Starting phenix.real_space_refine on Thu Nov 14 02:49:13 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ot9_17173/11_2024/8ot9_17173.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ot9_17173/11_2024/8ot9_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ot9_17173/11_2024/8ot9_17173.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ot9_17173/11_2024/8ot9_17173.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ot9_17173/11_2024/8ot9_17173.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ot9_17173/11_2024/8ot9_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-5513/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: 4.06, per 1000 atoms: 1.18 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: 0.81 Conformation dependent library (CDL) restraints added in 422.7 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: 0.56 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: 0.88 Time building geometry restraints manager: 0.94 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.780 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: 0.040 Process input model: 14.200 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.640 ------------------------------------------------------------------------------- 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 : 0.387 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: 0.3244 time to fit residues: 46.7501 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 : 0.437 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8733 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 : 0.394 Fit side-chains REVERT: A 349 ARG cc_start: 0.9141 (mtt-85) cc_final: 0.8869 (mtp85) REVERT: B 311 LYS cc_start: 0.9211 (mtmt) cc_final: 0.8532 (tttt) REVERT: C 331 LYS cc_start: 0.9053 (tttm) cc_final: 0.8820 (ttpt) REVERT: C 349 ARG cc_start: 0.9040 (mtt180) cc_final: 0.7497 (mmm160) REVERT: C 375 LYS cc_start: 0.8851 (tttt) cc_final: 0.8601 (ttmm) REVERT: D 311 LYS cc_start: 0.9159 (mtmt) cc_final: 0.8504 (tttt) REVERT: D 320 SER cc_start: 0.8833 (t) cc_final: 0.8395 (m) REVERT: D 368 ASN cc_start: 0.9043 (m110) cc_final: 0.8828 (m-40) REVERT: E 311 LYS cc_start: 0.9139 (mtmt) cc_final: 0.8840 (mmtt) REVERT: E 340 LYS cc_start: 0.8745 (mttt) cc_final: 0.8523 (mtpp) REVERT: E 375 LYS cc_start: 0.8763 (tttt) cc_final: 0.8512 (ttmm) REVERT: F 311 LYS cc_start: 0.9144 (mtmt) cc_final: 0.8484 (tttt) REVERT: F 349 ARG cc_start: 0.8760 (ptt-90) cc_final: 0.7099 (mmm160) outliers start: 12 outliers final: 4 residues processed: 99 average time/residue: 0.2535 time to fit residues: 28.5436 Evaluate side-chains 79 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 75 time to evaluate : 0.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain D residue 350 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 31 optimal weight: 5.9990 chunk 25 optimal weight: 9.9990 chunk 10 optimal weight: 8.9990 chunk 38 optimal weight: 7.9990 chunk 41 optimal weight: 0.9990 chunk 34 optimal weight: 10.0000 chunk 37 optimal weight: 9.9990 chunk 13 optimal weight: 0.9990 chunk 30 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 19 optimal weight: 8.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- 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 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8704 moved from start: 0.3293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3498 Z= 0.207 Angle : 0.594 5.780 4680 Z= 0.293 Chirality : 0.048 0.127 528 Planarity : 0.003 0.019 594 Dihedral : 4.908 12.743 462 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Rotamer: Outliers : 1.01 % Allowed : 14.39 % Favored : 84.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.85 (0.32), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.17 (0.24), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS B 330 PHE 0.006 0.001 PHE A 346 TYR 0.017 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 79 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 75 time to evaluate : 0.322 Fit side-chains REVERT: A 349 ARG cc_start: 0.9176 (mtt-85) cc_final: 0.8923 (mtp85) REVERT: B 311 LYS cc_start: 0.9133 (mtmt) cc_final: 0.8479 (tttt) REVERT: B 327 ASN cc_start: 0.9411 (m-40) cc_final: 0.9186 (m-40) REVERT: C 331 LYS cc_start: 0.9092 (tttm) cc_final: 0.8826 (ttpt) REVERT: C 349 ARG cc_start: 0.9094 (mtt180) cc_final: 0.7573 (mmm160) REVERT: C 375 LYS cc_start: 0.8880 (tttt) cc_final: 0.8597 (ttmm) REVERT: D 311 LYS cc_start: 0.9094 (mtmt) cc_final: 0.8442 (tttt) REVERT: D 320 SER cc_start: 0.8773 (t) cc_final: 0.8361 (m) REVERT: E 311 LYS cc_start: 0.9095 (mtmt) cc_final: 0.8823 (mttt) REVERT: E 375 LYS cc_start: 0.8747 (tttt) cc_final: 0.8521 (ttmm) REVERT: F 311 LYS cc_start: 0.9013 (mtmt) cc_final: 0.8448 (tttt) REVERT: F 349 ARG cc_start: 0.8703 (ptt-90) cc_final: 0.6926 (mmm160) outliers start: 4 outliers final: 1 residues processed: 76 average time/residue: 0.2261 time to fit residues: 19.7019 Evaluate side-chains 68 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 67 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 350 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 4 optimal weight: 9.9990 chunk 18 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 40 optimal weight: 10.0000 chunk 20 optimal weight: 10.0000 chunk 36 optimal weight: 10.0000 chunk 10 optimal weight: 6.9990 chunk 33 optimal weight: 9.9990 chunk 23 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 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 330 HIS ** D 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8735 moved from start: 0.3344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 3498 Z= 0.364 Angle : 0.650 5.876 4680 Z= 0.331 Chirality : 0.049 0.132 528 Planarity : 0.003 0.021 594 Dihedral : 5.039 12.817 462 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.26 % Allowed : 14.90 % Favored : 83.84 % 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: -2.68 (0.32), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.04 (0.24), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS B 362 PHE 0.009 0.002 PHE A 346 TYR 0.012 0.002 TYR B 310 ARG 0.003 0.000 ARG E 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 73 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 68 time to evaluate : 0.323 Fit side-chains REVERT: A 311 LYS cc_start: 0.9051 (mttm) cc_final: 0.8603 (pttm) REVERT: B 311 LYS cc_start: 0.9148 (mtmt) cc_final: 0.8481 (tttt) REVERT: C 349 ARG cc_start: 0.9048 (mtt180) cc_final: 0.7509 (mmm160) REVERT: C 375 LYS cc_start: 0.8879 (tttt) cc_final: 0.8617 (ttmm) REVERT: D 311 LYS cc_start: 0.9130 (mtmt) cc_final: 0.8461 (tttt) REVERT: D 320 SER cc_start: 0.8795 (t) cc_final: 0.8365 (m) REVERT: E 375 LYS cc_start: 0.8784 (tttt) cc_final: 0.8548 (ttmm) REVERT: F 311 LYS cc_start: 0.9045 (mtmt) cc_final: 0.8418 (tttt) REVERT: F 349 ARG cc_start: 0.8752 (ptt-90) cc_final: 0.7039 (mmm160) outliers start: 5 outliers final: 4 residues processed: 73 average time/residue: 0.2423 time to fit residues: 20.2964 Evaluate side-chains 65 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 61 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 SER 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 30 optimal weight: 2.9990 chunk 16 optimal weight: 6.9990 chunk 34 optimal weight: 6.9990 chunk 28 optimal weight: 0.0270 chunk 0 optimal weight: 2.9990 chunk 20 optimal weight: 6.9990 chunk 36 optimal weight: 7.9990 chunk 10 optimal weight: 8.9990 chunk 13 optimal weight: 3.9990 chunk 8 optimal weight: 3.9990 chunk 23 optimal weight: 0.7980 overall best weight: 2.1644 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8699 moved from start: 0.3582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 3498 Z= 0.195 Angle : 0.555 5.864 4680 Z= 0.277 Chirality : 0.047 0.122 528 Planarity : 0.003 0.020 594 Dihedral : 4.593 12.800 462 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % 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: -2.48 (0.33), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.88 (0.25), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 330 PHE 0.006 0.001 PHE A 346 TYR 0.013 0.002 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 72 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 67 time to evaluate : 0.431 Fit side-chains REVERT: A 311 LYS cc_start: 0.8954 (mttm) cc_final: 0.8525 (pttm) REVERT: B 311 LYS cc_start: 0.9127 (mtmt) cc_final: 0.8455 (tttt) REVERT: B 327 ASN cc_start: 0.9393 (m-40) cc_final: 0.9161 (m-40) REVERT: C 349 ARG cc_start: 0.9121 (mtt180) cc_final: 0.7558 (mmm160) REVERT: C 375 LYS cc_start: 0.8855 (tttt) cc_final: 0.8595 (ttmm) REVERT: D 320 SER cc_start: 0.8708 (t) cc_final: 0.8290 (m) REVERT: E 375 LYS cc_start: 0.8789 (tttt) cc_final: 0.8540 (ttmm) REVERT: F 311 LYS cc_start: 0.9008 (mtmt) cc_final: 0.8457 (tttt) REVERT: F 349 ARG cc_start: 0.8705 (ptt-90) cc_final: 0.6935 (mmm160) outliers start: 5 outliers final: 4 residues processed: 71 average time/residue: 0.2415 time to fit residues: 19.7747 Evaluate side-chains 63 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 59 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 SER 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 10 optimal weight: 10.0000 chunk 40 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 18 optimal weight: 9.9990 chunk 3 optimal weight: 10.0000 chunk 13 optimal weight: 4.9990 chunk 21 optimal weight: 8.9990 chunk 39 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 23 optimal weight: 6.9990 chunk 29 optimal weight: 0.0970 overall best weight: 2.0186 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8691 moved from start: 0.3706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 3498 Z= 0.183 Angle : 0.557 6.028 4680 Z= 0.275 Chirality : 0.047 0.119 528 Planarity : 0.003 0.026 594 Dihedral : 4.457 12.165 462 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % 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: -2.31 (0.33), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.75 (0.26), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS F 330 PHE 0.006 0.001 PHE A 346 TYR 0.014 0.002 TYR E 310 ARG 0.005 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 71 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 66 time to evaluate : 0.427 Fit side-chains REVERT: A 311 LYS cc_start: 0.8898 (mttm) cc_final: 0.8491 (pttm) REVERT: A 349 ARG cc_start: 0.9197 (mtt-85) cc_final: 0.8994 (mtp85) REVERT: B 311 LYS cc_start: 0.9119 (mtmt) cc_final: 0.8453 (tttt) REVERT: C 349 ARG cc_start: 0.9100 (mtt180) cc_final: 0.7511 (mmm160) REVERT: C 375 LYS cc_start: 0.8870 (tttt) cc_final: 0.8610 (ttmm) REVERT: D 320 SER cc_start: 0.8682 (t) cc_final: 0.8242 (m) REVERT: E 331 LYS cc_start: 0.8892 (tttp) cc_final: 0.8609 (ttmt) REVERT: E 375 LYS cc_start: 0.8741 (tttt) cc_final: 0.8494 (ttmm) REVERT: F 311 LYS cc_start: 0.8969 (mtmt) cc_final: 0.8448 (tttt) REVERT: F 349 ARG cc_start: 0.8683 (ptt-90) cc_final: 0.6919 (mmm160) outliers start: 5 outliers final: 5 residues processed: 70 average time/residue: 0.2592 time to fit residues: 20.9150 Evaluate side-chains 65 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 60 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain D residue 350 VAL Chi-restraints excluded: chain E residue 311 LYS 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 22 optimal weight: 0.4980 chunk 34 optimal weight: 3.9990 chunk 40 optimal weight: 5.9990 chunk 25 optimal weight: 6.9990 chunk 24 optimal weight: 8.9990 chunk 18 optimal weight: 10.0000 chunk 16 optimal weight: 10.0000 chunk 12 optimal weight: 6.9990 chunk 7 optimal weight: 9.9990 chunk 27 optimal weight: 3.9990 chunk 20 optimal weight: 10.0000 overall best weight: 4.2988 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8734 moved from start: 0.3633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.037 3498 Z= 0.371 Angle : 0.642 5.934 4680 Z= 0.324 Chirality : 0.049 0.121 528 Planarity : 0.003 0.030 594 Dihedral : 4.831 12.927 462 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.52 % Allowed : 17.42 % Favored : 81.06 % 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 (0.33), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.73 (0.25), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS D 330 PHE 0.009 0.002 PHE A 346 TYR 0.012 0.002 TYR B 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 67 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 61 time to evaluate : 0.419 Fit side-chains REVERT: A 311 LYS cc_start: 0.8935 (mttm) cc_final: 0.8526 (pttm) REVERT: B 311 LYS cc_start: 0.9123 (mtmt) cc_final: 0.8443 (tttt) REVERT: C 349 ARG cc_start: 0.8996 (mtt180) cc_final: 0.7444 (mmp-170) REVERT: C 375 LYS cc_start: 0.8901 (tttt) cc_final: 0.8624 (ttmm) REVERT: D 320 SER cc_start: 0.8792 (t) cc_final: 0.8360 (m) REVERT: E 325 LEU cc_start: 0.8724 (OUTLIER) cc_final: 0.8327 (tt) REVERT: E 375 LYS cc_start: 0.8815 (tttt) cc_final: 0.8561 (ttmm) REVERT: F 311 LYS cc_start: 0.8992 (mtmt) cc_final: 0.8388 (tttt) REVERT: F 349 ARG cc_start: 0.8765 (ptt-90) cc_final: 0.7025 (mmm160) outliers start: 6 outliers final: 5 residues processed: 66 average time/residue: 0.2516 time to fit residues: 19.1949 Evaluate side-chains 64 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 58 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain D residue 350 VAL Chi-restraints excluded: chain E residue 311 LYS Chi-restraints excluded: chain E residue 325 LEU 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 3 optimal weight: 8.9990 chunk 31 optimal weight: 6.9990 chunk 36 optimal weight: 9.9990 chunk 38 optimal weight: 7.9990 chunk 35 optimal weight: 8.9990 chunk 37 optimal weight: 3.9990 chunk 22 optimal weight: 4.9990 chunk 16 optimal weight: 8.9990 chunk 29 optimal weight: 7.9990 chunk 11 optimal weight: 10.0000 chunk 34 optimal weight: 5.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 327 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8760 moved from start: 0.3632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.043 3498 Z= 0.508 Angle : 0.726 7.841 4680 Z= 0.370 Chirality : 0.051 0.123 528 Planarity : 0.004 0.028 594 Dihedral : 5.178 13.446 462 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 1.52 % Allowed : 18.43 % 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: -2.45 (0.32), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.86 (0.25), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.002 HIS D 330 PHE 0.010 0.002 PHE C 346 TYR 0.016 0.003 TYR B 310 ARG 0.002 0.000 ARG C 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 70 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 64 time to evaluate : 0.348 Fit side-chains REVERT: B 311 LYS cc_start: 0.9173 (mtmt) cc_final: 0.8489 (tttt) REVERT: C 349 ARG cc_start: 0.9012 (mtt180) cc_final: 0.7453 (mmp-170) REVERT: C 375 LYS cc_start: 0.8926 (tttt) cc_final: 0.8691 (ttmm) REVERT: D 311 LYS cc_start: 0.9124 (mtmt) cc_final: 0.8473 (tttt) REVERT: D 320 SER cc_start: 0.8864 (t) cc_final: 0.8403 (m) REVERT: E 325 LEU cc_start: 0.8802 (OUTLIER) cc_final: 0.8353 (tt) REVERT: E 375 LYS cc_start: 0.8802 (tttt) cc_final: 0.8546 (ttmm) REVERT: F 311 LYS cc_start: 0.9068 (mtmt) cc_final: 0.8431 (tttt) REVERT: F 349 ARG cc_start: 0.8810 (ptt-90) cc_final: 0.7129 (mmm160) outliers start: 6 outliers final: 5 residues processed: 69 average time/residue: 0.2336 time to fit residues: 18.8016 Evaluate side-chains 67 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 61 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain D residue 350 VAL Chi-restraints excluded: chain E residue 311 LYS Chi-restraints excluded: chain E residue 325 LEU 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 35 optimal weight: 6.9990 chunk 37 optimal weight: 4.9990 chunk 24 optimal weight: 10.0000 chunk 39 optimal weight: 0.0050 chunk 18 optimal weight: 7.9990 chunk 27 optimal weight: 3.9990 chunk 41 optimal weight: 3.9990 chunk 38 optimal weight: 5.9990 chunk 33 optimal weight: 1.9990 chunk 3 optimal weight: 10.0000 chunk 25 optimal weight: 0.9990 overall best weight: 2.2002 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8705 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 : 0.003 0.032 3498 Z= 0.208 Angle : 0.605 6.341 4680 Z= 0.300 Chirality : 0.048 0.121 528 Planarity : 0.003 0.025 594 Dihedral : 4.653 12.331 462 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % 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: -2.26 (0.33), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.71 (0.25), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS F 330 PHE 0.006 0.001 PHE A 346 TYR 0.014 0.002 TYR E 310 ARG 0.001 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 73 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 66 time to evaluate : 0.436 Fit side-chains REVERT: A 311 LYS cc_start: 0.8818 (mttm) cc_final: 0.8377 (pttt) REVERT: A 349 ARG cc_start: 0.9170 (mtt-85) cc_final: 0.8969 (mtp85) REVERT: B 311 LYS cc_start: 0.9135 (mtmt) cc_final: 0.8440 (tttt) REVERT: B 356 SER cc_start: 0.8581 (OUTLIER) cc_final: 0.8348 (t) REVERT: C 349 ARG cc_start: 0.9010 (mtt180) cc_final: 0.7396 (mmm160) REVERT: C 375 LYS cc_start: 0.8878 (tttt) cc_final: 0.8619 (ttmm) REVERT: E 375 LYS cc_start: 0.8761 (tttt) cc_final: 0.8531 (ttmm) REVERT: F 311 LYS cc_start: 0.9009 (mtmt) cc_final: 0.8438 (tttt) REVERT: F 349 ARG cc_start: 0.8672 (ptt-90) cc_final: 0.6882 (mmm160) outliers start: 7 outliers final: 5 residues processed: 72 average time/residue: 0.2556 time to fit residues: 21.0832 Evaluate side-chains 69 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 63 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 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 E residue 311 LYS 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 20 optimal weight: 0.7980 chunk 26 optimal weight: 9.9990 chunk 35 optimal weight: 9.9990 chunk 10 optimal weight: 10.0000 chunk 30 optimal weight: 1.9990 chunk 4 optimal weight: 9.9990 chunk 9 optimal weight: 9.9990 chunk 33 optimal weight: 7.9990 chunk 13 optimal weight: 8.9990 chunk 34 optimal weight: 3.9990 chunk 6 optimal weight: 0.9980 overall best weight: 3.1586 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8717 moved from start: 0.3796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 3498 Z= 0.277 Angle : 0.641 7.979 4680 Z= 0.315 Chirality : 0.049 0.121 528 Planarity : 0.003 0.026 594 Dihedral : 4.711 12.475 462 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 1.52 % Allowed : 18.69 % Favored : 79.80 % 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: -2.21 (0.34), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.67 (0.26), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS D 330 PHE 0.007 0.002 PHE A 346 TYR 0.012 0.002 TYR E 310 ARG 0.001 0.000 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 71 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 65 time to evaluate : 0.426 Fit side-chains REVERT: A 311 LYS cc_start: 0.8772 (mttm) cc_final: 0.8370 (pttt) REVERT: B 311 LYS cc_start: 0.9144 (mtmt) cc_final: 0.8446 (tttt) REVERT: B 356 SER cc_start: 0.8601 (OUTLIER) cc_final: 0.8348 (t) REVERT: C 349 ARG cc_start: 0.9003 (mtt180) cc_final: 0.7366 (mmm160) REVERT: C 375 LYS cc_start: 0.8941 (tttt) cc_final: 0.8684 (ttmm) REVERT: E 375 LYS cc_start: 0.8778 (tttt) cc_final: 0.8544 (ttmm) REVERT: F 311 LYS cc_start: 0.9007 (mtmt) cc_final: 0.8423 (tttt) REVERT: F 349 ARG cc_start: 0.8726 (ptt-90) cc_final: 0.6961 (mmm160) outliers start: 6 outliers final: 5 residues processed: 70 average time/residue: 0.2453 time to fit residues: 19.7910 Evaluate side-chains 70 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 64 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 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 E residue 311 LYS 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 29 optimal weight: 0.8980 chunk 1 optimal weight: 5.9990 chunk 24 optimal weight: 9.9990 chunk 38 optimal weight: 8.9990 chunk 22 optimal weight: 8.9990 chunk 28 optimal weight: 0.0970 chunk 26 optimal weight: 8.9990 chunk 25 optimal weight: 0.8980 chunk 16 optimal weight: 9.9990 chunk 15 optimal weight: 2.9990 chunk 41 optimal weight: 5.9990 overall best weight: 2.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 329 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 = 0.3780 r_free = 0.3780 target = 0.116159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.102710 restraints weight = 5327.096| |-----------------------------------------------------------------------------| r_work (start): 0.3655 rms_B_bonded: 2.49 r_work: 0.3553 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3461 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 moved from start: 0.3918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3498 Z= 0.199 Angle : 0.610 8.179 4680 Z= 0.297 Chirality : 0.048 0.122 528 Planarity : 0.003 0.027 594 Dihedral : 4.528 12.324 462 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Rotamer: Outliers : 1.52 % Allowed : 18.94 % Favored : 79.55 % 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 (0.34), 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 0.004 0.001 HIS B 330 PHE 0.006 0.001 PHE A 346 TYR 0.014 0.002 TYR E 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: 1383.31 seconds wall clock time: 25 minutes 50.07 seconds (1550.07 seconds total)