Starting phenix.real_space_refine on Thu Nov 14 00:34:32 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ot6_17171/11_2024/8ot6_17171.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ot6_17171/11_2024/8ot6_17171.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ot6_17171/11_2024/8ot6_17171.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ot6_17171/11_2024/8ot6_17171.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ot6_17171/11_2024/8ot6_17171.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ot6_17171/11_2024/8ot6_17171.cif" } resolution = 2.0 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 5 5.16 5 C 1800 2.51 5 N 530 2.21 5 O 535 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 25 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: 2870 Number of models: 1 Model: "" Number of chains: 1 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} Restraints were copied for chains: C, B, E, D Time building chain proxies: 3.03, per 1000 atoms: 1.06 Number of scatterers: 2870 At special positions: 0 Unit cell: (139.256, 119.48, 32.96, 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 5 16.00 O 535 8.00 N 530 7.00 C 1800 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.74 Conformation dependent library (CDL) restraints added in 391.7 milliseconds 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 660 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 16 sheets defined 0.0% alpha, 56.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.40 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'B' and resid 306 through 310 removed outlier: 6.392A pdb=" N GLN A 307 " --> pdb=" O ILE B 308 " (cutoff:3.500A) removed outlier: 7.654A pdb=" N TYR B 310 " --> pdb=" O GLN A 307 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N VAL A 309 " --> pdb=" O TYR B 310 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 313 through 314 removed outlier: 6.764A pdb=" N VAL A 313 " --> pdb=" O ASP B 314 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 317 through 322 removed outlier: 6.445A pdb=" N LYS A 317 " --> pdb=" O VAL B 318 " (cutoff:3.500A) removed outlier: 8.172A pdb=" N SER B 320 " --> pdb=" O LYS A 317 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N THR A 319 " --> pdb=" O SER B 320 " (cutoff:3.500A) removed outlier: 8.458A pdb=" N CYS B 322 " --> pdb=" O THR A 319 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N LYS A 321 " --> pdb=" O CYS B 322 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 325 through 330 removed outlier: 6.800A pdb=" N GLY B 326 " --> pdb=" O LEU A 325 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N ASN A 327 " --> pdb=" O GLY B 326 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N GLY A 326 " --> pdb=" O ASN E 327 " (cutoff:3.500A) removed outlier: 8.602A pdb=" N HIS E 329 " --> pdb=" O GLY A 326 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N ILE A 328 " --> pdb=" O HIS E 329 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 337 through 346 removed outlier: 8.995A pdb=" N VAL A 337 " --> pdb=" O GLU B 338 " (cutoff:3.500A) removed outlier: 10.116A pdb=" N LYS B 340 " --> pdb=" O VAL A 337 " (cutoff:3.500A) removed outlier: 8.912A pdb=" N VAL A 339 " --> pdb=" O LYS B 340 " (cutoff:3.500A) removed outlier: 10.083A pdb=" N GLU B 342 " --> pdb=" O VAL A 339 " (cutoff:3.500A) removed outlier: 9.214A pdb=" N SER A 341 " --> pdb=" O GLU B 342 " (cutoff:3.500A) removed outlier: 9.316A pdb=" N LEU B 344 " --> pdb=" O SER A 341 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N LYS A 343 " --> pdb=" O LEU B 344 " (cutoff:3.500A) removed outlier: 8.093A pdb=" N PHE B 346 " --> pdb=" O LYS A 343 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N ASP A 345 " --> pdb=" O PHE B 346 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N GLU A 338 " --> pdb=" O VAL E 337 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N VAL E 339 " --> pdb=" O GLU A 338 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N LYS A 340 " --> pdb=" O VAL E 339 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N SER E 341 " --> pdb=" O LYS A 340 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N GLU A 342 " --> pdb=" O SER E 341 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N LYS E 343 " --> pdb=" O GLU A 342 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 350 through 357 removed outlier: 6.411A pdb=" N GLN A 351 " --> pdb=" O SER B 352 " (cutoff:3.500A) removed outlier: 8.066A pdb=" N ILE B 354 " --> pdb=" O GLN A 351 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N LYS A 353 " --> pdb=" O ILE B 354 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N SER B 356 " --> pdb=" O LYS A 353 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N GLY A 355 " --> pdb=" O SER B 356 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 360 through 362 removed outlier: 6.323A pdb=" N THR A 361 " --> pdb=" O HIS E 362 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 369 through 378 removed outlier: 6.618A pdb=" N LYS A 369 " --> pdb=" O LYS B 370 " (cutoff:3.500A) removed outlier: 8.147A pdb=" N GLU B 372 " --> pdb=" O LYS A 369 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N ILE A 371 " --> pdb=" O GLU B 372 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N HIS B 374 " --> pdb=" O ILE A 371 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N THR A 373 " --> pdb=" O HIS B 374 " (cutoff:3.500A) removed outlier: 7.946A pdb=" N LEU B 376 " --> pdb=" O THR A 373 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N LYS A 375 " --> pdb=" O LEU B 376 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N PHE B 378 " --> pdb=" O LYS A 375 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N THR A 377 " --> pdb=" O PHE B 378 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 306 through 310 Processing sheet with id=AB1, first strand: chain 'C' and resid 313 through 314 Processing sheet with id=AB2, first strand: chain 'C' and resid 317 through 322 Processing sheet with id=AB3, first strand: chain 'C' and resid 325 through 330 removed outlier: 6.141A pdb=" N GLY C 326 " --> pdb=" O ASN D 327 " (cutoff:3.500A) removed outlier: 8.601A pdb=" N HIS D 329 " --> pdb=" O GLY C 326 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N ILE C 328 " --> pdb=" O HIS D 329 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'C' and resid 337 through 346 removed outlier: 6.918A pdb=" N GLU C 338 " --> pdb=" O VAL D 337 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N VAL D 339 " --> pdb=" O GLU C 338 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N LYS C 340 " --> pdb=" O VAL D 339 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N SER D 341 " --> pdb=" O LYS C 340 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N GLU C 342 " --> pdb=" O SER D 341 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N LYS D 343 " --> pdb=" O GLU C 342 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 350 through 357 Processing sheet with id=AB6, first strand: chain 'C' and resid 360 through 362 removed outlier: 6.323A pdb=" N THR C 361 " --> pdb=" O HIS D 362 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'C' and resid 369 through 378 63 hydrogen bonds defined for protein. 189 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: 0.61 Time building geometry restraints manager: 0.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 628 1.34 - 1.45: 634 1.45 - 1.57: 1648 1.57 - 1.69: 0 1.69 - 1.81: 5 Bond restraints: 2915 Sorted by residual: bond pdb=" C LYS B 331 " pdb=" N PRO B 332 " ideal model delta sigma weight residual 1.331 1.355 -0.024 1.28e-02 6.10e+03 3.38e+00 bond pdb=" CA SER D 352 " pdb=" CB SER D 352 " ideal model delta sigma weight residual 1.533 1.498 0.035 1.90e-02 2.77e+03 3.37e+00 bond pdb=" CA SER A 352 " pdb=" CB SER A 352 " ideal model delta sigma weight residual 1.533 1.499 0.034 1.90e-02 2.77e+03 3.23e+00 bond pdb=" CA SER E 352 " pdb=" CB SER E 352 " ideal model delta sigma weight residual 1.533 1.499 0.034 1.90e-02 2.77e+03 3.23e+00 bond pdb=" CA SER C 352 " pdb=" CB SER C 352 " ideal model delta sigma weight residual 1.533 1.499 0.034 1.90e-02 2.77e+03 3.23e+00 ... (remaining 2910 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.04: 2697 1.04 - 2.07: 931 2.07 - 3.11: 184 3.11 - 4.14: 63 4.14 - 5.18: 25 Bond angle restraints: 3900 Sorted by residual: angle pdb=" N GLY D 326 " pdb=" CA GLY D 326 " pdb=" C GLY D 326 " ideal model delta sigma weight residual 110.69 115.87 -5.18 1.33e+00 5.65e-01 1.52e+01 angle pdb=" N GLY A 326 " pdb=" CA GLY A 326 " pdb=" C GLY A 326 " ideal model delta sigma weight residual 110.69 115.86 -5.17 1.33e+00 5.65e-01 1.51e+01 angle pdb=" N GLY E 326 " pdb=" CA GLY E 326 " pdb=" C GLY E 326 " ideal model delta sigma weight residual 110.69 115.86 -5.17 1.33e+00 5.65e-01 1.51e+01 angle pdb=" N GLY C 326 " pdb=" CA GLY C 326 " pdb=" C GLY C 326 " ideal model delta sigma weight residual 110.69 115.85 -5.16 1.33e+00 5.65e-01 1.51e+01 angle pdb=" N GLY B 326 " pdb=" CA GLY B 326 " pdb=" C GLY B 326 " ideal model delta sigma weight residual 110.69 115.85 -5.16 1.33e+00 5.65e-01 1.51e+01 ... (remaining 3895 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.54: 1684 15.54 - 31.08: 61 31.08 - 46.61: 25 46.61 - 62.15: 5 62.15 - 77.69: 5 Dihedral angle restraints: 1780 sinusoidal: 745 harmonic: 1035 Sorted by residual: dihedral pdb=" CA ILE C 360 " pdb=" C ILE C 360 " pdb=" N THR C 361 " pdb=" CA THR C 361 " ideal model delta harmonic sigma weight residual 180.00 161.23 18.77 0 5.00e+00 4.00e-02 1.41e+01 dihedral pdb=" CA ILE D 360 " pdb=" C ILE D 360 " pdb=" N THR D 361 " pdb=" CA THR D 361 " ideal model delta harmonic sigma weight residual 180.00 161.26 18.74 0 5.00e+00 4.00e-02 1.41e+01 dihedral pdb=" CA ILE A 360 " pdb=" C ILE A 360 " pdb=" N THR A 361 " pdb=" CA THR A 361 " ideal model delta harmonic sigma weight residual 180.00 161.26 18.74 0 5.00e+00 4.00e-02 1.40e+01 ... (remaining 1777 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 121 0.038 - 0.077: 175 0.077 - 0.115: 124 0.115 - 0.153: 5 0.153 - 0.192: 15 Chirality restraints: 440 Sorted by residual: chirality pdb=" CB ILE D 328 " pdb=" CA ILE D 328 " pdb=" CG1 ILE D 328 " pdb=" CG2 ILE D 328 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.19 2.00e-01 2.50e+01 9.20e-01 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 2.45 0.19 2.00e-01 2.50e+01 9.15e-01 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 2.45 0.19 2.00e-01 2.50e+01 9.10e-01 ... (remaining 437 not shown) Planarity restraints: 495 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL D 363 " 0.010 2.00e-02 2.50e+03 1.99e-02 3.94e+00 pdb=" C VAL D 363 " -0.034 2.00e-02 2.50e+03 pdb=" O VAL D 363 " 0.013 2.00e-02 2.50e+03 pdb=" N PRO D 364 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 363 " -0.010 2.00e-02 2.50e+03 1.97e-02 3.88e+00 pdb=" C VAL A 363 " 0.034 2.00e-02 2.50e+03 pdb=" O VAL A 363 " -0.013 2.00e-02 2.50e+03 pdb=" N PRO A 364 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL C 363 " 0.010 2.00e-02 2.50e+03 1.97e-02 3.86e+00 pdb=" C VAL C 363 " -0.034 2.00e-02 2.50e+03 pdb=" O VAL C 363 " 0.013 2.00e-02 2.50e+03 pdb=" N PRO C 364 " 0.011 2.00e-02 2.50e+03 ... (remaining 492 not shown) Histogram of nonbonded interaction distances: 2.63 - 3.08: 1689 3.08 - 3.54: 2595 3.54 - 3.99: 4320 3.99 - 4.45: 4408 4.45 - 4.90: 8692 Nonbonded interactions: 21704 Sorted by model distance: nonbonded pdb=" N ASP D 348 " pdb=" O ASP D 348 " model vdw 2.631 2.496 nonbonded pdb=" N ASP A 348 " pdb=" O ASP A 348 " model vdw 2.631 2.496 nonbonded pdb=" N ASP E 348 " pdb=" O ASP E 348 " model vdw 2.631 2.496 nonbonded pdb=" N ASP C 348 " pdb=" O ASP C 348 " model vdw 2.631 2.496 nonbonded pdb=" N ASP B 348 " pdb=" O ASP B 348 " model vdw 2.632 2.496 ... (remaining 21699 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' } 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: 3.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.430 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8984 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 : 0.007 0.037 2915 Z= 0.499 Angle : 1.165 5.180 3900 Z= 0.754 Chirality : 0.071 0.192 440 Planarity : 0.008 0.041 495 Dihedral : 11.962 77.688 1120 Min Nonbonded Distance : 2.631 Molprobity Statistics. All-atom Clashscore : 0.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.52 % Allowed : 0.00 % Favored : 98.48 % 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: -2.61 (0.36), residues: 365 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.98 (0.27), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.003 HIS C 329 PHE 0.007 0.003 PHE C 346 TYR 0.008 0.004 TYR C 310 ARG 0.005 0.001 ARG E 349 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 148 time to evaluate : 0.358 Fit side-chains REVERT: B 347 LYS cc_start: 0.8879 (mttm) cc_final: 0.8288 (pmtt) REVERT: B 379 ARG cc_start: 0.7889 (mtt180) cc_final: 0.7674 (ptt-90) REVERT: C 311 LYS cc_start: 0.8575 (mtmt) cc_final: 0.8369 (mtmt) REVERT: C 347 LYS cc_start: 0.8959 (mttm) cc_final: 0.8354 (pmtt) REVERT: C 379 ARG cc_start: 0.7844 (mtt180) cc_final: 0.7614 (ptt-90) REVERT: D 311 LYS cc_start: 0.8424 (mtmt) cc_final: 0.7870 (mptp) REVERT: D 349 ARG cc_start: 0.8872 (mtt180) cc_final: 0.7801 (mmm160) REVERT: E 311 LYS cc_start: 0.8519 (mtmt) cc_final: 0.8020 (mptp) REVERT: E 349 ARG cc_start: 0.8863 (mtt180) cc_final: 0.7952 (mmm160) outliers start: 5 outliers final: 1 residues processed: 153 average time/residue: 1.6150 time to fit residues: 251.1099 Evaluate side-chains 87 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 86 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 325 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 29 optimal weight: 0.5980 chunk 26 optimal weight: 4.9990 chunk 14 optimal weight: 7.9990 chunk 9 optimal weight: 6.9990 chunk 17 optimal weight: 7.9990 chunk 27 optimal weight: 0.7980 chunk 10 optimal weight: 5.9990 chunk 16 optimal weight: 7.9990 chunk 20 optimal weight: 0.0030 chunk 31 optimal weight: 10.0000 chunk 21 optimal weight: 3.9990 overall best weight: 2.0794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 GLN A 351 GLN B 351 GLN D 307 GLN D 351 GLN E 351 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9010 moved from start: 0.2485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 2915 Z= 0.223 Angle : 0.608 5.659 3900 Z= 0.298 Chirality : 0.049 0.141 440 Planarity : 0.003 0.022 495 Dihedral : 5.249 29.263 387 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 2.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 2.12 % Allowed : 13.03 % Favored : 84.85 % 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: -2.20 (0.36), residues: 365 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.67 (0.27), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS E 329 PHE 0.004 0.001 PHE A 346 TYR 0.009 0.002 TYR E 310 ARG 0.002 0.000 ARG D 379 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 85 time to evaluate : 0.378 Fit side-chains REVERT: A 338 GLU cc_start: 0.8647 (OUTLIER) cc_final: 0.7694 (tp30) REVERT: C 351 GLN cc_start: 0.8946 (mt0) cc_final: 0.8730 (mt0) REVERT: D 379 ARG cc_start: 0.5541 (OUTLIER) cc_final: 0.5290 (tpt170) REVERT: E 349 ARG cc_start: 0.8822 (mtt180) cc_final: 0.7915 (mmp-170) outliers start: 7 outliers final: 0 residues processed: 88 average time/residue: 1.3537 time to fit residues: 121.7372 Evaluate side-chains 85 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 83 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain D residue 379 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 8 optimal weight: 2.9990 chunk 31 optimal weight: 10.0000 chunk 34 optimal weight: 7.9990 chunk 28 optimal weight: 10.0000 chunk 10 optimal weight: 7.9990 chunk 25 optimal weight: 0.8980 chunk 23 optimal weight: 0.0470 chunk 16 optimal weight: 4.9990 chunk 3 optimal weight: 3.9990 chunk 15 optimal weight: 0.9990 chunk 21 optimal weight: 0.8980 overall best weight: 1.1682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 GLN A 351 GLN D 307 GLN E 351 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8981 moved from start: 0.2965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 2915 Z= 0.144 Angle : 0.530 5.188 3900 Z= 0.255 Chirality : 0.048 0.128 440 Planarity : 0.003 0.018 495 Dihedral : 4.688 13.629 385 Min Nonbonded Distance : 2.643 Molprobity Statistics. All-atom Clashscore : 1.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 1.82 % Allowed : 16.06 % Favored : 82.12 % 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: -2.01 (0.37), residues: 365 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.52 (0.28), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS C 374 PHE 0.004 0.001 PHE E 346 TYR 0.009 0.002 TYR E 310 ARG 0.001 0.000 ARG A 379 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 85 time to evaluate : 0.373 Fit side-chains REVERT: A 349 ARG cc_start: 0.8924 (OUTLIER) cc_final: 0.8709 (mtt180) REVERT: C 351 GLN cc_start: 0.8929 (mt0) cc_final: 0.8713 (mt0) REVERT: D 379 ARG cc_start: 0.5610 (OUTLIER) cc_final: 0.5061 (mmt-90) REVERT: E 349 ARG cc_start: 0.8801 (mtt180) cc_final: 0.7669 (mmp-170) outliers start: 6 outliers final: 0 residues processed: 87 average time/residue: 1.5342 time to fit residues: 136.2180 Evaluate side-chains 84 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 82 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 349 ARG Chi-restraints excluded: chain D residue 379 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 31 optimal weight: 5.9990 chunk 33 optimal weight: 7.9990 chunk 16 optimal weight: 9.9990 chunk 30 optimal weight: 0.0870 chunk 9 optimal weight: 5.9990 chunk 28 optimal weight: 9.9990 chunk 19 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 25 optimal weight: 9.9990 chunk 13 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 overall best weight: 3.2166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 GLN A 351 GLN B 351 GLN C 307 GLN D 307 GLN E 351 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9020 moved from start: 0.2963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 2915 Z= 0.306 Angle : 0.603 5.485 3900 Z= 0.301 Chirality : 0.049 0.144 440 Planarity : 0.003 0.023 495 Dihedral : 5.014 14.859 385 Min Nonbonded Distance : 2.639 Molprobity Statistics. All-atom Clashscore : 2.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 1.82 % Allowed : 17.58 % Favored : 80.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.98 (0.36), residues: 365 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.50 (0.27), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS E 329 PHE 0.006 0.002 PHE E 346 TYR 0.009 0.002 TYR E 310 ARG 0.003 0.000 ARG D 379 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 82 time to evaluate : 0.391 Fit side-chains REVERT: A 349 ARG cc_start: 0.8925 (OUTLIER) cc_final: 0.8683 (mtt180) REVERT: B 338 GLU cc_start: 0.8461 (OUTLIER) cc_final: 0.7912 (tp30) REVERT: D 379 ARG cc_start: 0.5643 (OUTLIER) cc_final: 0.5228 (mmt-90) REVERT: E 349 ARG cc_start: 0.8812 (mtt180) cc_final: 0.7538 (tpt90) outliers start: 6 outliers final: 0 residues processed: 83 average time/residue: 1.5156 time to fit residues: 128.3298 Evaluate side-chains 85 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 82 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 349 ARG Chi-restraints excluded: chain B residue 338 GLU Chi-restraints excluded: chain D residue 379 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 0 optimal weight: 10.0000 chunk 17 optimal weight: 10.0000 chunk 30 optimal weight: 5.9990 chunk 8 optimal weight: 0.4980 chunk 11 optimal weight: 4.9990 chunk 6 optimal weight: 5.9990 chunk 19 optimal weight: 6.9990 chunk 33 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 15 optimal weight: 0.8980 chunk 2 optimal weight: 0.9980 overall best weight: 2.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 GLN A 351 GLN B 351 GLN C 307 GLN D 307 GLN E 351 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9007 moved from start: 0.3074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 2915 Z= 0.211 Angle : 0.549 5.184 3900 Z= 0.272 Chirality : 0.049 0.134 440 Planarity : 0.003 0.019 495 Dihedral : 4.855 14.217 385 Min Nonbonded Distance : 2.639 Molprobity Statistics. All-atom Clashscore : 2.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 1.52 % Allowed : 18.48 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.91 (0.36), residues: 365 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.45 (0.28), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS E 329 PHE 0.005 0.002 PHE E 346 TYR 0.010 0.002 TYR E 310 ARG 0.002 0.000 ARG D 379 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 83 time to evaluate : 0.382 Fit side-chains REVERT: A 349 ARG cc_start: 0.8929 (OUTLIER) cc_final: 0.8688 (mtt180) REVERT: B 338 GLU cc_start: 0.8393 (OUTLIER) cc_final: 0.7884 (tp30) REVERT: C 351 GLN cc_start: 0.8950 (mt0) cc_final: 0.8723 (mt0) REVERT: D 379 ARG cc_start: 0.5385 (OUTLIER) cc_final: 0.4962 (mmt-90) REVERT: E 349 ARG cc_start: 0.8801 (mtt180) cc_final: 0.7546 (tpt90) outliers start: 5 outliers final: 0 residues processed: 84 average time/residue: 1.4662 time to fit residues: 125.6264 Evaluate side-chains 85 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 82 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 349 ARG Chi-restraints excluded: chain B residue 338 GLU Chi-restraints excluded: chain D residue 379 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 11 optimal weight: 3.9990 chunk 17 optimal weight: 0.1980 chunk 32 optimal weight: 10.0000 chunk 3 optimal weight: 9.9990 chunk 19 optimal weight: 6.9990 chunk 24 optimal weight: 2.9990 chunk 28 optimal weight: 6.9990 chunk 18 optimal weight: 3.9990 chunk 33 optimal weight: 6.9990 chunk 21 optimal weight: 7.9990 chunk 20 optimal weight: 10.0000 overall best weight: 3.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 GLN A 351 GLN B 307 GLN B 351 GLN C 307 GLN D 307 GLN E 351 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9027 moved from start: 0.3038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 2915 Z= 0.341 Angle : 0.611 5.413 3900 Z= 0.309 Chirality : 0.050 0.144 440 Planarity : 0.003 0.034 495 Dihedral : 5.115 14.805 385 Min Nonbonded Distance : 2.628 Molprobity Statistics. All-atom Clashscore : 2.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 1.82 % Allowed : 17.88 % 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: -1.88 (0.36), residues: 365 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.42 (0.27), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS D 329 PHE 0.007 0.002 PHE A 346 TYR 0.011 0.003 TYR E 310 ARG 0.003 0.001 ARG D 379 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 85 time to evaluate : 0.394 Fit side-chains REVERT: A 349 ARG cc_start: 0.8935 (OUTLIER) cc_final: 0.8686 (mtt180) REVERT: B 338 GLU cc_start: 0.8514 (OUTLIER) cc_final: 0.7940 (tp30) REVERT: D 379 ARG cc_start: 0.5246 (OUTLIER) cc_final: 0.4750 (mmt-90) REVERT: E 349 ARG cc_start: 0.8821 (mtt180) cc_final: 0.7533 (tpt90) outliers start: 6 outliers final: 1 residues processed: 88 average time/residue: 1.5494 time to fit residues: 138.9329 Evaluate side-chains 86 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 82 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 349 ARG Chi-restraints excluded: chain B residue 338 GLU Chi-restraints excluded: chain D residue 340 LYS Chi-restraints excluded: chain D residue 379 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 15 optimal weight: 0.9990 chunk 20 optimal weight: 0.0980 chunk 13 optimal weight: 0.9980 chunk 10 optimal weight: 5.9990 chunk 6 optimal weight: 0.7980 chunk 21 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 chunk 16 optimal weight: 7.9990 chunk 3 optimal weight: 6.9990 chunk 26 optimal weight: 0.0770 chunk 30 optimal weight: 7.9990 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 GLN A 351 GLN B 307 GLN C 307 GLN D 307 GLN E 351 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8956 moved from start: 0.3376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.001 0.013 2915 Z= 0.102 Angle : 0.494 5.725 3900 Z= 0.239 Chirality : 0.049 0.122 440 Planarity : 0.002 0.019 495 Dihedral : 4.441 13.005 385 Min Nonbonded Distance : 2.636 Molprobity Statistics. All-atom Clashscore : 1.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % Rotamer: Outliers : 0.61 % Allowed : 19.39 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.74 (0.37), residues: 365 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.31 (0.28), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS B 374 PHE 0.004 0.001 PHE E 346 TYR 0.011 0.002 TYR E 310 ARG 0.002 0.000 ARG B 379 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 85 time to evaluate : 0.352 Fit side-chains REVERT: D 379 ARG cc_start: 0.5258 (OUTLIER) cc_final: 0.4240 (mpt90) REVERT: E 349 ARG cc_start: 0.8762 (mtt180) cc_final: 0.7655 (mmp-170) outliers start: 2 outliers final: 0 residues processed: 86 average time/residue: 1.5075 time to fit residues: 132.1760 Evaluate side-chains 82 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 81 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 379 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 32 optimal weight: 9.9990 chunk 29 optimal weight: 9.9990 chunk 31 optimal weight: 9.9990 chunk 18 optimal weight: 0.6980 chunk 13 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 9 optimal weight: 0.0000 chunk 28 optimal weight: 5.9990 chunk 20 optimal weight: 10.0000 chunk 33 optimal weight: 1.9990 chunk 15 optimal weight: 0.3980 overall best weight: 1.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 307 GLN B 351 GLN C 307 GLN D 307 GLN E 351 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8978 moved from start: 0.3334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.015 2915 Z= 0.128 Angle : 0.512 6.723 3900 Z= 0.248 Chirality : 0.048 0.123 440 Planarity : 0.002 0.017 495 Dihedral : 4.479 13.250 385 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 1.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % Rotamer: Outliers : 0.30 % Allowed : 19.39 % 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: -1.67 (0.37), residues: 365 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.26 (0.28), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS B 374 PHE 0.005 0.001 PHE E 346 TYR 0.010 0.002 TYR E 310 ARG 0.001 0.000 ARG B 379 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 83 time to evaluate : 0.385 Fit side-chains REVERT: D 379 ARG cc_start: 0.5061 (OUTLIER) cc_final: 0.4225 (mmp-170) REVERT: E 349 ARG cc_start: 0.8774 (mtt180) cc_final: 0.7658 (mmp-170) outliers start: 1 outliers final: 0 residues processed: 83 average time/residue: 1.4828 time to fit residues: 125.5861 Evaluate side-chains 84 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 83 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 379 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 23 optimal weight: 7.9990 chunk 34 optimal weight: 7.9990 chunk 32 optimal weight: 9.9990 chunk 27 optimal weight: 4.9990 chunk 2 optimal weight: 6.9990 chunk 21 optimal weight: 3.9990 chunk 17 optimal weight: 9.9990 chunk 22 optimal weight: 9.9990 chunk 29 optimal weight: 9.9990 chunk 8 optimal weight: 3.9990 chunk 25 optimal weight: 6.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 351 GLN C 307 GLN D 307 GLN E 351 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9034 moved from start: 0.3088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.054 2915 Z= 0.483 Angle : 0.672 6.488 3900 Z= 0.345 Chirality : 0.052 0.154 440 Planarity : 0.004 0.053 495 Dihedral : 5.220 15.114 385 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 0.91 % Allowed : 19.09 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.74 (0.36), residues: 365 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.32 (0.28), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS E 329 PHE 0.009 0.003 PHE A 346 TYR 0.009 0.003 TYR E 310 ARG 0.004 0.001 ARG D 379 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 82 time to evaluate : 0.381 Fit side-chains REVERT: D 379 ARG cc_start: 0.5059 (OUTLIER) cc_final: 0.3937 (mmp80) REVERT: E 349 ARG cc_start: 0.8824 (mtt180) cc_final: 0.7514 (tpt90) outliers start: 3 outliers final: 0 residues processed: 83 average time/residue: 1.4805 time to fit residues: 125.3627 Evaluate side-chains 83 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 82 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 379 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 4 optimal weight: 0.8980 chunk 7 optimal weight: 5.9990 chunk 27 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 28 optimal weight: 0.9980 chunk 3 optimal weight: 5.9990 chunk 5 optimal weight: 1.9990 chunk 24 optimal weight: 0.0270 chunk 1 optimal weight: 9.9990 chunk 20 optimal weight: 0.6980 chunk 31 optimal weight: 8.9990 overall best weight: 0.9240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 GLN A 351 GLN C 307 GLN D 307 GLN E 351 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8976 moved from start: 0.3329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.015 2915 Z= 0.128 Angle : 0.524 7.019 3900 Z= 0.256 Chirality : 0.049 0.121 440 Planarity : 0.003 0.019 495 Dihedral : 4.628 13.561 385 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 2.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 0.30 % Allowed : 19.09 % Favored : 80.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.65 (0.37), residues: 365 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.25 (0.28), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS D 374 PHE 0.005 0.001 PHE A 346 TYR 0.011 0.002 TYR E 310 ARG 0.001 0.000 ARG B 379 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 82 time to evaluate : 0.394 Fit side-chains revert: symmetry clash REVERT: D 379 ARG cc_start: 0.5031 (OUTLIER) cc_final: 0.3782 (mpt90) REVERT: E 349 ARG cc_start: 0.8800 (mtt180) cc_final: 0.7698 (mmp-170) outliers start: 1 outliers final: 0 residues processed: 82 average time/residue: 1.5153 time to fit residues: 126.7231 Evaluate side-chains 82 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 81 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 379 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 18 optimal weight: 0.6980 chunk 23 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 22 optimal weight: 9.9990 chunk 21 optimal weight: 1.9990 chunk 20 optimal weight: 8.9990 chunk 13 optimal weight: 0.8980 chunk 12 optimal weight: 8.9990 chunk 34 optimal weight: 7.9990 chunk 1 optimal weight: 9.9990 chunk 33 optimal weight: 5.9990 overall best weight: 2.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 GLN B 351 GLN C 307 GLN D 307 GLN E 351 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.127349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.111510 restraints weight = 3096.035| |-----------------------------------------------------------------------------| r_work (start): 0.3697 rms_B_bonded: 1.22 r_work: 0.3599 rms_B_bonded: 1.43 restraints_weight: 0.5000 r_work: 0.3521 rms_B_bonded: 2.44 restraints_weight: 0.2500 r_work (final): 0.3521 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9021 moved from start: 0.3227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 2915 Z= 0.213 Angle : 0.565 7.377 3900 Z= 0.280 Chirality : 0.049 0.129 440 Planarity : 0.003 0.024 495 Dihedral : 4.834 14.401 385 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 2.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 0.61 % Allowed : 19.09 % 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: -1.65 (0.37), residues: 365 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.25 (0.28), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS E 329 PHE 0.006 0.002 PHE A 346 TYR 0.010 0.002 TYR E 310 ARG 0.002 0.000 ARG D 379 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2662.15 seconds wall clock time: 47 minutes 59.99 seconds (2879.99 seconds total)