------------------------| r_work (start): 0.3863 rms_B_bonded: 2.36 r_work: 0.3766 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3668 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.4024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3456 Z= 0.218 Angle : 0.580 6.804 4626 Z= 0.286 Chirality : 0.051 0.187 522 Planarity : 0.002 0.019 588 Dihedral : 5.064 16.867 456 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 2.31 % Allowed : 16.67 % Favored : 81.03 % 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: -2.33 (0.33), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.76 (0.26), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 329 PHE 0.006 0.001 PHE C 346 TYR 0.011 0.002 TYR B 310 ARG 0.001 0.000 ARG C 349 *********************** 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 86 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 77 time to evaluate : 0.426 Fit side-chains REVERT: D 347 LYS cc_start: 0.8093 (mttt) cc_final: 0.7590 (pttm) REVERT: F 342 GLU cc_start: 0.8245 (pt0) cc_final: 0.6786 (tp30) REVERT: E 374 HIS cc_start: 0.8395 (m-70) cc_final: 0.8000 (m-70) outliers start: 9 outliers final: 8 residues processed: 79 average time/residue: 0.0920 time to fit residues: 10.0859 Evaluate side-chains 83 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 75 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 C residue 342 GLU 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 12 optimal weight: 0.7980 chunk 32 optimal weight: 10.0000 chunk 18 optimal weight: 3.9990 chunk 10 optimal weight: 5.9990 chunk 16 optimal weight: 3.9990 chunk 13 optimal weight: 6.9990 chunk 40 optimal weight: 5.9990 chunk 14 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 33 optimal weight: 10.0000 chunk 38 optimal weight: 7.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- 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 = 0.4068 r_free = 0.4068 target = 0.141716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.128438 restraints weight = 5126.523| |-----------------------------------------------------------------------------| r_work (start): 0.3898 rms_B_bonded: 2.34 r_work: 0.3812 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3718 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.4151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 3456 Z= 0.290 Angle : 0.606 6.710 4626 Z= 0.302 Chirality : 0.051 0.206 522 Planarity : 0.002 0.020 588 Dihedral : 5.142 17.652 456 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % 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 (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: -2.38 (0.33), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.81 (0.25), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 329 PHE 0.006 0.001 PHE C 346 TYR 0.018 0.003 TYR E 310 ARG 0.000 0.000 ARG A 349 ********************** 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 82 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 73 time to evaluate : 0.449 Fit side-chains REVERT: D 347 LYS cc_start: 0.8149 (mttt) cc_final: 0.7636 (pttm) REVERT: F 342 GLU cc_start: 0.8256 (pt0) cc_final: 0.6818 (tp30) REVERT: E 374 HIS cc_start: 0.8417 (m-70) cc_final: 0.8012 (m-70) outliers start: 9 outliers final: 8 residues processed: 76 average time/residue: 0.1015 time to fit residues: 10.9166 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 : 0.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 A residue 328 ILE Chi-restraints excluded: chain C residue 306 VAL Chi-restraints excluded: chain C residue 342 GLU 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 28 optimal weight: 9.9990 chunk 19 optimal weight: 10.0000 chunk 2 optimal weight: 0.8980 chunk 40 optimal weight: 10.0000 chunk 35 optimal weight: 0.9980 chunk 13 optimal weight: 6.9990 chunk 4 optimal weight: 0.3980 chunk 33 optimal weight: 0.9980 chunk 3 optimal weight: 3.9990 chunk 7 optimal weight: 8.9990 chunk 14 optimal weight: 0.1980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.4101 r_free = 0.4101 target = 0.140400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.127452 restraints weight = 5428.857| |-----------------------------------------------------------------------------| r_work (start): 0.3930 rms_B_bonded: 2.34 r_work: 0.3846 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3752 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.4213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.013 3456 Z= 0.113 Angle : 0.521 6.560 4626 Z= 0.257 Chirality : 0.050 0.148 522 Planarity : 0.002 0.019 588 Dihedral : 4.564 13.506 456 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Rotamer: Outliers : 1.28 % Allowed : 17.69 % Favored : 81.03 % 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: -2.28 (0.34), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.73 (0.26), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 362 PHE 0.005 0.001 PHE C 346 TYR 0.008 0.002 TYR B 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: 2083.28 seconds wall clock time: 36 minutes 51.29 seconds (2211.29 seconds total)