Starting phenix.real_space_refine on Wed Mar 5 16:54:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8oth_17179/03_2025/8oth_17179.cif Found real_map, /net/cci-nas-00/data/ceres_data/8oth_17179/03_2025/8oth_17179.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8oth_17179/03_2025/8oth_17179.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8oth_17179/03_2025/8oth_17179.map" model { file = "/net/cci-nas-00/data/ceres_data/8oth_17179/03_2025/8oth_17179.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8oth_17179/03_2025/8oth_17179.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 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 35 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 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: 3.31, per 1000 atoms: 1.15 Number of scatterers: 2870 At special positions: 0 Unit cell: (135.464, 109.032, 33.04, 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: 0.62 Conformation dependent library (CDL) restraints added in 701.5 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, 42.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.39 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'D' and resid 306 through 310 removed outlier: 6.991A pdb=" N GLN A 307 " --> pdb=" O ILE D 308 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N TYR D 310 " --> pdb=" O GLN A 307 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N VAL A 309 " --> pdb=" O TYR D 310 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 313 through 314 removed outlier: 6.819A pdb=" N VAL A 313 " --> pdb=" O ASP D 314 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 319 through 328 removed outlier: 6.803A pdb=" N THR A 319 " --> pdb=" O SER D 320 " (cutoff:3.500A) removed outlier: 8.459A pdb=" N CYS D 322 " --> pdb=" O THR A 319 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N LYS A 321 " --> pdb=" O CYS D 322 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N SER D 324 " --> pdb=" O LYS A 321 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N GLY A 323 " --> pdb=" O SER D 324 " (cutoff:3.500A) removed outlier: 9.877A pdb=" N GLY D 326 " --> pdb=" O GLY A 323 " (cutoff:3.500A) removed outlier: 8.985A pdb=" N LEU A 325 " --> pdb=" O GLY D 326 " (cutoff:3.500A) removed outlier: 9.514A pdb=" N ILE D 328 " --> pdb=" O LEU A 325 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N ASN A 327 " --> pdb=" O ILE D 328 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N SER A 324 " --> pdb=" O GLY E 323 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N LEU E 325 " --> pdb=" O SER A 324 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N GLY A 326 " --> pdb=" O LEU E 325 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N ASN E 327 " --> pdb=" O GLY A 326 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 337 through 339 removed outlier: 6.481A pdb=" N VAL A 337 " --> pdb=" O GLU E 338 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 342 through 345 removed outlier: 6.926A pdb=" N LYS A 343 " --> pdb=" O GLU D 342 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N GLU A 342 " --> pdb=" O LYS E 343 " (cutoff:3.500A) removed outlier: 8.332A pdb=" N ASP E 345 " --> pdb=" O GLU A 342 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N LEU A 344 " --> pdb=" O ASP E 345 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 350 through 357 removed outlier: 6.460A pdb=" N VAL A 350 " --> pdb=" O GLN E 351 " (cutoff:3.500A) removed outlier: 8.416A pdb=" N LYS E 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N SER A 352 " --> pdb=" O LYS E 353 " (cutoff:3.500A) removed outlier: 8.221A pdb=" N GLY E 355 " --> pdb=" O SER A 352 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N ILE A 354 " --> pdb=" O GLY E 355 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N LEU E 357 " --> pdb=" O ILE A 354 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N SER A 356 " --> pdb=" O LEU E 357 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 369 through 373 removed outlier: 6.781A pdb=" N LYS A 369 " --> pdb=" O LYS D 370 " (cutoff:3.500A) removed outlier: 8.281A pdb=" N GLU D 372 " --> pdb=" O LYS A 369 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N ILE A 371 " --> pdb=" O GLU D 372 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 376 through 378 removed outlier: 6.498A pdb=" N LEU A 376 " --> pdb=" O THR E 377 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 306 through 310 removed outlier: 6.991A pdb=" N GLN B 307 " --> pdb=" O ILE C 308 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N TYR C 310 " --> pdb=" O GLN B 307 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N VAL B 309 " --> pdb=" O TYR C 310 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'B' and resid 313 through 314 removed outlier: 6.820A pdb=" N VAL B 313 " --> pdb=" O ASP C 314 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'B' and resid 319 through 328 removed outlier: 6.803A pdb=" N THR B 319 " --> pdb=" O SER C 320 " (cutoff:3.500A) removed outlier: 8.458A pdb=" N CYS C 322 " --> pdb=" O THR B 319 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N LYS B 321 " --> pdb=" O CYS C 322 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N SER C 324 " --> pdb=" O LYS B 321 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N GLY B 323 " --> pdb=" O SER C 324 " (cutoff:3.500A) removed outlier: 9.876A pdb=" N GLY C 326 " --> pdb=" O GLY B 323 " (cutoff:3.500A) removed outlier: 8.985A pdb=" N LEU B 325 " --> pdb=" O GLY C 326 " (cutoff:3.500A) removed outlier: 9.513A pdb=" N ILE C 328 " --> pdb=" O LEU B 325 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N ASN B 327 " --> pdb=" O ILE C 328 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'B' and resid 337 through 339 Processing sheet with id=AB4, first strand: chain 'B' and resid 342 through 345 removed outlier: 6.926A pdb=" N LYS B 343 " --> pdb=" O GLU C 342 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 350 through 357 Processing sheet with id=AB6, first strand: chain 'B' and resid 369 through 373 removed outlier: 6.780A pdb=" N LYS B 369 " --> pdb=" O LYS C 370 " (cutoff:3.500A) removed outlier: 8.281A pdb=" N GLU C 372 " --> pdb=" O LYS B 369 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N ILE B 371 " --> pdb=" O GLU C 372 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'B' and resid 376 through 378 40 hydrogen bonds defined for protein. 120 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: 0.60 Time building geometry restraints manager: 0.77 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: 727 1.34 - 1.46: 657 1.46 - 1.58: 1526 1.58 - 1.70: 0 1.70 - 1.82: 5 Bond restraints: 2915 Sorted by residual: bond pdb=" CG HIS B 330 " pdb=" CD2 HIS B 330 " ideal model delta sigma weight residual 1.354 1.322 0.032 1.10e-02 8.26e+03 8.21e+00 bond pdb=" CG HIS C 330 " pdb=" CD2 HIS C 330 " ideal model delta sigma weight residual 1.354 1.323 0.031 1.10e-02 8.26e+03 8.00e+00 bond pdb=" CG HIS A 330 " pdb=" CD2 HIS A 330 " ideal model delta sigma weight residual 1.354 1.323 0.031 1.10e-02 8.26e+03 7.92e+00 bond pdb=" CG HIS D 330 " pdb=" CD2 HIS D 330 " ideal model delta sigma weight residual 1.354 1.323 0.031 1.10e-02 8.26e+03 7.80e+00 bond pdb=" CG HIS E 330 " pdb=" CD2 HIS E 330 " ideal model delta sigma weight residual 1.354 1.323 0.031 1.10e-02 8.26e+03 7.75e+00 ... (remaining 2910 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.76: 3025 1.76 - 3.52: 767 3.52 - 5.28: 83 5.28 - 7.04: 20 7.04 - 8.80: 5 Bond angle restraints: 3900 Sorted by residual: angle pdb=" C HIS D 362 " pdb=" CA HIS D 362 " pdb=" CB HIS D 362 " ideal model delta sigma weight residual 110.22 119.02 -8.80 1.67e+00 3.59e-01 2.78e+01 angle pdb=" C HIS B 362 " pdb=" CA HIS B 362 " pdb=" CB HIS B 362 " ideal model delta sigma weight residual 110.22 119.02 -8.80 1.67e+00 3.59e-01 2.77e+01 angle pdb=" C HIS C 362 " pdb=" CA HIS C 362 " pdb=" CB HIS C 362 " ideal model delta sigma weight residual 110.22 119.01 -8.79 1.67e+00 3.59e-01 2.77e+01 angle pdb=" C HIS A 362 " pdb=" CA HIS A 362 " pdb=" CB HIS A 362 " ideal model delta sigma weight residual 110.22 119.00 -8.78 1.67e+00 3.59e-01 2.77e+01 angle pdb=" C HIS E 362 " pdb=" CA HIS E 362 " pdb=" CB HIS E 362 " ideal model delta sigma weight residual 110.22 119.00 -8.78 1.67e+00 3.59e-01 2.76e+01 ... (remaining 3895 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.74: 1540 14.74 - 29.48: 190 29.48 - 44.21: 40 44.21 - 58.95: 5 58.95 - 73.69: 5 Dihedral angle restraints: 1780 sinusoidal: 745 harmonic: 1035 Sorted by residual: dihedral pdb=" CA VAL D 318 " pdb=" C VAL D 318 " pdb=" N THR D 319 " pdb=" CA THR D 319 " ideal model delta harmonic sigma weight residual -180.00 -150.07 -29.93 0 5.00e+00 4.00e-02 3.58e+01 dihedral pdb=" CA VAL C 318 " pdb=" C VAL C 318 " pdb=" N THR C 319 " pdb=" CA THR C 319 " ideal model delta harmonic sigma weight residual -180.00 -150.07 -29.93 0 5.00e+00 4.00e-02 3.58e+01 dihedral pdb=" CA VAL B 318 " pdb=" C VAL B 318 " pdb=" N THR B 319 " pdb=" CA THR B 319 " ideal model delta harmonic sigma weight residual 180.00 -150.10 -29.90 0 5.00e+00 4.00e-02 3.57e+01 ... (remaining 1777 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 162 0.052 - 0.103: 166 0.103 - 0.155: 82 0.155 - 0.206: 25 0.206 - 0.258: 5 Chirality restraints: 440 Sorted by residual: chirality pdb=" CA ILE C 328 " pdb=" N ILE C 328 " pdb=" C ILE C 328 " pdb=" CB ILE C 328 " both_signs ideal model delta sigma weight residual False 2.43 2.69 -0.26 2.00e-01 2.50e+01 1.66e+00 chirality pdb=" CA ILE B 328 " pdb=" N ILE B 328 " pdb=" C ILE B 328 " pdb=" CB ILE B 328 " both_signs ideal model delta sigma weight residual False 2.43 2.69 -0.26 2.00e-01 2.50e+01 1.65e+00 chirality pdb=" CA ILE A 328 " pdb=" N ILE A 328 " pdb=" C ILE A 328 " pdb=" CB ILE A 328 " both_signs ideal model delta sigma weight residual False 2.43 2.69 -0.26 2.00e-01 2.50e+01 1.65e+00 ... (remaining 437 not shown) Planarity restraints: 495 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL D 363 " -0.022 2.00e-02 2.50e+03 4.33e-02 1.87e+01 pdb=" C VAL D 363 " 0.075 2.00e-02 2.50e+03 pdb=" O VAL D 363 " -0.027 2.00e-02 2.50e+03 pdb=" N PRO D 364 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 363 " 0.022 2.00e-02 2.50e+03 4.32e-02 1.87e+01 pdb=" C VAL B 363 " -0.075 2.00e-02 2.50e+03 pdb=" O VAL B 363 " 0.027 2.00e-02 2.50e+03 pdb=" N PRO B 364 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 363 " -0.022 2.00e-02 2.50e+03 4.32e-02 1.87e+01 pdb=" C VAL A 363 " 0.075 2.00e-02 2.50e+03 pdb=" O VAL A 363 " -0.027 2.00e-02 2.50e+03 pdb=" N PRO A 364 " -0.025 2.00e-02 2.50e+03 ... (remaining 492 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 598 2.81 - 3.33: 2681 3.33 - 3.85: 4409 3.85 - 4.38: 4732 4.38 - 4.90: 8981 Nonbonded interactions: 21401 Sorted by model distance: nonbonded pdb=" OG SER C 316 " pdb=" NZ LYS C 370 " model vdw 2.287 3.120 nonbonded pdb=" OG SER E 316 " pdb=" NZ LYS E 370 " model vdw 2.287 3.120 nonbonded pdb=" OG SER A 316 " pdb=" NZ LYS A 370 " model vdw 2.287 3.120 nonbonded pdb=" OG SER D 316 " pdb=" NZ LYS D 370 " model vdw 2.287 3.120 nonbonded pdb=" OG SER B 316 " pdb=" NZ LYS B 370 " model vdw 2.287 3.120 ... (remaining 21396 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' } 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: 5.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.670 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 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 0.041 2915 Z= 0.583 Angle : 1.555 8.805 3900 Z= 1.013 Chirality : 0.092 0.258 440 Planarity : 0.011 0.054 495 Dihedral : 14.035 73.685 1120 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.59 % Favored : 90.41 % Rotamer: Outliers : 1.52 % Allowed : 10.61 % Favored : 87.88 % 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: -4.34 (0.29), residues: 365 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.30 (0.22), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.011 0.004 HIS C 329 PHE 0.017 0.004 PHE D 346 TYR 0.035 0.013 TYR E 310 ARG 0.004 0.002 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 75 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 70 time to evaluate : 0.350 Fit side-chains REVERT: A 347 LYS cc_start: 0.8220 (mttt) cc_final: 0.7703 (mptt) REVERT: A 369 LYS cc_start: 0.8381 (mttt) cc_final: 0.7869 (mtpt) REVERT: A 378 PHE cc_start: 0.8163 (t80) cc_final: 0.7901 (t80) REVERT: B 311 LYS cc_start: 0.7562 (mtmt) cc_final: 0.7060 (mmmt) REVERT: B 321 LYS cc_start: 0.6802 (ttmt) cc_final: 0.6294 (tttt) REVERT: B 347 LYS cc_start: 0.8459 (mttt) cc_final: 0.7975 (mptt) REVERT: B 349 ARG cc_start: 0.8767 (mtt180) cc_final: 0.7743 (mmm160) REVERT: B 369 LYS cc_start: 0.8429 (mttt) cc_final: 0.7920 (mtpt) REVERT: C 321 LYS cc_start: 0.7545 (ttmt) cc_final: 0.7317 (ttmt) REVERT: C 349 ARG cc_start: 0.8804 (mtt180) cc_final: 0.7529 (pmt-80) REVERT: C 369 LYS cc_start: 0.8546 (mttt) cc_final: 0.8133 (mtpt) REVERT: D 321 LYS cc_start: 0.7550 (ttmt) cc_final: 0.7238 (ttmt) REVERT: D 347 LYS cc_start: 0.8559 (mttt) cc_final: 0.8321 (mptt) REVERT: D 349 ARG cc_start: 0.8801 (mtt180) cc_final: 0.7559 (pmt-80) REVERT: D 369 LYS cc_start: 0.8627 (mttt) cc_final: 0.8040 (mtmt) REVERT: E 311 LYS cc_start: 0.7622 (mtmt) cc_final: 0.7126 (mmmt) REVERT: E 321 LYS cc_start: 0.6808 (ttmt) cc_final: 0.6372 (ttpt) REVERT: E 347 LYS cc_start: 0.8389 (mttt) cc_final: 0.7987 (mptt) REVERT: E 349 ARG cc_start: 0.8725 (mtt180) cc_final: 0.7761 (mmp-170) REVERT: E 369 LYS cc_start: 0.8373 (mttt) cc_final: 0.7844 (mtpt) outliers start: 5 outliers final: 0 residues processed: 75 average time/residue: 0.2873 time to fit residues: 23.7975 Evaluate side-chains 52 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 52 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 29 optimal weight: 9.9990 chunk 26 optimal weight: 2.9990 chunk 14 optimal weight: 6.9990 chunk 9 optimal weight: 0.6980 chunk 17 optimal weight: 9.9990 chunk 27 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 16 optimal weight: 4.9990 chunk 20 optimal weight: 4.9990 chunk 31 optimal weight: 0.0980 chunk 21 optimal weight: 8.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 362 HIS B 362 HIS C 330 HIS C 362 HIS D 330 HIS D 362 HIS E 362 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4626 r_free = 0.4626 target = 0.158941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4337 r_free = 0.4337 target = 0.128577 restraints weight = 3402.230| |-----------------------------------------------------------------------------| r_work (start): 0.4343 rms_B_bonded: 2.67 r_work: 0.4239 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.4138 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.4138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.2526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 2915 Z= 0.209 Angle : 0.593 4.513 3900 Z= 0.303 Chirality : 0.049 0.128 440 Planarity : 0.003 0.028 495 Dihedral : 5.650 19.578 385 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.42 % Allowed : 13.03 % Favored : 84.55 % 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: -4.00 (0.29), residues: 365 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.04 (0.22), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS A 330 PHE 0.005 0.001 PHE D 378 TYR 0.015 0.004 TYR A 310 ARG 0.002 0.000 ARG C 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 80 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 72 time to evaluate : 0.356 Fit side-chains REVERT: A 347 LYS cc_start: 0.8041 (mttt) cc_final: 0.7797 (mmtm) REVERT: A 375 LYS cc_start: 0.7765 (tttt) cc_final: 0.7237 (mttt) REVERT: B 311 LYS cc_start: 0.7667 (mtmt) cc_final: 0.6919 (mmtt) REVERT: B 347 LYS cc_start: 0.8098 (mttt) cc_final: 0.7531 (mptt) REVERT: B 369 LYS cc_start: 0.7757 (mttt) cc_final: 0.7090 (mtpt) REVERT: B 375 LYS cc_start: 0.7765 (OUTLIER) cc_final: 0.7341 (mttt) REVERT: C 375 LYS cc_start: 0.8288 (ttmt) cc_final: 0.7952 (mttt) REVERT: D 321 LYS cc_start: 0.7390 (ttmt) cc_final: 0.6929 (ttmt) REVERT: D 347 LYS cc_start: 0.8388 (mttt) cc_final: 0.8135 (mptt) REVERT: D 369 LYS cc_start: 0.8090 (mttt) cc_final: 0.7340 (mtmt) REVERT: D 375 LYS cc_start: 0.8236 (ttmt) cc_final: 0.7861 (mttt) REVERT: E 311 LYS cc_start: 0.7738 (mtmt) cc_final: 0.7017 (mmtt) REVERT: E 331 LYS cc_start: 0.8426 (mtmt) cc_final: 0.8184 (mttm) REVERT: E 345 ASP cc_start: 0.7700 (m-30) cc_final: 0.6706 (t0) REVERT: E 349 ARG cc_start: 0.8444 (mtt180) cc_final: 0.7364 (mmm160) REVERT: E 369 LYS cc_start: 0.7506 (mttt) cc_final: 0.6907 (mtpt) outliers start: 8 outliers final: 6 residues processed: 72 average time/residue: 0.2521 time to fit residues: 20.4217 Evaluate side-chains 61 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 54 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 375 LYS Chi-restraints excluded: chain C residue 311 LYS Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain E residue 318 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 25 optimal weight: 2.9990 chunk 34 optimal weight: 10.0000 chunk 22 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 23 optimal weight: 0.0050 chunk 7 optimal weight: 10.0000 chunk 32 optimal weight: 10.0000 chunk 30 optimal weight: 0.7980 chunk 24 optimal weight: 0.9990 chunk 8 optimal weight: 7.9990 chunk 28 optimal weight: 0.0970 overall best weight: 0.9796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5106 r_free = 0.5106 target = 0.370632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 117)---------------| | r_work = 0.5445 r_free = 0.5445 target = 0.308207 restraints weight = 3748.855| |-----------------------------------------------------------------------------| r_work (start): 0.4502 rms_B_bonded: 0.97 r_work: 0.4414 rms_B_bonded: 1.09 restraints_weight: 0.5000 r_work: 0.4356 rms_B_bonded: 1.77 restraints_weight: 0.2500 r_work (final): 0.4356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.3092 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= 0.130 Angle : 0.469 3.520 3900 Z= 0.241 Chirality : 0.047 0.120 440 Planarity : 0.004 0.046 495 Dihedral : 4.447 16.051 385 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 1.82 % Allowed : 17.27 % Favored : 80.91 % 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: -3.32 (0.31), residues: 365 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.52 (0.24), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS B 330 PHE 0.004 0.001 PHE C 346 TYR 0.015 0.003 TYR A 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 66 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 60 time to evaluate : 0.316 Fit side-chains REVERT: A 375 LYS cc_start: 0.7823 (tttt) cc_final: 0.7375 (mttt) REVERT: B 311 LYS cc_start: 0.7754 (mtmt) cc_final: 0.7064 (mmtt) REVERT: B 347 LYS cc_start: 0.8068 (mttt) cc_final: 0.7716 (mptt) REVERT: B 349 ARG cc_start: 0.8508 (mtt180) cc_final: 0.7561 (mmm160) REVERT: B 369 LYS cc_start: 0.7815 (mttt) cc_final: 0.7165 (mtpt) REVERT: B 375 LYS cc_start: 0.7895 (ttmt) cc_final: 0.7526 (mttt) REVERT: C 347 LYS cc_start: 0.8516 (mptt) cc_final: 0.8030 (mptt) REVERT: C 369 LYS cc_start: 0.7936 (mttt) cc_final: 0.7350 (ttmt) REVERT: C 375 LYS cc_start: 0.8253 (ttmt) cc_final: 0.7996 (mttt) REVERT: D 369 LYS cc_start: 0.7987 (mttt) cc_final: 0.7383 (mtpt) REVERT: D 375 LYS cc_start: 0.8150 (ttmt) cc_final: 0.7867 (mttt) REVERT: E 311 LYS cc_start: 0.7793 (mtmt) cc_final: 0.7202 (mmtt) REVERT: E 331 LYS cc_start: 0.8451 (mtmt) cc_final: 0.8181 (mttm) REVERT: E 347 LYS cc_start: 0.8081 (mttp) cc_final: 0.7785 (mptt) REVERT: E 349 ARG cc_start: 0.8498 (mtt180) cc_final: 0.7557 (mmp-170) REVERT: E 369 LYS cc_start: 0.7550 (mttt) cc_final: 0.6979 (mtpt) REVERT: E 375 LYS cc_start: 0.8123 (tppt) cc_final: 0.7745 (mttt) outliers start: 6 outliers final: 6 residues processed: 61 average time/residue: 0.3117 time to fit residues: 20.9218 Evaluate side-chains 60 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 54 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 311 LYS Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain E residue 318 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 13 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 9 optimal weight: 0.0870 chunk 19 optimal weight: 1.9990 chunk 24 optimal weight: 6.9990 chunk 14 optimal weight: 10.0000 chunk 11 optimal weight: 3.9990 chunk 34 optimal weight: 10.0000 chunk 30 optimal weight: 7.9990 chunk 17 optimal weight: 9.9990 chunk 4 optimal weight: 8.9990 overall best weight: 3.2166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4921 r_free = 0.4921 target = 0.294080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.5152 r_free = 0.5152 target = 0.245699 restraints weight = 3386.131| |-----------------------------------------------------------------------------| r_work (start): 0.4409 rms_B_bonded: 1.23 r_work: 0.4337 rms_B_bonded: 1.30 restraints_weight: 0.5000 r_work: 0.4274 rms_B_bonded: 2.13 restraints_weight: 0.2500 r_work (final): 0.4274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.3312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 2915 Z= 0.290 Angle : 0.570 6.995 3900 Z= 0.292 Chirality : 0.048 0.129 440 Planarity : 0.004 0.053 495 Dihedral : 4.884 18.720 385 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 2.12 % Allowed : 19.70 % Favored : 78.18 % 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: -2.95 (0.33), residues: 365 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.24 (0.25), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.002 HIS B 330 PHE 0.006 0.002 PHE C 346 TYR 0.018 0.004 TYR A 310 ARG 0.001 0.000 ARG B 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 72 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 65 time to evaluate : 0.314 Fit side-chains REVERT: A 347 LYS cc_start: 0.8363 (mptt) cc_final: 0.7866 (mptt) REVERT: A 375 LYS cc_start: 0.8020 (tttt) cc_final: 0.7569 (mttt) REVERT: B 311 LYS cc_start: 0.7835 (mtmt) cc_final: 0.7128 (mmtt) REVERT: B 347 LYS cc_start: 0.8108 (mttt) cc_final: 0.7645 (mptt) REVERT: B 349 ARG cc_start: 0.8402 (mtt180) cc_final: 0.7441 (mmm160) REVERT: B 369 LYS cc_start: 0.7874 (mttt) cc_final: 0.7158 (mtpt) REVERT: B 375 LYS cc_start: 0.7911 (ttmt) cc_final: 0.7504 (mttt) REVERT: B 379 ARG cc_start: 0.7081 (tmt-80) cc_final: 0.6487 (ttp80) REVERT: C 347 LYS cc_start: 0.8510 (mptt) cc_final: 0.7852 (mptt) REVERT: C 369 LYS cc_start: 0.8097 (mttt) cc_final: 0.7456 (mtpt) REVERT: C 375 LYS cc_start: 0.8241 (ttmt) cc_final: 0.7959 (mttt) REVERT: D 321 LYS cc_start: 0.7560 (ttmt) cc_final: 0.7096 (ttmt) REVERT: D 348 ASP cc_start: 0.5967 (t0) cc_final: 0.5333 (p0) REVERT: D 369 LYS cc_start: 0.8160 (mttt) cc_final: 0.7469 (mtpt) REVERT: D 375 LYS cc_start: 0.8177 (ttmt) cc_final: 0.7875 (mttt) REVERT: E 311 LYS cc_start: 0.7811 (mtmt) cc_final: 0.7136 (mmtt) REVERT: E 331 LYS cc_start: 0.8598 (mtmt) cc_final: 0.8165 (mttm) REVERT: E 347 LYS cc_start: 0.8237 (mttp) cc_final: 0.7855 (mptt) REVERT: E 349 ARG cc_start: 0.8520 (mtt180) cc_final: 0.7538 (mmm160) REVERT: E 369 LYS cc_start: 0.7704 (mttt) cc_final: 0.6977 (mtpt) REVERT: E 375 LYS cc_start: 0.8115 (tppt) cc_final: 0.7643 (mttt) outliers start: 7 outliers final: 7 residues processed: 65 average time/residue: 0.3104 time to fit residues: 22.0918 Evaluate side-chains 65 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 58 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 311 LYS Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain C residue 311 LYS Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain E residue 318 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 28 optimal weight: 0.0980 chunk 7 optimal weight: 10.0000 chunk 14 optimal weight: 0.0970 chunk 15 optimal weight: 1.9990 chunk 18 optimal weight: 4.9990 chunk 4 optimal weight: 7.9990 chunk 26 optimal weight: 0.0570 chunk 34 optimal weight: 8.9990 chunk 22 optimal weight: 10.0000 chunk 24 optimal weight: 2.9990 chunk 8 optimal weight: 3.9990 overall best weight: 1.0500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4645 r_free = 0.4645 target = 0.162329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4356 r_free = 0.4356 target = 0.131009 restraints weight = 3348.844| |-----------------------------------------------------------------------------| r_work (start): 0.4366 rms_B_bonded: 2.66 r_work: 0.4269 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.4166 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.4166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.3662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.013 2915 Z= 0.126 Angle : 0.457 3.583 3900 Z= 0.234 Chirality : 0.046 0.121 440 Planarity : 0.004 0.053 495 Dihedral : 4.122 15.050 385 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 2.73 % Allowed : 21.21 % Favored : 76.06 % 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: -2.84 (0.35), residues: 365 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.15 (0.26), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS B 330 PHE 0.003 0.001 PHE D 346 TYR 0.012 0.002 TYR A 310 ARG 0.001 0.000 ARG C 349 *********************** 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 62 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 53 time to evaluate : 0.354 Fit side-chains REVERT: A 347 LYS cc_start: 0.8154 (mptt) cc_final: 0.7631 (mptt) REVERT: A 348 ASP cc_start: 0.8405 (OUTLIER) cc_final: 0.7945 (t70) REVERT: A 375 LYS cc_start: 0.7930 (tttt) cc_final: 0.7487 (mttt) REVERT: B 311 LYS cc_start: 0.7837 (mtmt) cc_final: 0.7113 (mmtt) REVERT: B 347 LYS cc_start: 0.7947 (mttt) cc_final: 0.7483 (mptt) REVERT: B 348 ASP cc_start: 0.8437 (OUTLIER) cc_final: 0.7966 (t70) REVERT: B 349 ARG cc_start: 0.8435 (mtt180) cc_final: 0.7346 (mmm160) REVERT: B 369 LYS cc_start: 0.7889 (mttt) cc_final: 0.7169 (mtpt) REVERT: B 375 LYS cc_start: 0.7938 (ttmt) cc_final: 0.7486 (mttt) REVERT: B 379 ARG cc_start: 0.7082 (tmt-80) cc_final: 0.6537 (ttp80) REVERT: C 322 CYS cc_start: 0.8320 (t) cc_final: 0.7985 (t) REVERT: C 347 LYS cc_start: 0.8464 (mptt) cc_final: 0.7769 (mptt) REVERT: C 369 LYS cc_start: 0.8193 (mttt) cc_final: 0.7520 (mtpt) REVERT: C 375 LYS cc_start: 0.8249 (ttmt) cc_final: 0.7962 (mttt) REVERT: D 322 CYS cc_start: 0.8303 (t) cc_final: 0.8044 (t) REVERT: D 369 LYS cc_start: 0.8138 (mttt) cc_final: 0.7480 (mtpt) REVERT: D 375 LYS cc_start: 0.8180 (ttmt) cc_final: 0.7853 (mttt) REVERT: E 311 LYS cc_start: 0.7763 (mtmt) cc_final: 0.7100 (mmtt) REVERT: E 331 LYS cc_start: 0.8565 (mtmt) cc_final: 0.8168 (mttm) REVERT: E 347 LYS cc_start: 0.8036 (mttp) cc_final: 0.7639 (mptt) REVERT: E 349 ARG cc_start: 0.8631 (mtt180) cc_final: 0.7432 (mmm160) REVERT: E 369 LYS cc_start: 0.7686 (mttt) cc_final: 0.6951 (mtpt) REVERT: E 375 LYS cc_start: 0.8145 (tppt) cc_final: 0.7623 (mttt) outliers start: 9 outliers final: 7 residues processed: 54 average time/residue: 0.3242 time to fit residues: 19.2865 Evaluate side-chains 60 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 51 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 311 LYS Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 348 ASP Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 348 ASP Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain E residue 318 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 2 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 22 optimal weight: 10.0000 chunk 4 optimal weight: 6.9990 chunk 20 optimal weight: 9.9990 chunk 3 optimal weight: 7.9990 chunk 6 optimal weight: 10.0000 chunk 28 optimal weight: 5.9990 chunk 31 optimal weight: 3.9990 chunk 8 optimal weight: 0.9990 chunk 9 optimal weight: 9.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4874 r_free = 0.4874 target = 0.289656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 86)----------------| | r_work = 0.5094 r_free = 0.5094 target = 0.241168 restraints weight = 3458.229| |-----------------------------------------------------------------------------| r_work (start): 0.4361 rms_B_bonded: 1.05 r_work: 0.4291 rms_B_bonded: 1.11 restraints_weight: 0.5000 r_work: 0.4229 rms_B_bonded: 1.82 restraints_weight: 0.2500 r_work: 0.4050 rms_B_bonded: 4.98 restraints_weight: 0.1250 r_work (final): 0.4050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.3584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.036 2915 Z= 0.433 Angle : 0.653 5.102 3900 Z= 0.347 Chirality : 0.050 0.132 440 Planarity : 0.005 0.046 495 Dihedral : 5.221 19.354 385 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 3.33 % Allowed : 21.21 % Favored : 75.45 % 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: -2.80 (0.35), residues: 365 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.13 (0.27), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.003 HIS B 330 PHE 0.008 0.002 PHE D 346 TYR 0.019 0.005 TYR A 310 ARG 0.001 0.000 ARG A 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 74 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 63 time to evaluate : 0.316 Fit side-chains REVERT: A 321 LYS cc_start: 0.6897 (ttmt) cc_final: 0.6539 (ttmt) REVERT: A 347 LYS cc_start: 0.8307 (mptt) cc_final: 0.7688 (mptt) REVERT: A 348 ASP cc_start: 0.8600 (OUTLIER) cc_final: 0.8200 (t70) REVERT: A 369 LYS cc_start: 0.8381 (mttt) cc_final: 0.7517 (mtpt) REVERT: A 375 LYS cc_start: 0.8128 (tttt) cc_final: 0.7718 (mttt) REVERT: B 311 LYS cc_start: 0.7810 (mtmt) cc_final: 0.7091 (mmtt) REVERT: B 347 LYS cc_start: 0.8151 (mttt) cc_final: 0.7634 (mptt) REVERT: B 349 ARG cc_start: 0.8437 (mtt180) cc_final: 0.7444 (mmm160) REVERT: B 369 LYS cc_start: 0.8181 (mttt) cc_final: 0.7397 (mtpt) REVERT: B 375 LYS cc_start: 0.8055 (ttmt) cc_final: 0.7621 (mttt) REVERT: B 379 ARG cc_start: 0.7143 (tmt-80) cc_final: 0.6629 (ttp80) REVERT: C 347 LYS cc_start: 0.8530 (mptt) cc_final: 0.7748 (mptt) REVERT: C 369 LYS cc_start: 0.8352 (mttt) cc_final: 0.7608 (mtpt) REVERT: C 375 LYS cc_start: 0.8256 (ttmt) cc_final: 0.7948 (mttt) REVERT: D 348 ASP cc_start: 0.6473 (t0) cc_final: 0.5891 (p0) REVERT: D 369 LYS cc_start: 0.8353 (mttt) cc_final: 0.7634 (mtpt) REVERT: D 375 LYS cc_start: 0.8310 (ttmt) cc_final: 0.7992 (mttt) REVERT: E 311 LYS cc_start: 0.7764 (mtmt) cc_final: 0.7017 (mmtt) REVERT: E 331 LYS cc_start: 0.8714 (mtmt) cc_final: 0.8345 (mttm) REVERT: E 347 LYS cc_start: 0.8244 (mttp) cc_final: 0.7817 (mptt) REVERT: E 349 ARG cc_start: 0.8560 (mtt180) cc_final: 0.7559 (mmm160) REVERT: E 369 LYS cc_start: 0.7995 (mttt) cc_final: 0.7304 (mtpt) REVERT: E 375 LYS cc_start: 0.8209 (tppt) cc_final: 0.7689 (mttt) outliers start: 11 outliers final: 10 residues processed: 65 average time/residue: 0.3167 time to fit residues: 22.5550 Evaluate side-chains 70 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 59 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 311 LYS Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 348 ASP Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain C residue 311 LYS Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 324 SER Chi-restraints excluded: chain D residue 311 LYS Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain E residue 318 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 26 optimal weight: 3.9990 chunk 17 optimal weight: 4.9990 chunk 7 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 1 optimal weight: 10.0000 chunk 21 optimal weight: 4.9990 chunk 34 optimal weight: 0.0030 chunk 14 optimal weight: 4.9990 chunk 20 optimal weight: 10.0000 chunk 4 optimal weight: 2.9990 chunk 8 optimal weight: 10.0000 overall best weight: 3.3998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4902 r_free = 0.4902 target = 0.293341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 92)----------------| | r_work = 0.5124 r_free = 0.5124 target = 0.245200 restraints weight = 3477.076| |-----------------------------------------------------------------------------| r_work (start): 0.4405 rms_B_bonded: 1.07 r_work: 0.4334 rms_B_bonded: 1.12 restraints_weight: 0.5000 r_work: 0.4276 rms_B_bonded: 1.83 restraints_weight: 0.2500 r_work (final): 0.4276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.3710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 2915 Z= 0.291 Angle : 0.588 6.262 3900 Z= 0.301 Chirality : 0.049 0.128 440 Planarity : 0.005 0.054 495 Dihedral : 4.826 17.343 385 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 3.94 % Allowed : 20.91 % Favored : 75.15 % 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: -2.67 (0.36), residues: 365 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.03 (0.28), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.002 HIS B 330 PHE 0.005 0.001 PHE D 346 TYR 0.013 0.004 TYR A 310 ARG 0.001 0.000 ARG A 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 71 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 58 time to evaluate : 0.354 Fit side-chains REVERT: A 347 LYS cc_start: 0.8377 (mptt) cc_final: 0.7832 (mptt) REVERT: A 348 ASP cc_start: 0.8424 (OUTLIER) cc_final: 0.8080 (t70) REVERT: A 375 LYS cc_start: 0.7952 (tttt) cc_final: 0.7582 (mttt) REVERT: B 311 LYS cc_start: 0.7838 (mtmt) cc_final: 0.7124 (mmtt) REVERT: B 347 LYS cc_start: 0.8118 (mttt) cc_final: 0.7671 (mptt) REVERT: B 348 ASP cc_start: 0.8338 (OUTLIER) cc_final: 0.7938 (t70) REVERT: B 349 ARG cc_start: 0.8446 (mtt180) cc_final: 0.7505 (mmm160) REVERT: B 369 LYS cc_start: 0.8132 (mttt) cc_final: 0.7367 (mtpt) REVERT: B 375 LYS cc_start: 0.7921 (OUTLIER) cc_final: 0.7521 (mttt) REVERT: B 379 ARG cc_start: 0.7036 (tmt-80) cc_final: 0.6566 (ttp80) REVERT: C 322 CYS cc_start: 0.8224 (t) cc_final: 0.7890 (t) REVERT: C 347 LYS cc_start: 0.8576 (mptt) cc_final: 0.7881 (mptt) REVERT: C 369 LYS cc_start: 0.8311 (mttt) cc_final: 0.7691 (mtpt) REVERT: C 375 LYS cc_start: 0.8205 (ttmt) cc_final: 0.7926 (mttt) REVERT: D 322 CYS cc_start: 0.8214 (t) cc_final: 0.7977 (t) REVERT: D 348 ASP cc_start: 0.6966 (t0) cc_final: 0.6307 (p0) REVERT: D 369 LYS cc_start: 0.8333 (mttt) cc_final: 0.7597 (mtpt) REVERT: D 375 LYS cc_start: 0.8216 (ttmt) cc_final: 0.7845 (mttt) REVERT: E 311 LYS cc_start: 0.7786 (mtmt) cc_final: 0.7049 (mmtt) REVERT: E 331 LYS cc_start: 0.8586 (mtmt) cc_final: 0.8267 (mttm) REVERT: E 347 LYS cc_start: 0.8209 (mttp) cc_final: 0.7864 (mptt) REVERT: E 349 ARG cc_start: 0.8563 (mtt180) cc_final: 0.7595 (mmm160) REVERT: E 369 LYS cc_start: 0.7939 (mttt) cc_final: 0.7242 (mtpt) REVERT: E 375 LYS cc_start: 0.8123 (tppt) cc_final: 0.7576 (mttt) outliers start: 13 outliers final: 10 residues processed: 60 average time/residue: 0.3170 time to fit residues: 20.9662 Evaluate side-chains 71 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 58 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 311 LYS Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 348 ASP Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 348 ASP Chi-restraints excluded: chain B residue 375 LYS Chi-restraints excluded: chain C residue 311 LYS Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 324 SER Chi-restraints excluded: chain D residue 311 LYS Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain E residue 318 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 27 optimal weight: 5.9990 chunk 32 optimal weight: 0.0870 chunk 2 optimal weight: 9.9990 chunk 30 optimal weight: 0.5980 chunk 17 optimal weight: 5.9990 chunk 11 optimal weight: 3.9990 chunk 28 optimal weight: 8.9990 chunk 10 optimal weight: 1.9990 chunk 6 optimal weight: 3.9990 chunk 29 optimal weight: 6.9990 chunk 24 optimal weight: 10.0000 overall best weight: 2.1364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4928 r_free = 0.4928 target = 0.297170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.5130 r_free = 0.5130 target = 0.250120 restraints weight = 3452.752| |-----------------------------------------------------------------------------| r_work (start): 0.4832 rms_B_bonded: 1.34 r_work: 0.5158 rms_B_bonded: 0.61 restraints_weight: 0.5000 r_work: 0.5132 rms_B_bonded: 0.93 restraints_weight: 0.2500 r_work: 0.4918 rms_B_bonded: 3.58 restraints_weight: 0.1250 r_work (final): 0.4918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.3881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.017 2915 Z= 0.195 Angle : 0.538 8.315 3900 Z= 0.266 Chirality : 0.048 0.121 440 Planarity : 0.004 0.050 495 Dihedral : 4.394 15.706 385 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 3.94 % Allowed : 20.91 % Favored : 75.15 % 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: -2.47 (0.38), residues: 365 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.87 (0.29), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS B 330 PHE 0.004 0.001 PHE D 346 TYR 0.013 0.003 TYR A 310 ARG 0.001 0.000 ARG C 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 75 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 62 time to evaluate : 0.321 Fit side-chains REVERT: A 321 LYS cc_start: 0.7757 (ttmt) cc_final: 0.7526 (ttmt) REVERT: A 369 LYS cc_start: 0.8366 (mttt) cc_final: 0.7968 (mtpt) REVERT: B 349 ARG cc_start: 0.8697 (mtt180) cc_final: 0.8426 (mmm160) REVERT: B 369 LYS cc_start: 0.8506 (mttt) cc_final: 0.8144 (mtpt) REVERT: C 369 LYS cc_start: 0.8209 (mttt) cc_final: 0.7846 (mtpt) REVERT: D 369 LYS cc_start: 0.8042 (mttt) cc_final: 0.7650 (mtpt) REVERT: E 349 ARG cc_start: 0.8614 (mtt180) cc_final: 0.8377 (mmm160) REVERT: E 369 LYS cc_start: 0.8012 (mttt) cc_final: 0.7752 (mtpt) outliers start: 13 outliers final: 10 residues processed: 64 average time/residue: 0.2939 time to fit residues: 20.8019 Evaluate side-chains 51 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 41 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 311 LYS Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain C residue 311 LYS Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 324 SER Chi-restraints excluded: chain D residue 311 LYS Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain E residue 318 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 29 optimal weight: 9.9990 chunk 14 optimal weight: 4.9990 chunk 18 optimal weight: 6.9990 chunk 4 optimal weight: 10.0000 chunk 32 optimal weight: 0.8980 chunk 7 optimal weight: 10.0000 chunk 25 optimal weight: 4.9990 chunk 16 optimal weight: 6.9990 chunk 26 optimal weight: 10.0000 chunk 34 optimal weight: 0.0270 chunk 22 optimal weight: 2.9990 overall best weight: 2.7844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4926 r_free = 0.4926 target = 0.294446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.5155 r_free = 0.5155 target = 0.244796 restraints weight = 3458.340| |-----------------------------------------------------------------------------| r_work (start): 0.4408 rms_B_bonded: 1.27 r_work: 0.4343 rms_B_bonded: 1.29 restraints_weight: 0.5000 r_work: 0.4280 rms_B_bonded: 2.13 restraints_weight: 0.2500 r_work (final): 0.4280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.4231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.021 2915 Z= 0.257 Angle : 0.666 7.897 3900 Z= 0.330 Chirality : 0.049 0.123 440 Planarity : 0.005 0.056 495 Dihedral : 4.502 16.168 385 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 3.03 % Allowed : 22.42 % Favored : 74.55 % 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: -2.43 (0.38), residues: 365 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.84 (0.29), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS B 330 PHE 0.006 0.001 PHE A 346 TYR 0.014 0.004 TYR A 310 ARG 0.001 0.000 ARG A 349 *********************** 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 55 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 45 time to evaluate : 0.356 Fit side-chains REVERT: A 375 LYS cc_start: 0.7958 (mttt) cc_final: 0.7398 (tppt) REVERT: B 349 ARG cc_start: 0.8507 (mtt180) cc_final: 0.7430 (mmm160) REVERT: B 375 LYS cc_start: 0.7697 (mttt) cc_final: 0.7272 (ttpt) REVERT: C 375 LYS cc_start: 0.8127 (mttt) cc_final: 0.7813 (tppt) REVERT: E 349 ARG cc_start: 0.8549 (mtt180) cc_final: 0.7546 (mmm160) REVERT: E 375 LYS cc_start: 0.7810 (mttt) cc_final: 0.7579 (tppt) outliers start: 10 outliers final: 10 residues processed: 48 average time/residue: 0.2743 time to fit residues: 14.8817 Evaluate side-chains 56 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 46 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 311 LYS Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain C residue 311 LYS Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 324 SER Chi-restraints excluded: chain D residue 311 LYS Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain E residue 318 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 11 optimal weight: 0.7980 chunk 8 optimal weight: 20.0000 chunk 2 optimal weight: 9.9990 chunk 23 optimal weight: 4.9990 chunk 10 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 18 optimal weight: 0.9990 chunk 7 optimal weight: 10.0000 chunk 16 optimal weight: 0.0980 chunk 24 optimal weight: 10.0000 chunk 29 optimal weight: 10.0000 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5073 r_free = 0.5073 target = 0.363745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 94)----------------| | r_work = 0.5413 r_free = 0.5413 target = 0.298396 restraints weight = 3925.166| |-----------------------------------------------------------------------------| r_work (start): 0.4483 rms_B_bonded: 1.06 r_work: 0.4412 rms_B_bonded: 1.09 restraints_weight: 0.5000 r_work: 0.4356 rms_B_bonded: 1.79 restraints_weight: 0.2500 r_work (final): 0.4356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.4451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 2915 Z= 0.166 Angle : 0.586 7.460 3900 Z= 0.286 Chirality : 0.047 0.119 440 Planarity : 0.004 0.053 495 Dihedral : 4.213 14.680 385 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 3.33 % Allowed : 22.12 % Favored : 74.55 % 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: -2.35 (0.39), residues: 365 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.78 (0.29), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS B 330 PHE 0.004 0.001 PHE D 346 TYR 0.011 0.003 TYR A 310 ARG 0.001 0.000 ARG D 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 59 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 48 time to evaluate : 0.357 Fit side-chains REVERT: A 348 ASP cc_start: 0.8306 (t70) cc_final: 0.7928 (t70) REVERT: A 375 LYS cc_start: 0.7888 (mttt) cc_final: 0.7569 (tppt) REVERT: B 349 ARG cc_start: 0.8538 (mtt180) cc_final: 0.7507 (mmm160) REVERT: B 375 LYS cc_start: 0.7706 (mttt) cc_final: 0.7311 (tppt) REVERT: C 375 LYS cc_start: 0.8093 (mttt) cc_final: 0.7808 (tppt) REVERT: D 369 LYS cc_start: 0.8269 (mttt) cc_final: 0.7535 (mtpt) REVERT: E 348 ASP cc_start: 0.8279 (OUTLIER) cc_final: 0.7882 (t70) REVERT: E 349 ARG cc_start: 0.8557 (mtt180) cc_final: 0.7564 (mmm160) outliers start: 11 outliers final: 9 residues processed: 50 average time/residue: 0.2741 time to fit residues: 15.4666 Evaluate side-chains 56 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 46 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 311 LYS Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain C residue 311 LYS Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 324 SER Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain E residue 318 VAL Chi-restraints excluded: chain E residue 348 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 23 optimal weight: 4.9990 chunk 12 optimal weight: 8.9990 chunk 27 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 18 optimal weight: 0.6980 chunk 3 optimal weight: 4.9990 chunk 31 optimal weight: 4.9990 chunk 7 optimal weight: 10.0000 chunk 10 optimal weight: 8.9990 chunk 34 optimal weight: 2.9990 chunk 14 optimal weight: 9.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4925 r_free = 0.4925 target = 0.293782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.5154 r_free = 0.5154 target = 0.243999 restraints weight = 3422.904| |-----------------------------------------------------------------------------| r_work (start): 0.4403 rms_B_bonded: 1.27 r_work: 0.4336 rms_B_bonded: 1.29 restraints_weight: 0.5000 r_work: 0.4270 rms_B_bonded: 2.14 restraints_weight: 0.2500 r_work (final): 0.4270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.4462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 2915 Z= 0.263 Angle : 0.637 7.519 3900 Z= 0.313 Chirality : 0.048 0.123 440 Planarity : 0.004 0.053 495 Dihedral : 4.508 16.019 385 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 3.03 % Allowed : 22.73 % Favored : 74.24 % 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: -2.36 (0.39), residues: 365 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.79 (0.29), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS B 330 PHE 0.005 0.001 PHE D 346 TYR 0.013 0.004 TYR A 310 ARG 0.001 0.000 ARG B 379 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2047.39 seconds wall clock time: 36 minutes 0.60 seconds (2160.60 seconds total)