Starting phenix.real_space_refine on Tue Feb 11 01:09:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ot9_17173/02_2025/8ot9_17173.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ot9_17173/02_2025/8ot9_17173.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ot9_17173/02_2025/8ot9_17173.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ot9_17173/02_2025/8ot9_17173.map" model { file = "/net/cci-nas-00/data/ceres_data/8ot9_17173/02_2025/8ot9_17173.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ot9_17173/02_2025/8ot9_17173.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 6 5.16 5 C 2160 2.51 5 N 636 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 27 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 3444 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 574 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "B" Number of atoms: 574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 574 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "C" Number of atoms: 574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 574 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "D" Number of atoms: 574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 574 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "E" Number of atoms: 574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 574 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "F" Number of atoms: 574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 574 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Time building chain proxies: 3.35, per 1000 atoms: 0.97 Number of scatterers: 3444 At special positions: 0 Unit cell: (98.056, 127.72, 37.08, 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 636 7.00 C 2160 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: 0.75 Conformation dependent library (CDL) restraints added in 400.7 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: 792 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 18 sheets defined 0.0% alpha, 34.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.62 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'C' and resid 308 through 310 removed outlier: 6.829A pdb=" N VAL A 309 " --> pdb=" O TYR E 310 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 313 through 314 removed outlier: 6.799A pdb=" N VAL A 313 " --> pdb=" O ASP E 314 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 324 through 330 removed outlier: 6.357A pdb=" N LEU A 325 " --> pdb=" O GLY C 326 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N ILE C 328 " --> pdb=" O LEU A 325 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N ASN A 327 " --> pdb=" O ILE C 328 " (cutoff:3.500A) removed outlier: 9.709A pdb=" N HIS C 330 " --> pdb=" O ASN A 327 " (cutoff:3.500A) removed outlier: 8.989A pdb=" N HIS A 329 " --> pdb=" O HIS C 330 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N ILE A 328 " --> pdb=" O ASN E 327 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N HIS E 329 " --> pdb=" O ILE A 328 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N HIS A 330 " --> pdb=" O HIS E 329 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 337 through 339 removed outlier: 6.023A pdb=" N VAL A 337 " --> pdb=" O GLU C 338 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 342 through 346 removed outlier: 6.900A pdb=" N LYS C 343 " --> pdb=" O GLU A 342 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N LYS A 343 " --> pdb=" O LEU E 344 " (cutoff:3.500A) removed outlier: 8.088A pdb=" N PHE E 346 " --> pdb=" O LYS A 343 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N ASP A 345 " --> pdb=" O PHE E 346 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 350 through 357 removed outlier: 6.358A pdb=" N VAL A 350 " --> pdb=" O GLN C 351 " (cutoff:3.500A) removed outlier: 8.318A pdb=" N LYS C 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N SER A 352 " --> pdb=" O LYS C 353 " (cutoff:3.500A) removed outlier: 8.594A pdb=" N GLY C 355 " --> pdb=" O SER A 352 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N ILE A 354 " --> pdb=" O GLY C 355 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N LEU C 357 " --> pdb=" O ILE A 354 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N SER A 356 " --> pdb=" O LEU C 357 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 360 through 362 removed outlier: 6.186A pdb=" N THR A 361 " --> pdb=" O HIS C 362 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 371 through 374 removed outlier: 6.841A pdb=" N ILE A 371 " --> pdb=" O GLU E 372 " (cutoff:3.500A) removed outlier: 7.893A pdb=" N HIS E 374 " --> pdb=" O ILE A 371 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N THR A 373 " --> pdb=" O HIS E 374 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 377 through 378 removed outlier: 6.549A pdb=" N THR A 377 " --> pdb=" O PHE E 378 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 308 through 310 removed outlier: 6.880A pdb=" N VAL B 309 " --> pdb=" O TYR D 310 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 313 through 314 removed outlier: 6.742A pdb=" N VAL B 313 " --> pdb=" O ASP D 314 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 324 through 325 removed outlier: 6.159A pdb=" N SER B 324 " --> pdb=" O LEU D 325 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 337 through 339 removed outlier: 6.034A pdb=" N VAL B 337 " --> pdb=" O GLU F 338 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 342 through 346 removed outlier: 8.685A pdb=" N GLU B 342 " --> pdb=" O LYS D 343 " (cutoff:3.500A) removed outlier: 8.003A pdb=" N ASP D 345 " --> pdb=" O GLU B 342 " (cutoff:3.500A) removed outlier: 9.024A pdb=" N LEU B 344 " --> pdb=" O ASP D 345 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N LEU F 344 " --> pdb=" O LYS B 343 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N ASP B 345 " --> pdb=" O LEU F 344 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N PHE F 346 " --> pdb=" O ASP B 345 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 350 through 357 removed outlier: 6.457A pdb=" N VAL B 350 " --> pdb=" O GLN F 351 " (cutoff:3.500A) removed outlier: 8.305A pdb=" N LYS F 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N SER B 352 " --> pdb=" O LYS F 353 " (cutoff:3.500A) removed outlier: 8.443A pdb=" N GLY F 355 " --> pdb=" O SER B 352 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N ILE B 354 " --> pdb=" O GLY F 355 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N LEU F 357 " --> pdb=" O ILE B 354 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N SER B 356 " --> pdb=" O LEU F 357 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 360 through 362 removed outlier: 6.223A pdb=" N THR B 361 " --> pdb=" O HIS F 362 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 371 through 374 removed outlier: 6.730A pdb=" N ILE B 371 " --> pdb=" O GLU D 372 " (cutoff:3.500A) removed outlier: 7.832A pdb=" N HIS D 374 " --> pdb=" O ILE B 371 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N THR B 373 " --> pdb=" O HIS D 374 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 377 through 378 removed outlier: 6.659A pdb=" N THR B 377 " --> pdb=" O PHE D 378 " (cutoff:3.500A) 44 hydrogen bonds defined for protein. 132 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.15 Time building geometry restraints manager: 0.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 918 1.33 - 1.45: 767 1.45 - 1.57: 1807 1.57 - 1.69: 0 1.69 - 1.81: 6 Bond restraints: 3498 Sorted by residual: bond pdb=" CG HIS F 362 " pdb=" CD2 HIS F 362 " ideal model delta sigma weight residual 1.354 1.292 0.062 1.10e-02 8.26e+03 3.16e+01 bond pdb=" CG HIS B 362 " pdb=" CD2 HIS B 362 " ideal model delta sigma weight residual 1.354 1.292 0.062 1.10e-02 8.26e+03 3.15e+01 bond pdb=" CG HIS D 362 " pdb=" CD2 HIS D 362 " ideal model delta sigma weight residual 1.354 1.292 0.062 1.10e-02 8.26e+03 3.13e+01 bond pdb=" CG HIS D 330 " pdb=" CD2 HIS D 330 " ideal model delta sigma weight residual 1.354 1.296 0.058 1.10e-02 8.26e+03 2.82e+01 bond pdb=" CG HIS F 330 " pdb=" CD2 HIS F 330 " ideal model delta sigma weight residual 1.354 1.296 0.058 1.10e-02 8.26e+03 2.77e+01 ... (remaining 3493 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.62: 3412 1.62 - 3.24: 917 3.24 - 4.86: 254 4.86 - 6.48: 79 6.48 - 8.10: 18 Bond angle restraints: 4680 Sorted by residual: angle pdb=" CB HIS B 362 " pdb=" CG HIS B 362 " pdb=" CD2 HIS B 362 " ideal model delta sigma weight residual 131.20 124.11 7.09 1.30e+00 5.92e-01 2.98e+01 angle pdb=" CB HIS F 362 " pdb=" CG HIS F 362 " pdb=" CD2 HIS F 362 " ideal model delta sigma weight residual 131.20 124.11 7.09 1.30e+00 5.92e-01 2.98e+01 angle pdb=" CB HIS D 362 " pdb=" CG HIS D 362 " pdb=" CD2 HIS D 362 " ideal model delta sigma weight residual 131.20 124.12 7.08 1.30e+00 5.92e-01 2.96e+01 angle pdb=" CB HIS D 362 " pdb=" CG HIS D 362 " pdb=" ND1 HIS D 362 " ideal model delta sigma weight residual 122.70 129.58 -6.88 1.50e+00 4.44e-01 2.10e+01 angle pdb=" C PRO C 332 " pdb=" CA PRO C 332 " pdb=" CB PRO C 332 " ideal model delta sigma weight residual 110.85 117.32 -6.47 1.41e+00 5.03e-01 2.10e+01 ... (remaining 4675 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.83: 1743 14.83 - 29.67: 312 29.67 - 44.50: 60 44.50 - 59.34: 18 59.34 - 74.17: 3 Dihedral angle restraints: 2136 sinusoidal: 894 harmonic: 1242 Sorted by residual: dihedral pdb=" CA VAL A 306 " pdb=" C VAL A 306 " pdb=" N GLN A 307 " pdb=" CA GLN A 307 " ideal model delta harmonic sigma weight residual 180.00 146.02 33.98 0 5.00e+00 4.00e-02 4.62e+01 dihedral pdb=" CA VAL C 306 " pdb=" C VAL C 306 " pdb=" N GLN C 307 " pdb=" CA GLN C 307 " ideal model delta harmonic sigma weight residual 180.00 146.02 33.98 0 5.00e+00 4.00e-02 4.62e+01 dihedral pdb=" CA VAL E 306 " pdb=" C VAL E 306 " pdb=" N GLN E 307 " pdb=" CA GLN E 307 " ideal model delta harmonic sigma weight residual 180.00 146.05 33.95 0 5.00e+00 4.00e-02 4.61e+01 ... (remaining 2133 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 286 0.073 - 0.146: 188 0.146 - 0.219: 36 0.219 - 0.291: 9 0.291 - 0.364: 9 Chirality restraints: 528 Sorted by residual: chirality pdb=" CB ILE C 328 " pdb=" CA ILE C 328 " pdb=" CG1 ILE C 328 " pdb=" CG2 ILE C 328 " both_signs ideal model delta sigma weight residual False 2.64 2.28 0.36 2.00e-01 2.50e+01 3.32e+00 chirality pdb=" CB ILE A 328 " pdb=" CA ILE A 328 " pdb=" CG1 ILE A 328 " pdb=" CG2 ILE A 328 " both_signs ideal model delta sigma weight residual False 2.64 2.28 0.36 2.00e-01 2.50e+01 3.29e+00 chirality pdb=" CB ILE E 328 " pdb=" CA ILE E 328 " pdb=" CG1 ILE E 328 " pdb=" CG2 ILE E 328 " both_signs ideal model delta sigma weight residual False 2.64 2.28 0.36 2.00e-01 2.50e+01 3.27e+00 ... (remaining 525 not shown) Planarity restraints: 594 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG F 349 " 0.234 9.50e-02 1.11e+02 1.05e-01 7.44e+00 pdb=" NE ARG F 349 " -0.019 2.00e-02 2.50e+03 pdb=" CZ ARG F 349 " 0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG F 349 " -0.007 2.00e-02 2.50e+03 pdb=" NH2 ARG F 349 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 349 " 0.234 9.50e-02 1.11e+02 1.05e-01 7.39e+00 pdb=" NE ARG B 349 " -0.019 2.00e-02 2.50e+03 pdb=" CZ ARG B 349 " 0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG B 349 " -0.007 2.00e-02 2.50e+03 pdb=" NH2 ARG B 349 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 349 " 0.234 9.50e-02 1.11e+02 1.05e-01 7.38e+00 pdb=" NE ARG D 349 " -0.019 2.00e-02 2.50e+03 pdb=" CZ ARG D 349 " 0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG D 349 " -0.007 2.00e-02 2.50e+03 pdb=" NH2 ARG D 349 " 0.004 2.00e-02 2.50e+03 ... (remaining 591 not shown) Histogram of nonbonded interaction distances: 2.41 - 2.91: 1305 2.91 - 3.41: 3126 3.41 - 3.91: 5461 3.91 - 4.40: 5760 4.40 - 4.90: 11555 Nonbonded interactions: 27207 Sorted by model distance: nonbonded pdb=" OG1 THR B 361 " pdb=" ND1 HIS F 330 " model vdw 2.415 3.120 nonbonded pdb=" ND1 HIS B 330 " pdb=" OG1 THR D 361 " model vdw 2.415 3.120 nonbonded pdb=" N GLY A 366 " pdb=" O GLY C 366 " model vdw 2.555 3.120 nonbonded pdb=" O GLY A 366 " pdb=" N GLY E 366 " model vdw 2.555 3.120 nonbonded pdb=" O PRO B 332 " pdb=" OG SER D 356 " model vdw 2.570 3.040 ... (remaining 27202 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: 2.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.160 Check model and map are aligned: 0.020 Set scattering table: 0.050 Process input model: 14.290 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8755 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 : 0.009 0.062 3498 Z= 0.590 Angle : 1.750 8.101 4680 Z= 1.116 Chirality : 0.099 0.364 528 Planarity : 0.013 0.105 594 Dihedral : 15.346 74.171 1344 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 6.82 % Allowed : 5.30 % Favored : 87.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 1.41 % 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: -5.00 (0.21), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.81 (0.16), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.014 0.006 HIS F 362 PHE 0.017 0.004 PHE F 346 TYR 0.025 0.006 TYR F 310 ARG 0.017 0.004 ARG C 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 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 115 time to evaluate : 0.445 Fit side-chains REVERT: A 331 LYS cc_start: 0.9130 (OUTLIER) cc_final: 0.8891 (ttpt) REVERT: A 348 ASP cc_start: 0.9022 (t0) cc_final: 0.8673 (t0) REVERT: B 311 LYS cc_start: 0.9019 (mtmt) cc_final: 0.8342 (tttt) REVERT: C 349 ARG cc_start: 0.9057 (mtt180) cc_final: 0.7479 (mmp-170) REVERT: C 375 LYS cc_start: 0.8746 (tttt) cc_final: 0.8507 (ttmm) REVERT: D 311 LYS cc_start: 0.9035 (mtmt) cc_final: 0.8410 (tttt) REVERT: D 349 ARG cc_start: 0.8988 (ptt-90) cc_final: 0.8715 (ptm-80) REVERT: E 311 LYS cc_start: 0.9046 (mtmt) cc_final: 0.8725 (mmtt) REVERT: E 340 LYS cc_start: 0.8736 (mttt) cc_final: 0.8535 (mtpp) REVERT: E 375 LYS cc_start: 0.8670 (tttt) cc_final: 0.8421 (ttmm) REVERT: F 311 LYS cc_start: 0.8922 (mtmt) cc_final: 0.8253 (tttt) REVERT: F 317 LYS cc_start: 0.8646 (pttt) cc_final: 0.8377 (pttp) REVERT: F 320 SER cc_start: 0.8939 (OUTLIER) cc_final: 0.8626 (m) REVERT: F 328 ILE cc_start: 0.9095 (OUTLIER) cc_final: 0.8810 (mm) REVERT: F 349 ARG cc_start: 0.8876 (ptt-90) cc_final: 0.7300 (mmm160) outliers start: 27 outliers final: 4 residues processed: 131 average time/residue: 0.3352 time to fit residues: 48.4084 Evaluate side-chains 73 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 66 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 331 LYS Chi-restraints excluded: chain B residue 356 SER Chi-restraints excluded: chain D residue 356 SER Chi-restraints excluded: chain E residue 320 SER Chi-restraints excluded: chain F residue 320 SER Chi-restraints excluded: chain F residue 328 ILE Chi-restraints excluded: chain F residue 356 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 9.9990 chunk 31 optimal weight: 6.9990 chunk 17 optimal weight: 0.9990 chunk 10 optimal weight: 6.9990 chunk 21 optimal weight: 5.9990 chunk 32 optimal weight: 4.9990 chunk 12 optimal weight: 6.9990 chunk 20 optimal weight: 2.9990 chunk 24 optimal weight: 9.9990 chunk 38 optimal weight: 8.9990 chunk 11 optimal weight: 1.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 307 GLN ** D 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 368 ASN E 330 HIS ** E 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 368 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.105109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.092418 restraints weight = 5372.432| |-----------------------------------------------------------------------------| r_work (start): 0.3551 rms_B_bonded: 2.43 r_work: 0.3440 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3350 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 moved from start: 0.2812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 3498 Z= 0.329 Angle : 0.688 6.790 4680 Z= 0.348 Chirality : 0.051 0.131 528 Planarity : 0.004 0.023 594 Dihedral : 7.224 52.251 473 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 3.03 % Allowed : 9.85 % Favored : 87.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.50 (0.28), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.66 (0.21), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS B 362 PHE 0.007 0.001 PHE F 378 TYR 0.025 0.003 TYR A 310 ARG 0.004 0.001 ARG A 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 102 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 90 time to evaluate : 0.406 Fit side-chains REVERT: A 311 LYS cc_start: 0.8953 (OUTLIER) cc_final: 0.8702 (mmtt) REVERT: A 343 LYS cc_start: 0.8361 (mttp) cc_final: 0.8081 (mttp) REVERT: A 349 ARG cc_start: 0.8674 (mtt-85) cc_final: 0.8353 (mtp85) REVERT: B 311 LYS cc_start: 0.9004 (mtmt) cc_final: 0.8226 (tttt) REVERT: C 331 LYS cc_start: 0.8909 (tttm) cc_final: 0.8505 (ttpt) REVERT: C 347 LYS cc_start: 0.8686 (mmtp) cc_final: 0.8451 (mmtp) REVERT: C 349 ARG cc_start: 0.8635 (mtt180) cc_final: 0.6909 (mmm160) REVERT: C 375 LYS cc_start: 0.8568 (tttt) cc_final: 0.8143 (ttmm) REVERT: D 311 LYS cc_start: 0.8966 (mtmt) cc_final: 0.8279 (tttt) REVERT: D 320 SER cc_start: 0.8748 (t) cc_final: 0.8083 (m) REVERT: D 368 ASN cc_start: 0.8645 (m110) cc_final: 0.8400 (m-40) REVERT: E 311 LYS cc_start: 0.8808 (mtmt) cc_final: 0.8371 (mmtt) REVERT: E 340 LYS cc_start: 0.8765 (mttt) cc_final: 0.8365 (mtpp) REVERT: E 375 LYS cc_start: 0.8649 (tttt) cc_final: 0.8225 (ttmm) REVERT: F 311 LYS cc_start: 0.8907 (mtmt) cc_final: 0.8167 (tttt) REVERT: F 349 ARG cc_start: 0.8398 (ptt-90) cc_final: 0.6635 (mmm160) REVERT: F 350 VAL cc_start: 0.9028 (OUTLIER) cc_final: 0.8802 (m) outliers start: 12 outliers final: 4 residues processed: 99 average time/residue: 0.2485 time to fit residues: 27.8707 Evaluate side-chains 83 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 77 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 311 LYS Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain D residue 350 VAL Chi-restraints excluded: chain F residue 350 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 19 optimal weight: 8.9990 chunk 34 optimal weight: 10.0000 chunk 7 optimal weight: 10.0000 chunk 24 optimal weight: 9.9990 chunk 22 optimal weight: 6.9990 chunk 27 optimal weight: 5.9990 chunk 0 optimal weight: 8.9990 chunk 1 optimal weight: 2.9990 chunk 3 optimal weight: 9.9990 chunk 16 optimal weight: 5.9990 chunk 25 optimal weight: 0.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 330 HIS ** D 362 HIS ** 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 = 0.3637 r_free = 0.3637 target = 0.102620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.089905 restraints weight = 5302.973| |-----------------------------------------------------------------------------| r_work (start): 0.3510 rms_B_bonded: 2.25 r_work: 0.3407 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3317 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8608 moved from start: 0.3210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 3498 Z= 0.401 Angle : 0.682 5.185 4680 Z= 0.348 Chirality : 0.050 0.133 528 Planarity : 0.003 0.023 594 Dihedral : 5.423 13.715 462 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 1.26 % Allowed : 13.64 % Favored : 85.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.03 (0.31), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.30 (0.23), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS B 362 PHE 0.009 0.002 PHE A 346 TYR 0.019 0.003 TYR A 310 ARG 0.002 0.000 ARG A 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 78 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 73 time to evaluate : 0.366 Fit side-chains REVERT: A 311 LYS cc_start: 0.8893 (OUTLIER) cc_final: 0.8580 (mmtt) REVERT: A 343 LYS cc_start: 0.8476 (mttp) cc_final: 0.8197 (mttp) REVERT: A 348 ASP cc_start: 0.9261 (t70) cc_final: 0.9049 (t70) REVERT: B 311 LYS cc_start: 0.9019 (mtmt) cc_final: 0.8298 (tttt) REVERT: C 349 ARG cc_start: 0.8677 (mtt180) cc_final: 0.6954 (mmm160) REVERT: C 375 LYS cc_start: 0.8658 (tttt) cc_final: 0.8169 (ttmm) REVERT: D 311 LYS cc_start: 0.8903 (mtmt) cc_final: 0.8267 (tttt) REVERT: D 320 SER cc_start: 0.8763 (t) cc_final: 0.8123 (m) REVERT: E 311 LYS cc_start: 0.8799 (mtmt) cc_final: 0.8444 (mttt) REVERT: E 375 LYS cc_start: 0.8649 (tttt) cc_final: 0.8259 (ttmm) REVERT: F 311 LYS cc_start: 0.8874 (mtmt) cc_final: 0.8213 (tttt) REVERT: F 349 ARG cc_start: 0.8439 (ptt-90) cc_final: 0.6737 (mmm160) outliers start: 5 outliers final: 2 residues processed: 77 average time/residue: 0.2365 time to fit residues: 21.0274 Evaluate side-chains 69 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 66 time to evaluate : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 311 LYS Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain D residue 350 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 26 optimal weight: 3.9990 chunk 13 optimal weight: 0.9990 chunk 7 optimal weight: 8.9990 chunk 33 optimal weight: 8.9990 chunk 29 optimal weight: 7.9990 chunk 22 optimal weight: 5.9990 chunk 25 optimal weight: 5.9990 chunk 18 optimal weight: 8.9990 chunk 21 optimal weight: 7.9990 chunk 14 optimal weight: 1.9990 chunk 11 optimal weight: 6.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.104388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.091645 restraints weight = 5373.876| |-----------------------------------------------------------------------------| r_work (start): 0.3538 rms_B_bonded: 2.31 r_work: 0.3432 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3342 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8583 moved from start: 0.3440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 3498 Z= 0.332 Angle : 0.636 6.163 4680 Z= 0.319 Chirality : 0.049 0.128 528 Planarity : 0.003 0.021 594 Dihedral : 5.017 12.736 462 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 1.26 % Allowed : 15.91 % Favored : 82.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.79 (0.31), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.12 (0.24), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS B 362 PHE 0.008 0.002 PHE A 346 TYR 0.021 0.003 TYR C 310 ARG 0.002 0.000 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 76 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 71 time to evaluate : 0.390 Fit side-chains REVERT: A 348 ASP cc_start: 0.9189 (t70) cc_final: 0.8783 (t0) REVERT: B 311 LYS cc_start: 0.8970 (mtmt) cc_final: 0.8239 (tttt) REVERT: C 349 ARG cc_start: 0.8756 (mtt180) cc_final: 0.6970 (mmm160) REVERT: C 375 LYS cc_start: 0.8622 (tttt) cc_final: 0.8186 (ttmm) REVERT: D 311 LYS cc_start: 0.8904 (mtmt) cc_final: 0.8240 (tttt) REVERT: D 320 SER cc_start: 0.8733 (t) cc_final: 0.8069 (m) REVERT: E 311 LYS cc_start: 0.8817 (mtmt) cc_final: 0.8440 (mttt) REVERT: E 314 ASP cc_start: 0.8712 (t0) cc_final: 0.8494 (t0) REVERT: E 375 LYS cc_start: 0.8685 (tttt) cc_final: 0.8272 (ttmm) REVERT: F 311 LYS cc_start: 0.8813 (mtmt) cc_final: 0.8146 (tttt) REVERT: F 349 ARG cc_start: 0.8400 (ptt-90) cc_final: 0.6575 (mmm160) outliers start: 5 outliers final: 3 residues processed: 73 average time/residue: 0.2470 time to fit residues: 20.5903 Evaluate side-chains 69 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 66 time to evaluate : 0.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain D residue 350 VAL Chi-restraints excluded: chain F residue 350 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 41 optimal weight: 0.2980 chunk 24 optimal weight: 9.9990 chunk 7 optimal weight: 10.0000 chunk 15 optimal weight: 0.8980 chunk 30 optimal weight: 7.9990 chunk 25 optimal weight: 7.9990 chunk 6 optimal weight: 9.9990 chunk 22 optimal weight: 10.0000 chunk 3 optimal weight: 10.0000 chunk 32 optimal weight: 8.9990 chunk 1 optimal weight: 7.9990 overall best weight: 5.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.101897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.089292 restraints weight = 5394.286| |-----------------------------------------------------------------------------| r_work (start): 0.3496 rms_B_bonded: 2.26 r_work: 0.3392 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3302 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8610 moved from start: 0.3534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 3498 Z= 0.430 Angle : 0.659 5.334 4680 Z= 0.337 Chirality : 0.050 0.128 528 Planarity : 0.003 0.026 594 Dihedral : 5.129 13.427 462 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.26 % Allowed : 16.16 % Favored : 82.58 % 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: -2.76 (0.31), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.09 (0.24), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS B 362 PHE 0.010 0.002 PHE A 346 TYR 0.019 0.003 TYR C 310 ARG 0.002 0.000 ARG C 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 79 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 74 time to evaluate : 0.386 Fit side-chains REVERT: A 311 LYS cc_start: 0.8855 (OUTLIER) cc_final: 0.8541 (mttm) REVERT: A 375 LYS cc_start: 0.8799 (ttmt) cc_final: 0.8450 (ttmm) REVERT: B 311 LYS cc_start: 0.8993 (mtmt) cc_final: 0.8261 (tttt) REVERT: C 349 ARG cc_start: 0.8706 (mtt180) cc_final: 0.6974 (mmm160) REVERT: C 375 LYS cc_start: 0.8703 (tttt) cc_final: 0.8244 (ttmm) REVERT: D 311 LYS cc_start: 0.8905 (mtmt) cc_final: 0.8276 (tttt) REVERT: D 320 SER cc_start: 0.8766 (t) cc_final: 0.8110 (m) REVERT: E 311 LYS cc_start: 0.8855 (mtmt) cc_final: 0.8473 (mttt) REVERT: E 375 LYS cc_start: 0.8662 (tttt) cc_final: 0.8252 (ttmm) REVERT: F 311 LYS cc_start: 0.8852 (mtmt) cc_final: 0.8189 (tttt) REVERT: F 349 ARG cc_start: 0.8407 (ptt-90) cc_final: 0.6616 (mmm160) outliers start: 5 outliers final: 4 residues processed: 78 average time/residue: 0.2483 time to fit residues: 22.0483 Evaluate side-chains 74 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 69 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 311 LYS Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain D residue 350 VAL Chi-restraints excluded: chain F residue 350 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 25 optimal weight: 2.9990 chunk 24 optimal weight: 6.9990 chunk 6 optimal weight: 8.9990 chunk 21 optimal weight: 0.5980 chunk 7 optimal weight: 5.9990 chunk 27 optimal weight: 10.0000 chunk 2 optimal weight: 8.9990 chunk 15 optimal weight: 7.9990 chunk 40 optimal weight: 5.9990 chunk 4 optimal weight: 3.9990 chunk 16 optimal weight: 0.9980 overall best weight: 2.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.105307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.092651 restraints weight = 5386.674| |-----------------------------------------------------------------------------| r_work (start): 0.3552 rms_B_bonded: 2.31 r_work: 0.3446 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3354 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.3682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 3498 Z= 0.255 Angle : 0.581 5.868 4680 Z= 0.291 Chirality : 0.048 0.122 528 Planarity : 0.003 0.024 594 Dihedral : 4.769 12.999 462 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 1.77 % Allowed : 16.16 % Favored : 82.07 % 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: -2.59 (0.32), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.97 (0.24), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS B 362 PHE 0.007 0.001 PHE A 346 TYR 0.016 0.003 TYR C 310 ARG 0.001 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 83 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 76 time to evaluate : 0.433 Fit side-chains REVERT: A 311 LYS cc_start: 0.8823 (OUTLIER) cc_final: 0.8513 (mttm) REVERT: A 375 LYS cc_start: 0.8749 (ttmt) cc_final: 0.8402 (ttmm) REVERT: B 311 LYS cc_start: 0.8934 (mtmt) cc_final: 0.8220 (tttt) REVERT: B 327 ASN cc_start: 0.9325 (m-40) cc_final: 0.8976 (m-40) REVERT: B 356 SER cc_start: 0.8353 (OUTLIER) cc_final: 0.7964 (t) REVERT: C 349 ARG cc_start: 0.8748 (mtt180) cc_final: 0.6960 (mmm160) REVERT: C 375 LYS cc_start: 0.8634 (tttt) cc_final: 0.8170 (ttmm) REVERT: E 311 LYS cc_start: 0.8821 (mtmt) cc_final: 0.8425 (mttt) REVERT: E 314 ASP cc_start: 0.8650 (t0) cc_final: 0.8438 (t0) REVERT: E 375 LYS cc_start: 0.8653 (tttt) cc_final: 0.8237 (ttmm) REVERT: F 311 LYS cc_start: 0.8778 (mtmt) cc_final: 0.8145 (tttt) REVERT: F 349 ARG cc_start: 0.8329 (ptt-90) cc_final: 0.6501 (mmm160) outliers start: 7 outliers final: 3 residues processed: 81 average time/residue: 0.2340 time to fit residues: 21.8456 Evaluate side-chains 70 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 65 time to evaluate : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 311 LYS Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 356 SER Chi-restraints excluded: chain F residue 350 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 36 optimal weight: 10.0000 chunk 15 optimal weight: 10.0000 chunk 26 optimal weight: 9.9990 chunk 16 optimal weight: 7.9990 chunk 2 optimal weight: 2.9990 chunk 9 optimal weight: 5.9990 chunk 20 optimal weight: 7.9990 chunk 3 optimal weight: 9.9990 chunk 37 optimal weight: 4.9990 chunk 24 optimal weight: 5.9990 chunk 39 optimal weight: 10.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.101007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.088517 restraints weight = 5479.258| |-----------------------------------------------------------------------------| r_work (start): 0.3487 rms_B_bonded: 2.25 r_work: 0.3381 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3291 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8623 moved from start: 0.3651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.043 3498 Z= 0.473 Angle : 0.693 7.962 4680 Z= 0.350 Chirality : 0.051 0.126 528 Planarity : 0.003 0.024 594 Dihedral : 5.178 13.169 462 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 1.77 % Allowed : 17.68 % Favored : 80.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.65 (0.32), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.01 (0.24), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.002 HIS B 362 PHE 0.010 0.002 PHE A 346 TYR 0.016 0.003 TYR C 310 ARG 0.002 0.000 ARG C 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 76 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 69 time to evaluate : 0.436 Fit side-chains REVERT: A 311 LYS cc_start: 0.8855 (OUTLIER) cc_final: 0.8536 (mttm) REVERT: A 375 LYS cc_start: 0.8816 (ttmt) cc_final: 0.8479 (ttmm) REVERT: B 311 LYS cc_start: 0.8979 (mtmt) cc_final: 0.8245 (tttt) REVERT: B 356 SER cc_start: 0.8431 (OUTLIER) cc_final: 0.8018 (t) REVERT: C 349 ARG cc_start: 0.8726 (mtt180) cc_final: 0.6961 (mmm160) REVERT: C 375 LYS cc_start: 0.8712 (tttt) cc_final: 0.8285 (ttmm) REVERT: D 311 LYS cc_start: 0.8907 (mtmt) cc_final: 0.8270 (tttt) REVERT: D 320 SER cc_start: 0.8737 (t) cc_final: 0.7874 (m) REVERT: E 311 LYS cc_start: 0.8862 (mtmt) cc_final: 0.8469 (mttt) REVERT: E 375 LYS cc_start: 0.8685 (tttt) cc_final: 0.8259 (ttmm) REVERT: F 311 LYS cc_start: 0.8833 (mtmt) cc_final: 0.8164 (tttt) REVERT: F 349 ARG cc_start: 0.8444 (ptt-90) cc_final: 0.6667 (mmm160) outliers start: 7 outliers final: 5 residues processed: 75 average time/residue: 0.2566 time to fit residues: 21.9145 Evaluate side-chains 74 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 67 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 311 LYS Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 356 SER Chi-restraints excluded: chain D residue 350 VAL Chi-restraints excluded: chain F residue 350 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 16 optimal weight: 2.9990 chunk 10 optimal weight: 5.9990 chunk 3 optimal weight: 9.9990 chunk 31 optimal weight: 7.9990 chunk 23 optimal weight: 4.9990 chunk 39 optimal weight: 6.9990 chunk 24 optimal weight: 3.9990 chunk 18 optimal weight: 7.9990 chunk 25 optimal weight: 3.9990 chunk 6 optimal weight: 6.9990 chunk 41 optimal weight: 4.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.102842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.090361 restraints weight = 5518.296| |-----------------------------------------------------------------------------| r_work (start): 0.3516 rms_B_bonded: 2.31 r_work: 0.3410 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3319 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8604 moved from start: 0.3738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 3498 Z= 0.360 Angle : 0.640 6.100 4680 Z= 0.322 Chirality : 0.050 0.123 528 Planarity : 0.003 0.032 594 Dihedral : 5.009 13.187 462 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.77 % Allowed : 17.93 % Favored : 80.30 % 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: -2.59 (0.33), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.96 (0.25), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS B 362 PHE 0.008 0.002 PHE A 346 TYR 0.016 0.003 TYR C 310 ARG 0.004 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 74 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 67 time to evaluate : 0.434 Fit side-chains REVERT: A 311 LYS cc_start: 0.8849 (OUTLIER) cc_final: 0.8530 (mttm) REVERT: A 375 LYS cc_start: 0.8796 (ttmt) cc_final: 0.8462 (ttmm) REVERT: B 311 LYS cc_start: 0.8953 (mtmt) cc_final: 0.8225 (tttt) REVERT: B 356 SER cc_start: 0.8386 (OUTLIER) cc_final: 0.7974 (t) REVERT: C 349 ARG cc_start: 0.8716 (mtt180) cc_final: 0.6930 (mmm160) REVERT: C 375 LYS cc_start: 0.8682 (tttt) cc_final: 0.8241 (ttmm) REVERT: E 311 LYS cc_start: 0.8834 (mtmt) cc_final: 0.8441 (mttt) REVERT: E 375 LYS cc_start: 0.8684 (tttt) cc_final: 0.8236 (ttmm) REVERT: F 311 LYS cc_start: 0.8817 (mtmt) cc_final: 0.8143 (tttt) REVERT: F 349 ARG cc_start: 0.8378 (ptt-90) cc_final: 0.6483 (mmm160) outliers start: 7 outliers final: 5 residues processed: 73 average time/residue: 0.2451 time to fit residues: 20.5364 Evaluate side-chains 74 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 67 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 311 LYS Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 356 SER Chi-restraints excluded: chain D residue 350 VAL Chi-restraints excluded: chain F residue 350 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 22 optimal weight: 10.0000 chunk 8 optimal weight: 4.9990 chunk 27 optimal weight: 5.9990 chunk 37 optimal weight: 9.9990 chunk 39 optimal weight: 10.0000 chunk 17 optimal weight: 9.9990 chunk 14 optimal weight: 6.9990 chunk 13 optimal weight: 0.0020 chunk 3 optimal weight: 3.9990 chunk 40 optimal weight: 4.9990 chunk 21 optimal weight: 5.9990 overall best weight: 3.9996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.103080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.090536 restraints weight = 5424.503| |-----------------------------------------------------------------------------| r_work (start): 0.3518 rms_B_bonded: 2.32 r_work: 0.3411 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3320 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8598 moved from start: 0.3787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 3498 Z= 0.343 Angle : 0.632 5.922 4680 Z= 0.317 Chirality : 0.049 0.124 528 Planarity : 0.003 0.025 594 Dihedral : 4.940 13.134 462 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 1.77 % Allowed : 18.18 % Favored : 80.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.55 (0.33), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.93 (0.25), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS B 362 PHE 0.007 0.002 PHE A 346 TYR 0.015 0.003 TYR C 310 ARG 0.003 0.000 ARG E 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 76 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 69 time to evaluate : 0.425 Fit side-chains REVERT: A 311 LYS cc_start: 0.8838 (OUTLIER) cc_final: 0.8518 (mttm) REVERT: A 375 LYS cc_start: 0.8793 (ttmt) cc_final: 0.8458 (ttmm) REVERT: B 311 LYS cc_start: 0.8946 (mtmt) cc_final: 0.8204 (tttt) REVERT: B 356 SER cc_start: 0.8369 (OUTLIER) cc_final: 0.7950 (t) REVERT: C 349 ARG cc_start: 0.8753 (mtt180) cc_final: 0.6949 (mmm160) REVERT: C 375 LYS cc_start: 0.8690 (tttt) cc_final: 0.8246 (ttmm) REVERT: D 320 SER cc_start: 0.8689 (t) cc_final: 0.7837 (m) REVERT: E 311 LYS cc_start: 0.8815 (mtmt) cc_final: 0.8414 (mttt) REVERT: E 375 LYS cc_start: 0.8693 (tttt) cc_final: 0.8243 (ttmm) REVERT: F 311 LYS cc_start: 0.8796 (mtmt) cc_final: 0.8114 (tttt) REVERT: F 349 ARG cc_start: 0.8385 (ptt-90) cc_final: 0.6495 (mmm160) outliers start: 7 outliers final: 5 residues processed: 75 average time/residue: 0.2439 time to fit residues: 20.9176 Evaluate side-chains 76 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 69 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 311 LYS Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 356 SER Chi-restraints excluded: chain D residue 350 VAL Chi-restraints excluded: chain F residue 350 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 24 optimal weight: 9.9990 chunk 8 optimal weight: 10.0000 chunk 32 optimal weight: 7.9990 chunk 23 optimal weight: 7.9990 chunk 16 optimal weight: 5.9990 chunk 27 optimal weight: 8.9990 chunk 18 optimal weight: 10.0000 chunk 38 optimal weight: 8.9990 chunk 15 optimal weight: 0.5980 chunk 1 optimal weight: 6.9990 chunk 19 optimal weight: 0.0980 overall best weight: 4.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.102476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.089994 restraints weight = 5529.300| |-----------------------------------------------------------------------------| r_work (start): 0.3511 rms_B_bonded: 2.31 r_work: 0.3405 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3313 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8601 moved from start: 0.3809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.035 3498 Z= 0.370 Angle : 0.644 6.242 4680 Z= 0.323 Chirality : 0.050 0.125 528 Planarity : 0.004 0.045 594 Dihedral : 4.990 13.237 462 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.77 % Allowed : 17.93 % Favored : 80.30 % 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: -2.54 (0.33), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.93 (0.25), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS B 362 PHE 0.008 0.002 PHE A 346 TYR 0.015 0.003 TYR C 310 ARG 0.008 0.001 ARG E 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 75 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 68 time to evaluate : 0.396 Fit side-chains REVERT: A 311 LYS cc_start: 0.8846 (OUTLIER) cc_final: 0.8520 (mttm) REVERT: A 375 LYS cc_start: 0.8799 (ttmt) cc_final: 0.8463 (ttmm) REVERT: B 311 LYS cc_start: 0.8956 (mtmt) cc_final: 0.8218 (tttt) REVERT: B 356 SER cc_start: 0.8376 (OUTLIER) cc_final: 0.7951 (t) REVERT: C 349 ARG cc_start: 0.8715 (mtt180) cc_final: 0.6913 (mmm160) REVERT: C 375 LYS cc_start: 0.8695 (tttt) cc_final: 0.8229 (ttmm) REVERT: E 311 LYS cc_start: 0.8833 (mtmt) cc_final: 0.8438 (mttt) REVERT: E 375 LYS cc_start: 0.8680 (tttt) cc_final: 0.8218 (ttmm) REVERT: F 311 LYS cc_start: 0.8820 (mtmt) cc_final: 0.8136 (tttt) REVERT: F 349 ARG cc_start: 0.8412 (ptt-90) cc_final: 0.6580 (mmm160) outliers start: 7 outliers final: 5 residues processed: 74 average time/residue: 0.2566 time to fit residues: 21.6921 Evaluate side-chains 74 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 67 time to evaluate : 0.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 311 LYS Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 356 SER Chi-restraints excluded: chain D residue 350 VAL Chi-restraints excluded: chain F residue 350 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 30 optimal weight: 0.0370 chunk 35 optimal weight: 7.9990 chunk 21 optimal weight: 10.0000 chunk 7 optimal weight: 0.9980 chunk 29 optimal weight: 0.1980 chunk 16 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 40 optimal weight: 10.0000 chunk 23 optimal weight: 0.9990 chunk 15 optimal weight: 0.9990 chunk 10 optimal weight: 10.0000 overall best weight: 0.6462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.112864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.100433 restraints weight = 5141.221| |-----------------------------------------------------------------------------| r_work (start): 0.3667 rms_B_bonded: 2.34 r_work: 0.3564 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3472 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.4128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 3498 Z= 0.103 Angle : 0.543 6.712 4680 Z= 0.261 Chirality : 0.048 0.122 528 Planarity : 0.003 0.029 594 Dihedral : 4.267 12.390 462 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 1.01 % Allowed : 18.69 % Favored : 80.30 % 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: -2.27 (0.34), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.72 (0.26), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS B 330 PHE 0.005 0.001 PHE F 346 TYR 0.015 0.002 TYR A 310 ARG 0.002 0.000 ARG A 349 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2057.96 seconds wall clock time: 37 minutes 18.20 seconds (2238.20 seconds total)