Starting phenix.real_space_refine on Wed Mar 5 20:10:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8otc_17174/03_2025/8otc_17174.cif Found real_map, /net/cci-nas-00/data/ceres_data/8otc_17174/03_2025/8otc_17174.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8otc_17174/03_2025/8otc_17174.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8otc_17174/03_2025/8otc_17174.map" model { file = "/net/cci-nas-00/data/ceres_data/8otc_17174/03_2025/8otc_17174.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8otc_17174/03_2025/8otc_17174.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 6 5.16 5 C 2160 2.51 5 N 636 2.21 5 O 642 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 36 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: 3444 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, F Time building chain proxies: 2.28, per 1000 atoms: 0.66 Number of scatterers: 3444 At special positions: 0 Unit cell: (125.248, 121.952, 38.728, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 6 16.00 O 642 8.00 N 636 7.00 C 2160 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.74 Conformation dependent library (CDL) restraints added in 387.8 milliseconds 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 792 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 14 sheets defined 0.0% alpha, 46.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.40 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'B' and resid 306 through 310 removed outlier: 6.179A pdb=" N VAL A 306 " --> pdb=" O GLN B 307 " (cutoff:3.500A) removed outlier: 7.775A pdb=" N VAL B 309 " --> pdb=" O VAL A 306 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N ILE A 308 " --> pdb=" O VAL B 309 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 313 through 314 removed outlier: 6.778A pdb=" N VAL A 313 " --> pdb=" O ASP E 314 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N VAL E 313 " --> pdb=" O ASP F 314 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 319 through 330 removed outlier: 6.767A pdb=" N SER A 324 " --> pdb=" O GLY B 323 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N LEU B 325 " --> pdb=" O SER A 324 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N GLY A 326 " --> pdb=" O LEU B 325 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ASN B 327 " --> pdb=" O GLY A 326 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N THR A 319 " --> pdb=" O SER E 320 " (cutoff:3.500A) removed outlier: 8.615A pdb=" N CYS E 322 " --> pdb=" O THR A 319 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N LYS A 321 " --> pdb=" O CYS E 322 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N SER E 324 " --> pdb=" O LYS A 321 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N GLY A 323 " --> pdb=" O SER E 324 " (cutoff:3.500A) removed outlier: 9.689A pdb=" N GLY E 326 " --> pdb=" O GLY A 323 " (cutoff:3.500A) removed outlier: 8.816A pdb=" N LEU A 325 " --> pdb=" O GLY E 326 " (cutoff:3.500A) removed outlier: 9.630A pdb=" N ILE E 328 " --> pdb=" O LEU A 325 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N ASN A 327 " --> pdb=" O ILE E 328 " (cutoff:3.500A) removed outlier: 8.152A pdb=" N HIS E 330 " --> pdb=" O ASN A 327 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N HIS A 329 " --> pdb=" O HIS E 330 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N THR E 319 " --> pdb=" O SER F 320 " (cutoff:3.500A) removed outlier: 8.616A pdb=" N CYS F 322 " --> pdb=" O THR E 319 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N LYS E 321 " --> pdb=" O CYS F 322 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N SER F 324 " --> pdb=" O LYS E 321 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N GLY E 323 " --> pdb=" O SER F 324 " (cutoff:3.500A) removed outlier: 9.689A pdb=" N GLY F 326 " --> pdb=" O GLY E 323 " (cutoff:3.500A) removed outlier: 8.816A pdb=" N LEU E 325 " --> pdb=" O GLY F 326 " (cutoff:3.500A) removed outlier: 9.630A pdb=" N ILE F 328 " --> pdb=" O LEU E 325 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N ASN E 327 " --> pdb=" O ILE F 328 " (cutoff:3.500A) removed outlier: 8.152A pdb=" N HIS F 330 " --> pdb=" O ASN E 327 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N HIS E 329 " --> pdb=" O HIS F 330 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 337 through 342 removed outlier: 6.407A pdb=" N GLU A 338 " --> pdb=" O VAL E 339 " (cutoff:3.500A) removed outlier: 8.185A pdb=" N SER E 341 " --> pdb=" O GLU A 338 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N LYS A 340 " --> pdb=" O SER E 341 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N GLU E 338 " --> pdb=" O VAL F 339 " (cutoff:3.500A) removed outlier: 8.185A pdb=" N SER F 341 " --> pdb=" O GLU E 338 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N LYS E 340 " --> pdb=" O SER F 341 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 353 through 357 removed outlier: 6.133A pdb=" N ILE A 354 " --> pdb=" O GLY B 355 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N LEU B 357 " --> pdb=" O ILE A 354 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N SER A 356 " --> pdb=" O LEU B 357 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 360 through 362 removed outlier: 5.952A pdb=" N THR A 361 " --> pdb=" O HIS B 362 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 370 through 378 removed outlier: 6.498A pdb=" N LYS A 370 " --> pdb=" O ILE B 371 " (cutoff:3.500A) removed outlier: 8.503A pdb=" N THR B 373 " --> pdb=" O LYS A 370 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N GLU A 372 " --> pdb=" O THR B 373 " (cutoff:3.500A) removed outlier: 8.183A pdb=" N LYS B 375 " --> pdb=" O GLU A 372 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N HIS A 374 " --> pdb=" O LYS B 375 " (cutoff:3.500A) removed outlier: 7.496A pdb=" N THR B 377 " --> pdb=" O HIS A 374 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N LEU A 376 " --> pdb=" O THR B 377 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 306 through 310 Processing sheet with id=AA9, first strand: chain 'C' and resid 313 through 314 removed outlier: 6.778A pdb=" N VAL C 313 " --> pdb=" O ASP D 314 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'C' and resid 319 through 330 removed outlier: 6.676A pdb=" N THR C 319 " --> pdb=" O SER D 320 " (cutoff:3.500A) removed outlier: 8.615A pdb=" N CYS D 322 " --> pdb=" O THR C 319 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N LYS C 321 " --> pdb=" O CYS D 322 " (cutoff:3.500A) removed outlier: 7.213A pdb=" N SER D 324 " --> pdb=" O LYS C 321 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N GLY C 323 " --> pdb=" O SER D 324 " (cutoff:3.500A) removed outlier: 9.690A pdb=" N GLY D 326 " --> pdb=" O GLY C 323 " (cutoff:3.500A) removed outlier: 8.816A pdb=" N LEU C 325 " --> pdb=" O GLY D 326 " (cutoff:3.500A) removed outlier: 9.630A pdb=" N ILE D 328 " --> pdb=" O LEU C 325 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N ASN C 327 " --> pdb=" O ILE D 328 " (cutoff:3.500A) removed outlier: 8.153A pdb=" N HIS D 330 " --> pdb=" O ASN C 327 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N HIS C 329 " --> pdb=" O HIS D 330 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'C' and resid 337 through 342 removed outlier: 6.407A pdb=" N GLU C 338 " --> pdb=" O VAL D 339 " (cutoff:3.500A) removed outlier: 8.185A pdb=" N SER D 341 " --> pdb=" O GLU C 338 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N LYS C 340 " --> pdb=" O SER D 341 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'C' and resid 353 through 357 Processing sheet with id=AB4, first strand: chain 'C' and resid 360 through 362 Processing sheet with id=AB5, first strand: chain 'C' and resid 370 through 378 67 hydrogen bonds defined for protein. 201 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: 0.62 Time building geometry restraints manager: 0.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 818 1.34 - 1.46: 885 1.46 - 1.58: 1789 1.58 - 1.70: 0 1.70 - 1.82: 6 Bond restraints: 3498 Sorted by residual: bond pdb=" C ARG D 379 " pdb=" O ARG D 379 " ideal model delta sigma weight residual 1.231 1.296 -0.065 2.00e-02 2.50e+03 1.07e+01 bond pdb=" C ARG F 379 " pdb=" O ARG F 379 " ideal model delta sigma weight residual 1.231 1.296 -0.065 2.00e-02 2.50e+03 1.07e+01 bond pdb=" C ARG E 379 " pdb=" O ARG E 379 " ideal model delta sigma weight residual 1.231 1.296 -0.065 2.00e-02 2.50e+03 1.07e+01 bond pdb=" C ARG C 379 " pdb=" O ARG C 379 " ideal model delta sigma weight residual 1.231 1.296 -0.065 2.00e-02 2.50e+03 1.07e+01 bond pdb=" C ARG A 379 " pdb=" O ARG A 379 " ideal model delta sigma weight residual 1.231 1.296 -0.065 2.00e-02 2.50e+03 1.06e+01 ... (remaining 3493 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.43: 3653 1.43 - 2.87: 833 2.87 - 4.30: 134 4.30 - 5.73: 48 5.73 - 7.16: 12 Bond angle restraints: 4680 Sorted by residual: angle pdb=" CA ASP E 348 " pdb=" CB ASP E 348 " pdb=" CG ASP E 348 " ideal model delta sigma weight residual 112.60 117.35 -4.75 1.00e+00 1.00e+00 2.26e+01 angle pdb=" CA ASP C 348 " pdb=" CB ASP C 348 " pdb=" CG ASP C 348 " ideal model delta sigma weight residual 112.60 117.35 -4.75 1.00e+00 1.00e+00 2.25e+01 angle pdb=" CA ASP B 348 " pdb=" CB ASP B 348 " pdb=" CG ASP B 348 " ideal model delta sigma weight residual 112.60 117.33 -4.73 1.00e+00 1.00e+00 2.24e+01 angle pdb=" CA ASP D 348 " pdb=" CB ASP D 348 " pdb=" CG ASP D 348 " ideal model delta sigma weight residual 112.60 117.33 -4.73 1.00e+00 1.00e+00 2.23e+01 angle pdb=" CA ASP A 348 " pdb=" CB ASP A 348 " pdb=" CG ASP A 348 " ideal model delta sigma weight residual 112.60 117.32 -4.72 1.00e+00 1.00e+00 2.23e+01 ... (remaining 4675 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.25: 1824 13.25 - 26.50: 240 26.50 - 39.75: 66 39.75 - 53.00: 0 53.00 - 66.26: 6 Dihedral angle restraints: 2136 sinusoidal: 894 harmonic: 1242 Sorted by residual: dihedral pdb=" CA GLY B 365 " pdb=" C GLY B 365 " pdb=" N GLY B 366 " pdb=" CA GLY B 366 " ideal model delta harmonic sigma weight residual 180.00 157.97 22.03 0 5.00e+00 4.00e-02 1.94e+01 dihedral pdb=" CA GLY E 365 " pdb=" C GLY E 365 " pdb=" N GLY E 366 " pdb=" CA GLY E 366 " ideal model delta harmonic sigma weight residual 180.00 157.99 22.01 0 5.00e+00 4.00e-02 1.94e+01 dihedral pdb=" CA GLY F 365 " pdb=" C GLY F 365 " pdb=" N GLY F 366 " pdb=" CA GLY F 366 " ideal model delta harmonic sigma weight residual 180.00 157.99 22.01 0 5.00e+00 4.00e-02 1.94e+01 ... (remaining 2133 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 177 0.040 - 0.079: 136 0.079 - 0.118: 144 0.118 - 0.158: 59 0.158 - 0.197: 12 Chirality restraints: 528 Sorted by residual: chirality pdb=" CB ILE B 328 " pdb=" CA ILE B 328 " pdb=" CG1 ILE B 328 " pdb=" CG2 ILE B 328 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.20 2.00e-01 2.50e+01 9.70e-01 chirality pdb=" CB ILE A 328 " pdb=" CA ILE A 328 " pdb=" CG1 ILE A 328 " pdb=" CG2 ILE A 328 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.20 2.00e-01 2.50e+01 9.60e-01 chirality pdb=" CB ILE D 328 " pdb=" CA ILE D 328 " pdb=" CG1 ILE D 328 " pdb=" CG2 ILE D 328 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.20 2.00e-01 2.50e+01 9.59e-01 ... (remaining 525 not shown) Planarity restraints: 594 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL D 363 " 0.010 2.00e-02 2.50e+03 1.99e-02 3.94e+00 pdb=" C VAL D 363 " -0.034 2.00e-02 2.50e+03 pdb=" O VAL D 363 " 0.013 2.00e-02 2.50e+03 pdb=" N PRO D 364 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL F 363 " -0.010 2.00e-02 2.50e+03 1.98e-02 3.90e+00 pdb=" C VAL F 363 " 0.034 2.00e-02 2.50e+03 pdb=" O VAL F 363 " -0.013 2.00e-02 2.50e+03 pdb=" N PRO F 364 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL C 363 " 0.010 2.00e-02 2.50e+03 1.97e-02 3.89e+00 pdb=" C VAL C 363 " -0.034 2.00e-02 2.50e+03 pdb=" O VAL C 363 " 0.013 2.00e-02 2.50e+03 pdb=" N PRO C 364 " 0.011 2.00e-02 2.50e+03 ... (remaining 591 not shown) Histogram of nonbonded interaction distances: 2.54 - 3.01: 1677 3.01 - 3.48: 3262 3.48 - 3.95: 5432 3.95 - 4.43: 5280 4.43 - 4.90: 10635 Nonbonded interactions: 26286 Sorted by model distance: nonbonded pdb=" OG SER F 316 " pdb=" NZ LYS F 370 " model vdw 2.536 3.120 nonbonded pdb=" OG SER C 316 " pdb=" NZ LYS C 370 " model vdw 2.536 3.120 nonbonded pdb=" OG SER D 316 " pdb=" NZ LYS D 370 " model vdw 2.536 3.120 nonbonded pdb=" OG SER E 316 " pdb=" NZ LYS E 370 " model vdw 2.536 3.120 nonbonded pdb=" OG SER A 316 " pdb=" NZ LYS A 370 " model vdw 2.537 3.120 ... (remaining 26281 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' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.950 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 12.300 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:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 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 0.065 3498 Z= 0.572 Angle : 1.336 7.165 4680 Z= 0.870 Chirality : 0.080 0.197 528 Planarity : 0.007 0.033 594 Dihedral : 12.550 66.255 1344 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 1.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 1.52 % Allowed : 7.58 % Favored : 90.91 % 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: -3.28 (0.28), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.49 (0.21), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.003 HIS F 330 PHE 0.014 0.004 PHE F 346 TYR 0.018 0.008 TYR F 310 ARG 0.001 0.000 ARG E 379 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 49 time to evaluate : 0.438 Fit side-chains REVERT: A 369 LYS cc_start: 0.7605 (mttt) cc_final: 0.7328 (mtpt) REVERT: B 348 ASP cc_start: 0.7680 (t0) cc_final: 0.7401 (t0) REVERT: B 349 ARG cc_start: 0.8277 (mtt180) cc_final: 0.7693 (mmm160) REVERT: B 369 LYS cc_start: 0.7590 (mttt) cc_final: 0.7272 (mtpt) REVERT: C 348 ASP cc_start: 0.7847 (t0) cc_final: 0.7568 (t0) REVERT: C 349 ARG cc_start: 0.8384 (mtt180) cc_final: 0.7675 (mmm160) REVERT: C 369 LYS cc_start: 0.7829 (mttt) cc_final: 0.7470 (mtpt) REVERT: D 369 LYS cc_start: 0.7939 (mttt) cc_final: 0.7633 (mtpt) REVERT: E 349 ARG cc_start: 0.8502 (mtt180) cc_final: 0.8239 (mtp180) REVERT: E 369 LYS cc_start: 0.7754 (mttt) cc_final: 0.7428 (mtmt) REVERT: F 369 LYS cc_start: 0.7928 (mttt) cc_final: 0.7682 (mtpt) outliers start: 6 outliers final: 2 residues processed: 55 average time/residue: 0.3435 time to fit residues: 21.0852 Evaluate side-chains 50 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 48 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain C residue 325 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 6.9990 chunk 31 optimal weight: 8.9990 chunk 17 optimal weight: 0.7980 chunk 10 optimal weight: 7.9990 chunk 21 optimal weight: 0.0050 chunk 32 optimal weight: 2.9990 chunk 12 optimal weight: 4.9990 chunk 20 optimal weight: 10.0000 chunk 24 optimal weight: 0.7980 chunk 38 optimal weight: 4.9990 chunk 11 optimal weight: 5.9990 overall best weight: 1.9198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 330 HIS D 362 HIS ** F 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4405 r_free = 0.4405 target = 0.184445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.148405 restraints weight = 3803.313| |-----------------------------------------------------------------------------| r_work (start): 0.4020 rms_B_bonded: 2.30 r_work: 0.3928 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3834 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.2119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3498 Z= 0.231 Angle : 0.533 5.119 4680 Z= 0.284 Chirality : 0.049 0.132 528 Planarity : 0.004 0.032 594 Dihedral : 5.557 35.438 466 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 0.51 % Allowed : 10.61 % Favored : 88.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.61 (0.31), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.98 (0.24), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS B 330 PHE 0.006 0.001 PHE C 378 TYR 0.012 0.003 TYR A 310 ARG 0.001 0.000 ARG F 349 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 54 time to evaluate : 0.399 Fit side-chains REVERT: A 369 LYS cc_start: 0.7661 (mttt) cc_final: 0.7158 (mtmt) REVERT: B 349 ARG cc_start: 0.8038 (mtt180) cc_final: 0.7377 (mmm160) REVERT: B 369 LYS cc_start: 0.7645 (mttt) cc_final: 0.7195 (mtpt) REVERT: C 325 LEU cc_start: 0.7821 (OUTLIER) cc_final: 0.7590 (tt) REVERT: C 348 ASP cc_start: 0.7439 (t0) cc_final: 0.7219 (t0) REVERT: C 349 ARG cc_start: 0.8157 (mtt180) cc_final: 0.7335 (mmm160) REVERT: C 369 LYS cc_start: 0.7725 (mttt) cc_final: 0.7218 (mtpt) REVERT: D 369 LYS cc_start: 0.7990 (mttt) cc_final: 0.7492 (mtmt) REVERT: E 369 LYS cc_start: 0.7665 (mttt) cc_final: 0.7241 (mtmt) REVERT: F 369 LYS cc_start: 0.8122 (mttt) cc_final: 0.7677 (mtpt) outliers start: 2 outliers final: 1 residues processed: 56 average time/residue: 0.2878 time to fit residues: 18.4134 Evaluate side-chains 43 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 41 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain C residue 325 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 19 optimal weight: 1.9990 chunk 34 optimal weight: 7.9990 chunk 7 optimal weight: 5.9990 chunk 24 optimal weight: 9.9990 chunk 22 optimal weight: 9.9990 chunk 27 optimal weight: 7.9990 chunk 0 optimal weight: 6.9990 chunk 1 optimal weight: 10.0000 chunk 3 optimal weight: 9.9990 chunk 16 optimal weight: 7.9990 chunk 25 optimal weight: 0.2980 overall best weight: 4.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4334 r_free = 0.4334 target = 0.177998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.141923 restraints weight = 3841.415| |-----------------------------------------------------------------------------| r_work (start): 0.3944 rms_B_bonded: 2.31 r_work: 0.3856 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3765 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.2892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.047 3498 Z= 0.476 Angle : 0.643 5.036 4680 Z= 0.342 Chirality : 0.053 0.148 528 Planarity : 0.005 0.039 594 Dihedral : 5.814 31.581 466 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 1.77 % Allowed : 15.66 % Favored : 82.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.27 (0.33), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.72 (0.25), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS C 330 PHE 0.013 0.002 PHE C 378 TYR 0.012 0.004 TYR E 310 ARG 0.005 0.001 ARG B 349 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 52 time to evaluate : 0.376 Fit side-chains REVERT: A 369 LYS cc_start: 0.7895 (mttt) cc_final: 0.7388 (mtmt) REVERT: B 349 ARG cc_start: 0.8010 (mtt180) cc_final: 0.7418 (mmm160) REVERT: B 369 LYS cc_start: 0.7782 (mttt) cc_final: 0.7328 (mtpt) REVERT: C 349 ARG cc_start: 0.8168 (mtt180) cc_final: 0.7383 (mmm160) REVERT: C 369 LYS cc_start: 0.7885 (mttt) cc_final: 0.7429 (mtpt) REVERT: D 369 LYS cc_start: 0.8104 (mttt) cc_final: 0.7627 (mtmt) REVERT: E 369 LYS cc_start: 0.7713 (mttt) cc_final: 0.7301 (mtmt) REVERT: F 369 LYS cc_start: 0.8100 (mttt) cc_final: 0.7674 (mtpt) outliers start: 7 outliers final: 5 residues processed: 58 average time/residue: 0.3503 time to fit residues: 22.4506 Evaluate side-chains 53 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 48 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain C residue 324 SER Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain E residue 324 SER Chi-restraints excluded: chain F residue 324 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 26 optimal weight: 7.9990 chunk 13 optimal weight: 1.9990 chunk 7 optimal weight: 7.9990 chunk 33 optimal weight: 0.6980 chunk 29 optimal weight: 7.9990 chunk 22 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 18 optimal weight: 0.7980 chunk 21 optimal weight: 10.0000 chunk 14 optimal weight: 0.7980 chunk 11 optimal weight: 3.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 336 GLN ** F 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4370 r_free = 0.4370 target = 0.179570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.146389 restraints weight = 4032.137| |-----------------------------------------------------------------------------| r_work (start): 0.4031 rms_B_bonded: 2.14 r_work: 0.3938 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3849 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.3352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 3498 Z= 0.173 Angle : 0.512 3.937 4680 Z= 0.273 Chirality : 0.049 0.136 528 Planarity : 0.003 0.029 594 Dihedral : 4.728 14.834 462 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.52 % Allowed : 17.68 % Favored : 80.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.91 (0.35), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.45 (0.26), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS E 330 PHE 0.005 0.001 PHE C 378 TYR 0.021 0.003 TYR A 310 ARG 0.002 0.000 ARG C 349 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 51 time to evaluate : 0.395 Fit side-chains REVERT: A 369 LYS cc_start: 0.7857 (mttt) cc_final: 0.7451 (mtpt) REVERT: B 349 ARG cc_start: 0.8167 (mtt180) cc_final: 0.7518 (mmm160) REVERT: B 369 LYS cc_start: 0.7875 (mttt) cc_final: 0.7466 (mtpt) REVERT: C 349 ARG cc_start: 0.8190 (mtt180) cc_final: 0.7418 (mmm160) REVERT: C 369 LYS cc_start: 0.7994 (mttt) cc_final: 0.7550 (mtpt) REVERT: D 369 LYS cc_start: 0.8135 (mttt) cc_final: 0.7654 (mtmt) REVERT: E 369 LYS cc_start: 0.7764 (mttt) cc_final: 0.7380 (mtmt) REVERT: F 369 LYS cc_start: 0.8153 (mttt) cc_final: 0.7756 (mtpt) outliers start: 6 outliers final: 6 residues processed: 57 average time/residue: 0.3989 time to fit residues: 25.0555 Evaluate side-chains 55 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 49 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain C residue 324 SER Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain E residue 324 SER Chi-restraints excluded: chain F residue 324 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 41 optimal weight: 10.0000 chunk 24 optimal weight: 7.9990 chunk 7 optimal weight: 10.0000 chunk 15 optimal weight: 0.4980 chunk 30 optimal weight: 7.9990 chunk 25 optimal weight: 3.9990 chunk 6 optimal weight: 9.9990 chunk 22 optimal weight: 4.9990 chunk 3 optimal weight: 7.9990 chunk 32 optimal weight: 5.9990 chunk 1 optimal weight: 5.9990 overall best weight: 4.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 374 HIS ** E 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4288 r_free = 0.4288 target = 0.171437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.140914 restraints weight = 4053.739| |-----------------------------------------------------------------------------| r_work (start): 0.3982 rms_B_bonded: 2.07 r_work: 0.3884 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3797 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.4112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 3498 Z= 0.441 Angle : 0.641 4.296 4680 Z= 0.343 Chirality : 0.052 0.151 528 Planarity : 0.004 0.031 594 Dihedral : 5.402 13.887 462 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 1.52 % Allowed : 19.70 % Favored : 78.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.94 (0.34), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.47 (0.26), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS E 374 PHE 0.010 0.002 PHE C 378 TYR 0.022 0.004 TYR A 310 ARG 0.003 0.000 ARG C 349 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 57 time to evaluate : 0.423 Fit side-chains REVERT: A 369 LYS cc_start: 0.7943 (mttt) cc_final: 0.7553 (mtpt) REVERT: B 349 ARG cc_start: 0.8134 (mtt180) cc_final: 0.7543 (mmm160) REVERT: B 369 LYS cc_start: 0.7884 (mttt) cc_final: 0.7472 (mtpt) REVERT: C 349 ARG cc_start: 0.8221 (mtt180) cc_final: 0.7528 (mmm160) REVERT: C 369 LYS cc_start: 0.8050 (mttt) cc_final: 0.7600 (mtmt) REVERT: D 369 LYS cc_start: 0.8072 (mttt) cc_final: 0.7639 (mtmt) REVERT: E 369 LYS cc_start: 0.7813 (mttt) cc_final: 0.7409 (mtmt) REVERT: F 369 LYS cc_start: 0.8155 (mttt) cc_final: 0.7782 (mtpt) outliers start: 6 outliers final: 6 residues processed: 63 average time/residue: 0.3891 time to fit residues: 26.9312 Evaluate side-chains 61 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 55 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain C residue 324 SER Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain E residue 324 SER Chi-restraints excluded: chain F residue 324 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 25 optimal weight: 2.9990 chunk 24 optimal weight: 0.0470 chunk 6 optimal weight: 2.9990 chunk 21 optimal weight: 0.7980 chunk 7 optimal weight: 5.9990 chunk 27 optimal weight: 8.9990 chunk 2 optimal weight: 0.9990 chunk 15 optimal weight: 5.9990 chunk 40 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 chunk 16 optimal weight: 0.0370 overall best weight: 0.5760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4382 r_free = 0.4382 target = 0.177609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.148720 restraints weight = 4083.715| |-----------------------------------------------------------------------------| r_work (start): 0.4067 rms_B_bonded: 2.06 r_work: 0.3955 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3866 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.4335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 3498 Z= 0.130 Angle : 0.510 4.081 4680 Z= 0.275 Chirality : 0.049 0.137 528 Planarity : 0.003 0.029 594 Dihedral : 4.551 13.818 462 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 1.77 % Allowed : 20.71 % Favored : 77.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.66 (0.35), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.26 (0.27), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 330 PHE 0.002 0.001 PHE C 378 TYR 0.018 0.003 TYR E 310 ARG 0.001 0.000 ARG C 379 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 50 time to evaluate : 0.451 Fit side-chains REVERT: A 369 LYS cc_start: 0.7945 (mttt) cc_final: 0.7504 (mtpt) REVERT: B 349 ARG cc_start: 0.8123 (mtt180) cc_final: 0.7385 (mmm160) REVERT: B 369 LYS cc_start: 0.7893 (mttt) cc_final: 0.7477 (mtpt) REVERT: C 325 LEU cc_start: 0.7622 (OUTLIER) cc_final: 0.7395 (tt) REVERT: C 349 ARG cc_start: 0.8265 (mtt180) cc_final: 0.7532 (mmm160) REVERT: C 369 LYS cc_start: 0.7992 (mttt) cc_final: 0.7553 (mtmt) REVERT: D 369 LYS cc_start: 0.8035 (mttt) cc_final: 0.7634 (mtmt) REVERT: E 369 LYS cc_start: 0.7833 (mttt) cc_final: 0.7377 (mtpt) REVERT: F 331 LYS cc_start: 0.8795 (mtpp) cc_final: 0.8086 (tttt) REVERT: F 369 LYS cc_start: 0.8024 (mttt) cc_final: 0.7678 (mtpt) outliers start: 7 outliers final: 5 residues processed: 57 average time/residue: 0.3428 time to fit residues: 21.8477 Evaluate side-chains 53 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 47 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain F residue 324 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 36 optimal weight: 0.0070 chunk 15 optimal weight: 6.9990 chunk 26 optimal weight: 5.9990 chunk 16 optimal weight: 0.5980 chunk 2 optimal weight: 3.9990 chunk 9 optimal weight: 3.9990 chunk 20 optimal weight: 6.9990 chunk 3 optimal weight: 3.9990 chunk 37 optimal weight: 0.0970 chunk 24 optimal weight: 10.0000 chunk 39 optimal weight: 2.9990 overall best weight: 1.5400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4354 r_free = 0.4354 target = 0.175593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.144376 restraints weight = 4162.360| |-----------------------------------------------------------------------------| r_work (start): 0.4025 rms_B_bonded: 2.17 r_work: 0.3928 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3841 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.4434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 3498 Z= 0.187 Angle : 0.536 5.225 4680 Z= 0.284 Chirality : 0.049 0.139 528 Planarity : 0.003 0.028 594 Dihedral : 4.509 15.481 462 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 2.02 % Allowed : 21.46 % Favored : 76.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.63 (0.35), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.23 (0.27), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS E 330 PHE 0.004 0.001 PHE C 378 TYR 0.018 0.003 TYR A 310 ARG 0.001 0.000 ARG E 379 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 48 time to evaluate : 0.384 Fit side-chains REVERT: A 369 LYS cc_start: 0.7892 (mttt) cc_final: 0.7465 (mtpt) REVERT: B 349 ARG cc_start: 0.8230 (mtt180) cc_final: 0.7479 (mmm160) REVERT: B 369 LYS cc_start: 0.7918 (mttt) cc_final: 0.7489 (mtpt) REVERT: C 325 LEU cc_start: 0.7705 (OUTLIER) cc_final: 0.7453 (tt) REVERT: C 349 ARG cc_start: 0.8261 (mtt180) cc_final: 0.7433 (mmm160) REVERT: C 369 LYS cc_start: 0.8002 (mttt) cc_final: 0.7550 (mtpt) REVERT: D 369 LYS cc_start: 0.7987 (mttt) cc_final: 0.7580 (mtmt) REVERT: E 369 LYS cc_start: 0.7858 (mttt) cc_final: 0.7409 (mtpt) REVERT: F 331 LYS cc_start: 0.8841 (mtpp) cc_final: 0.8146 (tttp) REVERT: F 369 LYS cc_start: 0.8083 (mttt) cc_final: 0.7716 (mtpt) outliers start: 8 outliers final: 7 residues processed: 56 average time/residue: 0.4460 time to fit residues: 27.9951 Evaluate side-chains 55 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 47 time to evaluate : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain C residue 324 SER Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain E residue 324 SER Chi-restraints excluded: chain F residue 324 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 16 optimal weight: 2.9990 chunk 10 optimal weight: 5.9990 chunk 3 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 23 optimal weight: 0.6980 chunk 39 optimal weight: 4.9990 chunk 24 optimal weight: 0.0020 chunk 18 optimal weight: 0.9990 chunk 25 optimal weight: 0.6980 chunk 6 optimal weight: 9.9990 chunk 41 optimal weight: 10.0000 overall best weight: 1.0792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 362 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4387 r_free = 0.4387 target = 0.180447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.149256 restraints weight = 4148.503| |-----------------------------------------------------------------------------| r_work (start): 0.4066 rms_B_bonded: 2.16 r_work: 0.3975 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3885 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.4627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 3498 Z= 0.152 Angle : 0.515 4.869 4680 Z= 0.273 Chirality : 0.049 0.136 528 Planarity : 0.003 0.029 594 Dihedral : 4.306 14.155 462 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 2.27 % Allowed : 22.47 % Favored : 75.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.56 (0.35), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.18 (0.27), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS E 330 PHE 0.003 0.001 PHE C 378 TYR 0.016 0.003 TYR A 310 ARG 0.002 0.000 ARG C 349 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 48 time to evaluate : 0.420 Fit side-chains REVERT: A 369 LYS cc_start: 0.7854 (mttt) cc_final: 0.7401 (mtpt) REVERT: B 349 ARG cc_start: 0.8167 (mtt180) cc_final: 0.7399 (mmm160) REVERT: B 369 LYS cc_start: 0.7929 (mttt) cc_final: 0.7469 (mtpt) REVERT: C 325 LEU cc_start: 0.7703 (OUTLIER) cc_final: 0.7413 (tt) REVERT: C 349 ARG cc_start: 0.8301 (mtt180) cc_final: 0.7414 (mmm160) REVERT: C 369 LYS cc_start: 0.7955 (mttt) cc_final: 0.7493 (mtpt) REVERT: D 369 LYS cc_start: 0.7969 (mttt) cc_final: 0.7563 (mtmt) REVERT: E 369 LYS cc_start: 0.7857 (mttt) cc_final: 0.7390 (mtpt) REVERT: F 331 LYS cc_start: 0.8857 (mtpp) cc_final: 0.8130 (tttt) REVERT: F 369 LYS cc_start: 0.8053 (mttt) cc_final: 0.7695 (mtpt) outliers start: 9 outliers final: 7 residues processed: 57 average time/residue: 0.3170 time to fit residues: 20.1813 Evaluate side-chains 56 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 48 time to evaluate : 0.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain C residue 324 SER Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain E residue 324 SER Chi-restraints excluded: chain F residue 324 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 22 optimal weight: 9.9990 chunk 8 optimal weight: 9.9990 chunk 27 optimal weight: 0.7980 chunk 37 optimal weight: 6.9990 chunk 39 optimal weight: 0.9990 chunk 17 optimal weight: 7.9990 chunk 14 optimal weight: 10.0000 chunk 13 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 40 optimal weight: 0.3980 chunk 21 optimal weight: 5.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4377 r_free = 0.4377 target = 0.179707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.148438 restraints weight = 4097.101| |-----------------------------------------------------------------------------| r_work (start): 0.4060 rms_B_bonded: 2.16 r_work: 0.3969 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3883 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.4707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 3498 Z= 0.164 Angle : 0.521 5.232 4680 Z= 0.277 Chirality : 0.049 0.138 528 Planarity : 0.003 0.028 594 Dihedral : 4.261 13.083 462 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 2.02 % Allowed : 22.98 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.50 (0.35), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.13 (0.27), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS E 330 PHE 0.004 0.001 PHE E 346 TYR 0.015 0.002 TYR A 310 ARG 0.002 0.000 ARG E 379 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 51 time to evaluate : 0.390 Fit side-chains REVERT: A 369 LYS cc_start: 0.7867 (mttt) cc_final: 0.7432 (mtpt) REVERT: B 349 ARG cc_start: 0.8160 (mtt180) cc_final: 0.7359 (mmm160) REVERT: B 369 LYS cc_start: 0.7929 (mttt) cc_final: 0.7475 (mtpt) REVERT: C 325 LEU cc_start: 0.7691 (OUTLIER) cc_final: 0.7404 (tt) REVERT: C 349 ARG cc_start: 0.8274 (mtt180) cc_final: 0.7444 (mmm160) REVERT: C 369 LYS cc_start: 0.7933 (mttt) cc_final: 0.7478 (mtpt) REVERT: C 379 ARG cc_start: 0.6683 (tpt90) cc_final: 0.5938 (tmt170) REVERT: D 369 LYS cc_start: 0.7940 (mttt) cc_final: 0.7547 (mtmt) REVERT: E 369 LYS cc_start: 0.7858 (mttt) cc_final: 0.7417 (mtpt) REVERT: F 331 LYS cc_start: 0.8845 (mtpp) cc_final: 0.8142 (tttt) REVERT: F 369 LYS cc_start: 0.8074 (mttt) cc_final: 0.7670 (mtpt) outliers start: 8 outliers final: 6 residues processed: 59 average time/residue: 0.3199 time to fit residues: 21.0748 Evaluate side-chains 57 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 50 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain E residue 324 SER Chi-restraints excluded: chain F residue 324 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 24 optimal weight: 9.9990 chunk 8 optimal weight: 9.9990 chunk 32 optimal weight: 4.9990 chunk 23 optimal weight: 0.9990 chunk 16 optimal weight: 0.9980 chunk 27 optimal weight: 9.9990 chunk 18 optimal weight: 4.9990 chunk 38 optimal weight: 0.0060 chunk 15 optimal weight: 5.9990 chunk 1 optimal weight: 3.9990 chunk 19 optimal weight: 3.9990 overall best weight: 2.0002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4338 r_free = 0.4338 target = 0.173463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.142596 restraints weight = 4185.345| |-----------------------------------------------------------------------------| r_work (start): 0.4013 rms_B_bonded: 2.15 r_work: 0.3916 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3828 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.4757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3498 Z= 0.225 Angle : 0.561 5.421 4680 Z= 0.299 Chirality : 0.049 0.140 528 Planarity : 0.003 0.029 594 Dihedral : 4.533 13.094 462 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 2.02 % Allowed : 23.48 % Favored : 74.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.54 (0.35), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.17 (0.27), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS E 330 PHE 0.006 0.001 PHE F 346 TYR 0.017 0.003 TYR D 310 ARG 0.002 0.000 ARG E 379 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 46 time to evaluate : 0.384 Fit side-chains REVERT: A 369 LYS cc_start: 0.7965 (mttt) cc_final: 0.7541 (mtpt) REVERT: B 349 ARG cc_start: 0.8299 (mtt180) cc_final: 0.7442 (mmm160) REVERT: B 369 LYS cc_start: 0.7997 (mttt) cc_final: 0.7534 (mtpt) REVERT: C 325 LEU cc_start: 0.7757 (OUTLIER) cc_final: 0.7495 (tt) REVERT: C 349 ARG cc_start: 0.8265 (mtt180) cc_final: 0.7475 (mmm160) REVERT: C 369 LYS cc_start: 0.7991 (mttt) cc_final: 0.7546 (mtpt) REVERT: D 369 LYS cc_start: 0.7959 (mttt) cc_final: 0.7614 (mtmt) REVERT: E 369 LYS cc_start: 0.7839 (mttt) cc_final: 0.7406 (mtpt) REVERT: F 331 LYS cc_start: 0.8842 (mtpp) cc_final: 0.8127 (tttt) REVERT: F 369 LYS cc_start: 0.8103 (mttt) cc_final: 0.7711 (mtpt) outliers start: 8 outliers final: 7 residues processed: 54 average time/residue: 0.3428 time to fit residues: 20.6543 Evaluate side-chains 54 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 46 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain C residue 324 SER Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain E residue 324 SER Chi-restraints excluded: chain F residue 324 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 30 optimal weight: 10.0000 chunk 35 optimal weight: 7.9990 chunk 21 optimal weight: 8.9990 chunk 7 optimal weight: 1.9990 chunk 29 optimal weight: 10.0000 chunk 16 optimal weight: 7.9990 chunk 22 optimal weight: 6.9990 chunk 40 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 chunk 10 optimal weight: 7.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4315 r_free = 0.4315 target = 0.173253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.142628 restraints weight = 4234.571| |-----------------------------------------------------------------------------| r_work (start): 0.3994 rms_B_bonded: 2.18 r_work: 0.3900 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3811 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.4865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 3498 Z= 0.344 Angle : 0.619 5.291 4680 Z= 0.331 Chirality : 0.051 0.148 528 Planarity : 0.004 0.028 594 Dihedral : 5.060 13.871 462 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 2.02 % Allowed : 22.98 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.75 (0.34), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.33 (0.26), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS E 330 PHE 0.008 0.001 PHE F 346 TYR 0.019 0.003 TYR D 310 ARG 0.002 0.000 ARG E 379 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2464.52 seconds wall clock time: 43 minutes 16.71 seconds (2596.71 seconds total)