Starting phenix.real_space_refine on Fri Dec 27 05:43:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8oth_17179/12_2024/8oth_17179.cif Found real_map, /net/cci-nas-00/data/ceres_data/8oth_17179/12_2024/8oth_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_17179/12_2024/8oth_17179.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8oth_17179/12_2024/8oth_17179.map" model { file = "/net/cci-nas-00/data/ceres_data/8oth_17179/12_2024/8oth_17179.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8oth_17179/12_2024/8oth_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-5532/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: 2.50, per 1000 atoms: 0.87 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 351.7 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, 42.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.42 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: 0.61 Time building geometry restraints manager: 0.72 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: 0.00 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: 2.650 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: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 11.700 Find NCS groups from input model: 0.090 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:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.430 ------------------------------------------------------------------------------- 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 : 0.334 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: 0.2796 time to fit residues: 23.1635 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 : 0.318 ------------------------------------------------------------------------------- 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: 8.9990 chunk 21 optimal weight: 8.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.2483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 2915 Z= 0.278 Angle : 0.627 5.266 3900 Z= 0.325 Chirality : 0.050 0.131 440 Planarity : 0.004 0.029 495 Dihedral : 5.934 21.050 385 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 2.42 % Allowed : 13.94 % Favored : 83.64 % 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: -4.02 (0.29), residues: 365 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.05 (0.22), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS A 330 PHE 0.006 0.001 PHE C 346 TYR 0.017 0.004 TYR A 310 ARG 0.001 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 83 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 75 time to evaluate : 0.357 Fit side-chains REVERT: A 347 LYS cc_start: 0.8172 (mttt) cc_final: 0.7787 (mptt) REVERT: A 375 LYS cc_start: 0.7906 (tttt) cc_final: 0.7421 (mttt) REVERT: B 311 LYS cc_start: 0.7710 (mtmt) cc_final: 0.7081 (mmtt) REVERT: B 347 LYS cc_start: 0.8288 (mttt) cc_final: 0.7855 (mptt) REVERT: B 349 ARG cc_start: 0.8822 (mtt180) cc_final: 0.7916 (mmp-170) REVERT: B 369 LYS cc_start: 0.8389 (mttt) cc_final: 0.7904 (mtpt) REVERT: B 375 LYS cc_start: 0.7929 (OUTLIER) cc_final: 0.7534 (mttt) REVERT: C 321 LYS cc_start: 0.7504 (ttmt) cc_final: 0.7302 (ttmt) REVERT: C 349 ARG cc_start: 0.8835 (mtt180) cc_final: 0.7451 (pmt-80) REVERT: C 375 LYS cc_start: 0.8599 (ttmt) cc_final: 0.8149 (mttt) REVERT: D 321 LYS cc_start: 0.7446 (ttmt) cc_final: 0.7138 (ttmt) REVERT: D 347 LYS cc_start: 0.8522 (mttt) cc_final: 0.8294 (mptt) REVERT: D 369 LYS cc_start: 0.8410 (mttt) cc_final: 0.7918 (mtpt) REVERT: D 375 LYS cc_start: 0.8507 (ttmt) cc_final: 0.8077 (mttt) REVERT: E 311 LYS cc_start: 0.7782 (mtmt) cc_final: 0.7193 (mmtt) REVERT: E 347 LYS cc_start: 0.8284 (mttt) cc_final: 0.7835 (mptt) REVERT: E 349 ARG cc_start: 0.8854 (mtt180) cc_final: 0.7822 (mmm160) REVERT: E 369 LYS cc_start: 0.8077 (mttt) cc_final: 0.7611 (mtpt) outliers start: 8 outliers final: 6 residues processed: 75 average time/residue: 0.2891 time to fit residues: 23.9301 Evaluate side-chains 59 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 52 time to evaluate : 0.341 ------------------------------------------------------------------------------- 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 8 optimal weight: 0.0060 chunk 31 optimal weight: 3.9990 chunk 34 optimal weight: 0.0470 chunk 28 optimal weight: 5.9990 chunk 10 optimal weight: 8.9990 chunk 25 optimal weight: 0.9980 chunk 23 optimal weight: 0.8980 chunk 16 optimal weight: 8.9990 chunk 3 optimal weight: 4.9990 chunk 15 optimal weight: 7.9990 chunk 21 optimal weight: 8.9990 overall best weight: 1.1896 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.3109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 2915 Z= 0.142 Angle : 0.492 4.286 3900 Z= 0.252 Chirality : 0.047 0.121 440 Planarity : 0.004 0.049 495 Dihedral : 4.644 16.896 385 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 2.12 % Allowed : 19.39 % Favored : 78.48 % 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: -3.36 (0.31), residues: 365 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.56 (0.24), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS A 330 PHE 0.003 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 59 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 52 time to evaluate : 0.413 Fit side-chains REVERT: A 347 LYS cc_start: 0.8105 (mttt) cc_final: 0.7737 (mptt) REVERT: A 375 LYS cc_start: 0.7919 (tttt) cc_final: 0.7469 (mttt) REVERT: B 311 LYS cc_start: 0.7899 (mtmt) cc_final: 0.7268 (mmtt) REVERT: B 347 LYS cc_start: 0.8121 (mttt) cc_final: 0.7910 (mptt) REVERT: B 349 ARG cc_start: 0.8887 (mtt180) cc_final: 0.7875 (mmp-170) REVERT: B 369 LYS cc_start: 0.8383 (mttt) cc_final: 0.7904 (mtpt) REVERT: B 375 LYS cc_start: 0.8077 (OUTLIER) cc_final: 0.7660 (mttt) REVERT: C 347 LYS cc_start: 0.8365 (mptt) cc_final: 0.8039 (mptt) REVERT: C 369 LYS cc_start: 0.8340 (mttt) cc_final: 0.7935 (mtpt) REVERT: C 375 LYS cc_start: 0.8602 (ttmt) cc_final: 0.8177 (mttt) REVERT: D 321 LYS cc_start: 0.7324 (ttmt) cc_final: 0.7029 (ttmt) REVERT: D 347 LYS cc_start: 0.8511 (mttt) cc_final: 0.8300 (mptt) REVERT: D 369 LYS cc_start: 0.8337 (mttt) cc_final: 0.7899 (mtpt) REVERT: D 375 LYS cc_start: 0.8483 (ttmt) cc_final: 0.8053 (mttt) REVERT: E 311 LYS cc_start: 0.7745 (mtmt) cc_final: 0.7160 (mmtt) REVERT: E 347 LYS cc_start: 0.8212 (mttt) cc_final: 0.7783 (mptt) REVERT: E 349 ARG cc_start: 0.8924 (mtt180) cc_final: 0.7862 (mmp-170) REVERT: E 369 LYS cc_start: 0.8062 (mttt) cc_final: 0.7627 (mtpt) REVERT: E 375 LYS cc_start: 0.8343 (tppt) cc_final: 0.7872 (mttt) outliers start: 7 outliers final: 6 residues processed: 52 average time/residue: 0.3027 time to fit residues: 17.4666 Evaluate side-chains 56 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 49 time to evaluate : 0.340 ------------------------------------------------------------------------------- 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 B residue 375 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 31 optimal weight: 6.9990 chunk 33 optimal weight: 4.9990 chunk 16 optimal weight: 10.0000 chunk 30 optimal weight: 7.9990 chunk 9 optimal weight: 10.0000 chunk 28 optimal weight: 1.9990 chunk 19 optimal weight: 7.9990 chunk 0 optimal weight: 1.9990 chunk 25 optimal weight: 7.9990 chunk 13 optimal weight: 2.9990 chunk 23 optimal weight: 9.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.3158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.028 2915 Z= 0.330 Angle : 0.598 6.956 3900 Z= 0.310 Chirality : 0.049 0.133 440 Planarity : 0.005 0.050 495 Dihedral : 5.097 19.105 385 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 2.12 % Allowed : 19.39 % Favored : 78.48 % 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: -3.09 (0.33), residues: 365 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.35 (0.25), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.003 HIS B 330 PHE 0.005 0.002 PHE D 346 TYR 0.019 0.005 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 68 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 61 time to evaluate : 0.319 Fit side-chains REVERT: A 347 LYS cc_start: 0.8165 (mttt) cc_final: 0.7712 (mptt) REVERT: A 375 LYS cc_start: 0.8097 (tttt) cc_final: 0.7657 (mttt) REVERT: B 311 LYS cc_start: 0.7842 (mtmt) cc_final: 0.7231 (mmtt) REVERT: B 347 LYS cc_start: 0.8235 (mttt) cc_final: 0.7796 (mptt) REVERT: B 349 ARG cc_start: 0.8824 (mtt180) cc_final: 0.7824 (mmm160) REVERT: B 369 LYS cc_start: 0.8457 (mttt) cc_final: 0.7935 (mtpt) REVERT: B 375 LYS cc_start: 0.8084 (ttmt) cc_final: 0.7670 (mttt) REVERT: C 347 LYS cc_start: 0.8382 (mptt) cc_final: 0.8005 (mptt) REVERT: C 349 ARG cc_start: 0.8913 (mtt180) cc_final: 0.7539 (pmt-80) REVERT: C 369 LYS cc_start: 0.8489 (mttt) cc_final: 0.8007 (mtpt) REVERT: C 375 LYS cc_start: 0.8579 (ttmt) cc_final: 0.8138 (mttt) REVERT: D 321 LYS cc_start: 0.7498 (ttmt) cc_final: 0.7225 (ttmt) REVERT: D 347 LYS cc_start: 0.8500 (mttt) cc_final: 0.8224 (mptt) REVERT: D 348 ASP cc_start: 0.6945 (t0) cc_final: 0.6395 (p0) REVERT: D 369 LYS cc_start: 0.8509 (mttt) cc_final: 0.7998 (mtpt) REVERT: D 375 LYS cc_start: 0.8517 (ttmt) cc_final: 0.8073 (mttt) REVERT: E 311 LYS cc_start: 0.7873 (mtmt) cc_final: 0.7231 (mmtt) REVERT: E 347 LYS cc_start: 0.8340 (mttt) cc_final: 0.7849 (mptt) REVERT: E 349 ARG cc_start: 0.8950 (mtt180) cc_final: 0.7886 (mmm160) REVERT: E 369 LYS cc_start: 0.8240 (mttt) cc_final: 0.7694 (mtpt) REVERT: E 375 LYS cc_start: 0.8274 (tppt) cc_final: 0.7802 (mttt) outliers start: 7 outliers final: 7 residues processed: 61 average time/residue: 0.3417 time to fit residues: 22.8741 Evaluate side-chains 64 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 57 time to evaluate : 0.358 ------------------------------------------------------------------------------- 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 0 optimal weight: 10.0000 chunk 17 optimal weight: 6.9990 chunk 30 optimal weight: 6.9990 chunk 8 optimal weight: 0.8980 chunk 11 optimal weight: 0.6980 chunk 6 optimal weight: 8.9990 chunk 19 optimal weight: 0.9990 chunk 33 optimal weight: 6.9990 chunk 28 optimal weight: 1.9990 chunk 15 optimal weight: 0.5980 chunk 2 optimal weight: 5.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.3624 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= 0.125 Angle : 0.480 6.921 3900 Z= 0.239 Chirality : 0.046 0.117 440 Planarity : 0.004 0.054 495 Dihedral : 4.194 15.131 385 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % Rotamer: Outliers : 2.42 % Allowed : 20.00 % Favored : 77.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.90 (0.35), residues: 365 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.20 (0.26), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS A 330 PHE 0.002 0.001 PHE C 346 TYR 0.012 0.002 TYR A 310 ARG 0.001 0.000 ARG C 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 63 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 55 time to evaluate : 0.336 Fit side-chains REVERT: A 347 LYS cc_start: 0.8064 (mttt) cc_final: 0.7660 (mptt) REVERT: A 348 ASP cc_start: 0.8932 (OUTLIER) cc_final: 0.8669 (t70) REVERT: A 375 LYS cc_start: 0.7990 (tttt) cc_final: 0.7554 (mttt) REVERT: B 311 LYS cc_start: 0.7881 (mtmt) cc_final: 0.7264 (mmtt) REVERT: B 347 LYS cc_start: 0.8047 (mttt) cc_final: 0.7687 (mptt) REVERT: B 348 ASP cc_start: 0.8954 (OUTLIER) cc_final: 0.8638 (t70) REVERT: B 349 ARG cc_start: 0.8876 (mtt180) cc_final: 0.7838 (mmm160) REVERT: B 369 LYS cc_start: 0.8438 (mttt) cc_final: 0.7928 (mtpt) REVERT: B 375 LYS cc_start: 0.8092 (ttmt) cc_final: 0.7657 (mttt) REVERT: B 379 ARG cc_start: 0.7687 (tmt-80) cc_final: 0.7353 (ttp80) REVERT: C 322 CYS cc_start: 0.8633 (t) cc_final: 0.8381 (t) REVERT: C 347 LYS cc_start: 0.8348 (mptt) cc_final: 0.7968 (mptt) REVERT: C 369 LYS cc_start: 0.8426 (mttt) cc_final: 0.7969 (mtpt) REVERT: C 375 LYS cc_start: 0.8548 (ttmt) cc_final: 0.8113 (mttt) REVERT: D 347 LYS cc_start: 0.8481 (mttt) cc_final: 0.8241 (mptt) REVERT: D 348 ASP cc_start: 0.7038 (t0) cc_final: 0.6522 (p0) REVERT: D 369 LYS cc_start: 0.8353 (mttt) cc_final: 0.7883 (mtpt) REVERT: D 375 LYS cc_start: 0.8486 (ttmt) cc_final: 0.8057 (mttt) REVERT: E 311 LYS cc_start: 0.7824 (mtmt) cc_final: 0.7238 (mmtt) REVERT: E 347 LYS cc_start: 0.8214 (mttt) cc_final: 0.7755 (mptt) REVERT: E 349 ARG cc_start: 0.9014 (mtt180) cc_final: 0.7862 (mmm160) REVERT: E 369 LYS cc_start: 0.8210 (mttt) cc_final: 0.7677 (mtpt) REVERT: E 375 LYS cc_start: 0.8309 (tppt) cc_final: 0.7806 (mttt) outliers start: 8 outliers final: 6 residues processed: 55 average time/residue: 0.3096 time to fit residues: 18.8703 Evaluate side-chains 58 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 50 time to evaluate : 0.344 ------------------------------------------------------------------------------- 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 E residue 318 VAL 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: 4.9990 chunk 32 optimal weight: 10.0000 chunk 3 optimal weight: 4.9990 chunk 19 optimal weight: 6.9990 chunk 24 optimal weight: 2.9990 chunk 28 optimal weight: 0.0000 chunk 18 optimal weight: 4.9990 chunk 33 optimal weight: 6.9990 chunk 21 optimal weight: 10.0000 chunk 20 optimal weight: 3.9990 overall best weight: 3.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.3587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 2915 Z= 0.264 Angle : 0.540 5.075 3900 Z= 0.278 Chirality : 0.048 0.124 440 Planarity : 0.004 0.047 495 Dihedral : 4.534 16.713 385 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 3.33 % Allowed : 20.30 % Favored : 76.36 % 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: -2.72 (0.36), residues: 365 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.07 (0.27), 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 0.016 0.004 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 68 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 57 time to evaluate : 0.360 Fit side-chains REVERT: A 347 LYS cc_start: 0.8157 (mttt) cc_final: 0.7692 (mptt) REVERT: A 348 ASP cc_start: 0.9000 (OUTLIER) cc_final: 0.8733 (t70) REVERT: A 375 LYS cc_start: 0.8065 (tttt) cc_final: 0.7637 (mttt) REVERT: B 311 LYS cc_start: 0.7857 (mtmt) cc_final: 0.7223 (mmtt) REVERT: B 347 LYS cc_start: 0.8116 (mttt) cc_final: 0.7723 (mptt) REVERT: B 349 ARG cc_start: 0.8836 (mtt180) cc_final: 0.7853 (mmm160) REVERT: B 369 LYS cc_start: 0.8492 (mttt) cc_final: 0.7960 (mtpt) REVERT: B 375 LYS cc_start: 0.8100 (ttmt) cc_final: 0.7663 (mttt) REVERT: B 379 ARG cc_start: 0.7708 (tmt-80) cc_final: 0.7373 (ttp80) REVERT: C 322 CYS cc_start: 0.8627 (t) cc_final: 0.8339 (t) REVERT: C 347 LYS cc_start: 0.8343 (mptt) cc_final: 0.7898 (mptt) REVERT: C 369 LYS cc_start: 0.8537 (mttt) cc_final: 0.8039 (mtpt) REVERT: C 375 LYS cc_start: 0.8530 (ttmt) cc_final: 0.8076 (mttt) REVERT: D 347 LYS cc_start: 0.8461 (mttt) cc_final: 0.8223 (mptt) REVERT: D 348 ASP cc_start: 0.7115 (t0) cc_final: 0.6589 (p0) REVERT: D 369 LYS cc_start: 0.8517 (mttt) cc_final: 0.8015 (mtpt) REVERT: D 375 LYS cc_start: 0.8533 (ttmt) cc_final: 0.8086 (mttt) REVERT: E 311 LYS cc_start: 0.7838 (mtmt) cc_final: 0.7210 (mmtt) REVERT: E 347 LYS cc_start: 0.8343 (mttt) cc_final: 0.7878 (mptt) REVERT: E 349 ARG cc_start: 0.8949 (mtt180) cc_final: 0.7860 (mmm160) REVERT: E 369 LYS cc_start: 0.8305 (mttt) cc_final: 0.7869 (mtpt) REVERT: E 375 LYS cc_start: 0.8283 (tppt) cc_final: 0.7778 (mttt) outliers start: 11 outliers final: 10 residues processed: 59 average time/residue: 0.3041 time to fit residues: 19.8479 Evaluate side-chains 63 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 52 time to evaluate : 0.391 ------------------------------------------------------------------------------- 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 15 optimal weight: 8.9990 chunk 20 optimal weight: 9.9990 chunk 13 optimal weight: 3.9990 chunk 10 optimal weight: 8.9990 chunk 6 optimal weight: 7.9990 chunk 21 optimal weight: 9.9990 chunk 22 optimal weight: 10.0000 chunk 16 optimal weight: 8.9990 chunk 3 optimal weight: 2.9990 chunk 26 optimal weight: 0.7980 chunk 30 optimal weight: 9.9990 overall best weight: 4.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.3645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.037 2915 Z= 0.417 Angle : 0.655 6.896 3900 Z= 0.343 Chirality : 0.051 0.132 440 Planarity : 0.005 0.055 495 Dihedral : 5.125 18.951 385 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 3.64 % Allowed : 20.61 % Favored : 75.76 % 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: -2.75 (0.36), residues: 365 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.09 (0.27), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.003 HIS B 330 PHE 0.007 0.002 PHE D 346 TYR 0.016 0.005 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 72 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 60 time to evaluate : 0.353 Fit side-chains REVERT: A 347 LYS cc_start: 0.8179 (mttt) cc_final: 0.7684 (mptt) REVERT: A 348 ASP cc_start: 0.9030 (OUTLIER) cc_final: 0.8749 (t70) REVERT: A 375 LYS cc_start: 0.8065 (tttt) cc_final: 0.7633 (mttt) REVERT: B 311 LYS cc_start: 0.7807 (mtmt) cc_final: 0.7176 (mmtt) REVERT: B 347 LYS cc_start: 0.8192 (mttt) cc_final: 0.7771 (mptt) REVERT: B 348 ASP cc_start: 0.9044 (OUTLIER) cc_final: 0.8716 (t70) REVERT: B 349 ARG cc_start: 0.8871 (mtt180) cc_final: 0.7851 (mmm160) REVERT: B 369 LYS cc_start: 0.8638 (mttt) cc_final: 0.8090 (mtpt) REVERT: B 375 LYS cc_start: 0.8101 (ttmt) cc_final: 0.7653 (mttt) REVERT: B 379 ARG cc_start: 0.7710 (tmt-80) cc_final: 0.7363 (ttp80) REVERT: C 347 LYS cc_start: 0.8334 (mptt) cc_final: 0.7841 (mptt) REVERT: C 369 LYS cc_start: 0.8621 (mttt) cc_final: 0.8201 (mtpt) REVERT: D 347 LYS cc_start: 0.8450 (mttt) cc_final: 0.8222 (mptt) REVERT: D 369 LYS cc_start: 0.8653 (mttt) cc_final: 0.8121 (mtpt) REVERT: E 311 LYS cc_start: 0.7851 (mtmt) cc_final: 0.7180 (mmtt) REVERT: E 347 LYS cc_start: 0.8429 (mttt) cc_final: 0.7925 (mptt) REVERT: E 349 ARG cc_start: 0.8930 (mtt180) cc_final: 0.7904 (mmm160) REVERT: E 369 LYS cc_start: 0.8404 (mttt) cc_final: 0.7871 (mtpt) REVERT: E 375 LYS cc_start: 0.8203 (tppt) cc_final: 0.7714 (mttt) outliers start: 12 outliers final: 10 residues processed: 62 average time/residue: 0.3085 time to fit residues: 21.0512 Evaluate side-chains 69 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 57 time to evaluate : 0.352 ------------------------------------------------------------------------------- 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 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 32 optimal weight: 0.9980 chunk 29 optimal weight: 5.9990 chunk 31 optimal weight: 5.9990 chunk 18 optimal weight: 7.9990 chunk 13 optimal weight: 0.5980 chunk 24 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 28 optimal weight: 10.0000 chunk 20 optimal weight: 0.8980 chunk 33 optimal weight: 3.9990 chunk 15 optimal weight: 9.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.3845 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= 0.139 Angle : 0.529 8.635 3900 Z= 0.257 Chirality : 0.047 0.121 440 Planarity : 0.004 0.055 495 Dihedral : 4.327 15.363 385 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % 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: -2.46 (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 A 330 PHE 0.002 0.001 PHE A 346 TYR 0.012 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 68 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 57 time to evaluate : 0.339 Fit side-chains REVERT: A 347 LYS cc_start: 0.8085 (mttt) cc_final: 0.7619 (mptt) REVERT: A 348 ASP cc_start: 0.8927 (OUTLIER) cc_final: 0.8637 (t70) REVERT: A 375 LYS cc_start: 0.8009 (tttt) cc_final: 0.7598 (mttt) REVERT: B 311 LYS cc_start: 0.7889 (mtmt) cc_final: 0.7272 (mmtt) REVERT: B 347 LYS cc_start: 0.7999 (mttt) cc_final: 0.7612 (mptt) REVERT: B 348 ASP cc_start: 0.8975 (OUTLIER) cc_final: 0.8645 (t70) REVERT: B 349 ARG cc_start: 0.8860 (mtt180) cc_final: 0.7801 (mmm160) REVERT: B 369 LYS cc_start: 0.8613 (mttt) cc_final: 0.8102 (mtpt) REVERT: B 375 LYS cc_start: 0.8100 (ttmt) cc_final: 0.7638 (mttt) REVERT: B 379 ARG cc_start: 0.7681 (tmt-80) cc_final: 0.7345 (ttp80) REVERT: C 322 CYS cc_start: 0.8510 (t) cc_final: 0.8253 (t) REVERT: C 347 LYS cc_start: 0.8321 (mptt) cc_final: 0.7903 (mptt) REVERT: C 369 LYS cc_start: 0.8618 (mttt) cc_final: 0.8187 (mtpt) REVERT: C 375 LYS cc_start: 0.8565 (ttmt) cc_final: 0.8092 (mttt) REVERT: D 369 LYS cc_start: 0.8555 (mttt) cc_final: 0.8045 (mtpt) REVERT: D 375 LYS cc_start: 0.8522 (ttmt) cc_final: 0.8024 (mttt) REVERT: E 311 LYS cc_start: 0.7897 (mtmt) cc_final: 0.7264 (mmtt) REVERT: E 347 LYS cc_start: 0.8251 (mttt) cc_final: 0.7801 (mptt) REVERT: E 349 ARG cc_start: 0.8977 (mtt180) cc_final: 0.7866 (mmm160) REVERT: E 369 LYS cc_start: 0.8398 (mttt) cc_final: 0.7894 (mtpt) REVERT: E 375 LYS cc_start: 0.8233 (tppt) cc_final: 0.7729 (mttt) outliers start: 11 outliers final: 9 residues processed: 58 average time/residue: 0.3096 time to fit residues: 19.8577 Evaluate side-chains 64 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 53 time to evaluate : 0.325 ------------------------------------------------------------------------------- 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 311 LYS Chi-restraints excluded: chain C residue 318 VAL 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 23 optimal weight: 0.4980 chunk 34 optimal weight: 0.9990 chunk 32 optimal weight: 6.9990 chunk 27 optimal weight: 0.0980 chunk 2 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 17 optimal weight: 6.9990 chunk 22 optimal weight: 6.9990 chunk 29 optimal weight: 9.9990 chunk 8 optimal weight: 4.9990 chunk 25 optimal weight: 6.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.4010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.014 2915 Z= 0.139 Angle : 0.515 7.677 3900 Z= 0.249 Chirality : 0.047 0.117 440 Planarity : 0.004 0.057 495 Dihedral : 4.050 14.546 385 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 3.64 % Allowed : 20.91 % 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: -2.36 (0.39), residues: 365 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.79 (0.30), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS A 330 PHE 0.003 0.001 PHE D 346 TYR 0.014 0.003 TYR A 310 ARG 0.001 0.000 ARG D 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 67 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 55 time to evaluate : 0.366 Fit side-chains REVERT: A 347 LYS cc_start: 0.8031 (mttt) cc_final: 0.7598 (mptt) REVERT: A 348 ASP cc_start: 0.8929 (OUTLIER) cc_final: 0.8590 (t70) REVERT: A 375 LYS cc_start: 0.7966 (tttt) cc_final: 0.7594 (mttt) REVERT: B 311 LYS cc_start: 0.7903 (mtmt) cc_final: 0.7291 (mmtt) REVERT: B 347 LYS cc_start: 0.7967 (mttt) cc_final: 0.7651 (mptt) REVERT: B 348 ASP cc_start: 0.8937 (OUTLIER) cc_final: 0.8591 (t70) REVERT: B 349 ARG cc_start: 0.8847 (mtt180) cc_final: 0.7776 (mmm160) REVERT: B 369 LYS cc_start: 0.8637 (mttt) cc_final: 0.8117 (mtpt) REVERT: B 375 LYS cc_start: 0.8108 (ttmt) cc_final: 0.7653 (mttt) REVERT: B 379 ARG cc_start: 0.7697 (tmt-80) cc_final: 0.7353 (ttp80) REVERT: C 322 CYS cc_start: 0.8476 (t) cc_final: 0.8241 (t) REVERT: C 347 LYS cc_start: 0.8308 (mptt) cc_final: 0.7886 (mptt) REVERT: C 369 LYS cc_start: 0.8634 (mttt) cc_final: 0.8219 (mtpt) REVERT: C 375 LYS cc_start: 0.8578 (ttmt) cc_final: 0.8119 (mttt) REVERT: D 369 LYS cc_start: 0.8515 (mttt) cc_final: 0.8015 (mtpt) REVERT: D 375 LYS cc_start: 0.8515 (ttmt) cc_final: 0.8021 (mttt) REVERT: E 311 LYS cc_start: 0.7852 (mtmt) cc_final: 0.7218 (mmtt) REVERT: E 347 LYS cc_start: 0.8179 (mttt) cc_final: 0.7740 (mptt) REVERT: E 349 ARG cc_start: 0.8987 (mtt180) cc_final: 0.7893 (mmm160) REVERT: E 369 LYS cc_start: 0.8390 (mttt) cc_final: 0.7895 (mtpt) REVERT: E 375 LYS cc_start: 0.8240 (tppt) cc_final: 0.7714 (mttt) outliers start: 12 outliers final: 9 residues processed: 57 average time/residue: 0.3202 time to fit residues: 20.1222 Evaluate side-chains 65 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 54 time to evaluate : 0.336 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 4 optimal weight: 10.0000 chunk 7 optimal weight: 10.0000 chunk 27 optimal weight: 7.9990 chunk 11 optimal weight: 0.0970 chunk 28 optimal weight: 5.9990 chunk 3 optimal weight: 7.9990 chunk 5 optimal weight: 5.9990 chunk 24 optimal weight: 0.9990 chunk 1 optimal weight: 0.8980 chunk 20 optimal weight: 8.9990 chunk 31 optimal weight: 1.9990 overall best weight: 1.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.4111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 2915 Z= 0.184 Angle : 0.545 7.377 3900 Z= 0.265 Chirality : 0.047 0.119 440 Planarity : 0.004 0.054 495 Dihedral : 4.146 14.980 385 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % 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: -2.30 (0.39), residues: 365 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.74 (0.30), 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 0.003 TYR A 310 ARG 0.001 0.000 ARG D 349 ********************** 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 66 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 55 time to evaluate : 0.357 Fit side-chains REVERT: A 347 LYS cc_start: 0.8116 (mttt) cc_final: 0.7652 (mptt) REVERT: A 348 ASP cc_start: 0.8961 (OUTLIER) cc_final: 0.8611 (t70) REVERT: A 375 LYS cc_start: 0.7994 (tttt) cc_final: 0.7605 (mttt) REVERT: B 311 LYS cc_start: 0.7920 (mtmt) cc_final: 0.7302 (mmtt) REVERT: B 347 LYS cc_start: 0.8015 (mttt) cc_final: 0.7612 (mptt) REVERT: B 348 ASP cc_start: 0.8992 (OUTLIER) cc_final: 0.8646 (t70) REVERT: B 349 ARG cc_start: 0.8817 (mtt180) cc_final: 0.7767 (mmm160) REVERT: B 369 LYS cc_start: 0.8643 (mttt) cc_final: 0.8123 (mtpt) REVERT: B 375 LYS cc_start: 0.8119 (ttmt) cc_final: 0.7652 (mttt) REVERT: B 379 ARG cc_start: 0.7687 (tmt-80) cc_final: 0.7346 (ttp80) REVERT: C 322 CYS cc_start: 0.8515 (t) cc_final: 0.8278 (t) REVERT: C 369 LYS cc_start: 0.8654 (mttt) cc_final: 0.8241 (mtpt) REVERT: C 375 LYS cc_start: 0.8584 (ttmt) cc_final: 0.8108 (mttt) REVERT: D 369 LYS cc_start: 0.8549 (mttt) cc_final: 0.8050 (mtpt) REVERT: D 375 LYS cc_start: 0.8539 (ttmt) cc_final: 0.8041 (mttt) REVERT: E 311 LYS cc_start: 0.7838 (mtmt) cc_final: 0.7204 (mmtt) REVERT: E 347 LYS cc_start: 0.8268 (mttt) cc_final: 0.7828 (mptt) REVERT: E 349 ARG cc_start: 0.8965 (mtt180) cc_final: 0.7882 (mmm160) REVERT: E 369 LYS cc_start: 0.8410 (mttt) cc_final: 0.7907 (mtpt) REVERT: E 375 LYS cc_start: 0.8218 (tppt) cc_final: 0.7698 (mttt) outliers start: 11 outliers final: 9 residues processed: 57 average time/residue: 0.3007 time to fit residues: 18.9748 Evaluate side-chains 65 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 54 time to evaluate : 0.413 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 18 optimal weight: 2.9990 chunk 23 optimal weight: 0.1980 chunk 0 optimal weight: 10.0000 chunk 22 optimal weight: 10.0000 chunk 21 optimal weight: 2.9990 chunk 20 optimal weight: 10.0000 chunk 13 optimal weight: 6.9990 chunk 12 optimal weight: 6.9990 chunk 34 optimal weight: 4.9990 chunk 1 optimal weight: 0.0770 chunk 33 optimal weight: 7.9990 overall best weight: 2.2544 ------------------------------------------------------------------------------- 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 = 0.5045 r_free = 0.5045 target = 0.361009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 107)---------------| | r_work = 0.5386 r_free = 0.5386 target = 0.295746 restraints weight = 3843.622| |-----------------------------------------------------------------------------| r_work (start): 0.4462 rms_B_bonded: 1.05 r_work: 0.4390 rms_B_bonded: 1.09 restraints_weight: 0.5000 r_work: 0.4333 rms_B_bonded: 1.80 restraints_weight: 0.2500 r_work (final): 0.4333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.4137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 2915 Z= 0.205 Angle : 0.584 8.586 3900 Z= 0.278 Chirality : 0.048 0.121 440 Planarity : 0.004 0.054 495 Dihedral : 4.226 15.159 385 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 3.33 % Allowed : 21.82 % Favored : 74.85 % 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: -2.25 (0.39), residues: 365 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.71 (0.30), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS B 330 PHE 0.003 0.001 PHE E 346 TYR 0.013 0.003 TYR A 310 ARG 0.001 0.000 ARG D 379 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1266.59 seconds wall clock time: 23 minutes 54.61 seconds (1434.61 seconds total)