Starting phenix.real_space_refine on Fri Aug 22 13:43:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8otc_17174/08_2025/8otc_17174.cif Found real_map, /net/cci-nas-00/data/ceres_data/8otc_17174/08_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_17174/08_2025/8otc_17174.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8otc_17174/08_2025/8otc_17174.map" model { file = "/net/cci-nas-00/data/ceres_data/8otc_17174/08_2025/8otc_17174.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8otc_17174/08_2025/8otc_17174.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: B, C, D, E, F Time building chain proxies: 0.54, per 1000 atoms: 0.16 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: 0.15 Conformation dependent library (CDL) restraints added in 200.6 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 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: 0.15 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: 0.45 Time building geometry restraints manager: 0.23 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.760 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: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 4.380 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.000 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:0.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.180 ------------------------------------------------------------------------------- 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= 0.549 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.001 0.000 ARG E 379 TYR 0.018 0.008 TYR F 310 PHE 0.014 0.004 PHE F 346 HIS 0.009 0.003 HIS F 330 Details of bonding type rmsd covalent geometry : bond 0.00854 ( 3498) covalent geometry : angle 1.33614 ( 4680) hydrogen bonds : bond 0.14302 ( 67) hydrogen bonds : angle 8.19157 ( 201) *********************** 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 : 0.086 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: 0.7570 (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: 0.1312 time to fit residues: 7.9607 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 : 0.099 ------------------------------------------------------------------------------- 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 24 optimal weight: 6.9990 chunk 26 optimal weight: 1.9990 chunk 2 optimal weight: 0.8980 chunk 16 optimal weight: 8.9990 chunk 32 optimal weight: 4.9990 chunk 31 optimal weight: 3.9990 chunk 25 optimal weight: 4.9990 chunk 19 optimal weight: 2.9990 chunk 30 optimal weight: 6.9990 chunk 22 optimal weight: 7.9990 chunk 37 optimal weight: 0.7980 overall best weight: 2.1386 ------------------------------------------------------------------------------- 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 = 0.4396 r_free = 0.4396 target = 0.183791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.147477 restraints weight = 3886.815| |-----------------------------------------------------------------------------| r_work (start): 0.4006 rms_B_bonded: 2.35 r_work: 0.3913 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3818 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.2113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 3498 Z= 0.158 Angle : 0.545 5.206 4680 Z= 0.290 Chirality : 0.049 0.131 528 Planarity : 0.004 0.030 594 Dihedral : 5.599 35.086 466 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 0.25 % Allowed : 11.11 % Favored : 88.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.64 (0.31), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.00 (0.24), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG F 349 TYR 0.011 0.004 TYR A 310 PHE 0.007 0.001 PHE C 378 HIS 0.006 0.001 HIS B 330 Details of bonding type rmsd covalent geometry : bond 0.00365 ( 3498) covalent geometry : angle 0.54484 ( 4680) hydrogen bonds : bond 0.01452 ( 67) hydrogen bonds : angle 5.65792 ( 201) *********************** 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 55 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 54 time to evaluate : 0.141 Fit side-chains REVERT: A 369 LYS cc_start: 0.7703 (mttt) cc_final: 0.7211 (mtmt) REVERT: B 349 ARG cc_start: 0.8028 (mtt180) cc_final: 0.7388 (mmm160) REVERT: B 369 LYS cc_start: 0.7662 (mttt) cc_final: 0.7241 (mtpt) REVERT: C 325 LEU cc_start: 0.7835 (OUTLIER) cc_final: 0.7599 (tt) REVERT: C 348 ASP cc_start: 0.7441 (t0) cc_final: 0.7236 (t0) REVERT: C 349 ARG cc_start: 0.8167 (mtt180) cc_final: 0.7354 (mmm160) REVERT: C 369 LYS cc_start: 0.7760 (mttt) cc_final: 0.7264 (mtpt) REVERT: D 369 LYS cc_start: 0.8002 (mttt) cc_final: 0.7506 (mtmt) REVERT: E 369 LYS cc_start: 0.7657 (mttt) cc_final: 0.7242 (mtmt) REVERT: F 369 LYS cc_start: 0.8127 (mttt) cc_final: 0.7687 (mtpt) outliers start: 1 outliers final: 0 residues processed: 55 average time/residue: 0.1242 time to fit residues: 7.6700 Evaluate side-chains 43 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 42 time to evaluate : 0.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 0 optimal weight: 10.0000 chunk 26 optimal weight: 8.9990 chunk 8 optimal weight: 9.9990 chunk 9 optimal weight: 7.9990 chunk 31 optimal weight: 9.9990 chunk 34 optimal weight: 8.9990 chunk 2 optimal weight: 0.9980 chunk 32 optimal weight: 7.9990 chunk 20 optimal weight: 3.9990 chunk 14 optimal weight: 10.0000 chunk 11 optimal weight: 6.9990 overall best weight: 5.5988 ------------------------------------------------------------------------------- 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 = 0.4331 r_free = 0.4331 target = 0.177639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.141865 restraints weight = 3869.817| |-----------------------------------------------------------------------------| r_work (start): 0.3929 rms_B_bonded: 2.31 r_work: 0.3841 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3749 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.3259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.054 3498 Z= 0.359 Angle : 0.705 4.738 4680 Z= 0.378 Chirality : 0.055 0.152 528 Planarity : 0.006 0.036 594 Dihedral : 6.067 29.171 464 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 2.02 % Allowed : 15.91 % Favored : 82.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.22 (0.33), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.68 (0.26), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 349 TYR 0.013 0.004 TYR F 310 PHE 0.015 0.003 PHE C 378 HIS 0.007 0.002 HIS E 330 Details of bonding type rmsd covalent geometry : bond 0.00830 ( 3498) covalent geometry : angle 0.70532 ( 4680) hydrogen bonds : bond 0.02066 ( 67) hydrogen bonds : angle 6.02194 ( 201) *********************** 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 68 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 60 time to evaluate : 0.142 Fit side-chains REVERT: A 348 ASP cc_start: 0.7683 (t0) cc_final: 0.7454 (t0) REVERT: A 369 LYS cc_start: 0.7860 (mttt) cc_final: 0.7375 (mtmt) REVERT: A 378 PHE cc_start: 0.7300 (t80) cc_final: 0.7039 (t80) REVERT: B 369 LYS cc_start: 0.7765 (mttt) cc_final: 0.7322 (mtpt) REVERT: C 348 ASP cc_start: 0.7580 (t0) cc_final: 0.7366 (t0) REVERT: C 349 ARG cc_start: 0.8148 (mtt180) cc_final: 0.7327 (mmm160) REVERT: C 369 LYS cc_start: 0.7876 (mttt) cc_final: 0.7360 (mtmt) REVERT: D 369 LYS cc_start: 0.8168 (mttt) cc_final: 0.7670 (mtmt) REVERT: E 369 LYS cc_start: 0.7760 (mttt) cc_final: 0.7300 (mtmt) REVERT: F 369 LYS cc_start: 0.8057 (mttt) cc_final: 0.7663 (mtpt) outliers start: 8 outliers final: 6 residues processed: 67 average time/residue: 0.1585 time to fit residues: 11.6369 Evaluate side-chains 58 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 52 time to evaluate : 0.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 3 optimal weight: 2.9990 chunk 40 optimal weight: 5.9990 chunk 14 optimal weight: 7.9990 chunk 25 optimal weight: 2.9990 chunk 16 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 31 optimal weight: 4.9990 chunk 6 optimal weight: 1.9990 chunk 35 optimal weight: 5.9990 chunk 9 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- 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 = 0.4291 r_free = 0.4291 target = 0.170455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.139736 restraints weight = 4123.527| |-----------------------------------------------------------------------------| r_work (start): 0.3988 rms_B_bonded: 2.21 r_work: 0.3884 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3795 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.4024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 3498 Z= 0.213 Angle : 0.599 4.454 4680 Z= 0.318 Chirality : 0.051 0.145 528 Planarity : 0.004 0.030 594 Dihedral : 5.343 14.679 462 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.02 % Allowed : 19.95 % Favored : 78.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.11 (0.33), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.60 (0.25), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 379 TYR 0.019 0.004 TYR D 310 PHE 0.008 0.002 PHE B 378 HIS 0.005 0.001 HIS E 330 Details of bonding type rmsd covalent geometry : bond 0.00490 ( 3498) covalent geometry : angle 0.59940 ( 4680) hydrogen bonds : bond 0.01566 ( 67) hydrogen bonds : angle 5.50613 ( 201) *********************** 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 63 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 55 time to evaluate : 0.086 Fit side-chains REVERT: A 369 LYS cc_start: 0.7931 (mttt) cc_final: 0.7487 (mtpt) REVERT: B 349 ARG cc_start: 0.8137 (mtt180) cc_final: 0.7503 (mmm160) REVERT: B 369 LYS cc_start: 0.7922 (mttt) cc_final: 0.7473 (mtpt) REVERT: C 349 ARG cc_start: 0.8203 (mtt180) cc_final: 0.7419 (mmm160) REVERT: C 369 LYS cc_start: 0.8075 (mttt) cc_final: 0.7635 (mtpt) REVERT: D 369 LYS cc_start: 0.8122 (mttt) cc_final: 0.7662 (mtmt) REVERT: E 369 LYS cc_start: 0.7830 (mttt) cc_final: 0.7413 (mtmt) REVERT: F 369 LYS cc_start: 0.8122 (mttt) cc_final: 0.7716 (mtpt) outliers start: 8 outliers final: 7 residues processed: 62 average time/residue: 0.1417 time to fit residues: 9.6382 Evaluate side-chains 58 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 51 time to evaluate : 0.089 ------------------------------------------------------------------------------- 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 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 21 optimal weight: 0.4980 chunk 17 optimal weight: 6.9990 chunk 32 optimal weight: 5.9990 chunk 24 optimal weight: 2.9990 chunk 28 optimal weight: 9.9990 chunk 6 optimal weight: 2.9990 chunk 36 optimal weight: 10.0000 chunk 0 optimal weight: 7.9990 chunk 41 optimal weight: 7.9990 chunk 26 optimal weight: 0.5980 chunk 5 optimal weight: 3.9990 overall best weight: 2.2186 ------------------------------------------------------------------------------- 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 = 0.4324 r_free = 0.4324 target = 0.174088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.144063 restraints weight = 4088.057| |-----------------------------------------------------------------------------| r_work (start): 0.4015 rms_B_bonded: 2.10 r_work: 0.3916 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3829 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.4214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 3498 Z= 0.155 Angle : 0.555 4.209 4680 Z= 0.297 Chirality : 0.050 0.143 528 Planarity : 0.003 0.028 594 Dihedral : 4.944 14.984 462 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.02 % Allowed : 21.72 % Favored : 76.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.001 0.000 ARG C 349 TYR 0.020 0.004 TYR A 310 PHE 0.007 0.001 PHE C 378 HIS 0.004 0.001 HIS E 330 Details of bonding type rmsd covalent geometry : bond 0.00356 ( 3498) covalent geometry : angle 0.55537 ( 4680) hydrogen bonds : bond 0.01266 ( 67) hydrogen bonds : angle 5.19514 ( 201) *********************** 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 57 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 49 time to evaluate : 0.125 Fit side-chains REVERT: A 369 LYS cc_start: 0.7943 (mttt) cc_final: 0.7520 (mtpt) REVERT: B 349 ARG cc_start: 0.8088 (mtt180) cc_final: 0.7473 (mmm160) REVERT: B 369 LYS cc_start: 0.7953 (mttt) cc_final: 0.7524 (mtpt) REVERT: C 349 ARG cc_start: 0.8217 (mtt180) cc_final: 0.7486 (mmm160) REVERT: C 369 LYS cc_start: 0.8128 (mttt) cc_final: 0.7689 (mtpt) REVERT: D 369 LYS cc_start: 0.8031 (mttt) cc_final: 0.7615 (mtmt) REVERT: D 379 ARG cc_start: 0.5472 (ptp90) cc_final: 0.5030 (ptp90) REVERT: E 369 LYS cc_start: 0.7852 (mttt) cc_final: 0.7394 (mtpt) REVERT: F 331 LYS cc_start: 0.8869 (mtpp) cc_final: 0.8146 (tttp) REVERT: F 369 LYS cc_start: 0.8056 (mttt) cc_final: 0.7653 (mtpt) outliers start: 8 outliers final: 7 residues processed: 56 average time/residue: 0.1498 time to fit residues: 9.2859 Evaluate side-chains 55 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 48 time to evaluate : 0.149 ------------------------------------------------------------------------------- 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 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 33 optimal weight: 2.9990 chunk 14 optimal weight: 10.0000 chunk 24 optimal weight: 7.9990 chunk 2 optimal weight: 4.9990 chunk 6 optimal weight: 9.9990 chunk 13 optimal weight: 2.9990 chunk 9 optimal weight: 0.9990 chunk 10 optimal weight: 7.9990 chunk 7 optimal weight: 8.9990 chunk 31 optimal weight: 7.9990 chunk 15 optimal weight: 6.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 374 HIS C 374 HIS ** E 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 374 HIS ** F 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4286 r_free = 0.4286 target = 0.171109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.140902 restraints weight = 4079.559| |-----------------------------------------------------------------------------| r_work (start): 0.3981 rms_B_bonded: 2.15 r_work: 0.3875 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3788 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.4544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.038 3498 Z= 0.249 Angle : 0.628 4.615 4680 Z= 0.336 Chirality : 0.052 0.152 528 Planarity : 0.004 0.029 594 Dihedral : 5.408 13.925 462 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.78 % Allowed : 23.23 % Favored : 73.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.11 (0.33), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.60 (0.25), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 379 TYR 0.022 0.005 TYR A 310 PHE 0.009 0.002 PHE C 378 HIS 0.008 0.002 HIS E 330 Details of bonding type rmsd covalent geometry : bond 0.00574 ( 3498) covalent geometry : angle 0.62792 ( 4680) hydrogen bonds : bond 0.01472 ( 67) hydrogen bonds : angle 5.25461 ( 201) *********************** 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 62 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 51 time to evaluate : 0.103 Fit side-chains REVERT: A 349 ARG cc_start: 0.8229 (mtt180) cc_final: 0.7874 (mtt90) REVERT: A 369 LYS cc_start: 0.7911 (mttt) cc_final: 0.7476 (mtpt) REVERT: B 349 ARG cc_start: 0.8096 (mtt180) cc_final: 0.7386 (mmm160) REVERT: B 369 LYS cc_start: 0.7972 (mttt) cc_final: 0.7514 (mtpt) REVERT: C 349 ARG cc_start: 0.8221 (mtt180) cc_final: 0.7433 (mmm160) REVERT: C 369 LYS cc_start: 0.8062 (mttt) cc_final: 0.7611 (mtpt) REVERT: D 369 LYS cc_start: 0.8023 (mttt) cc_final: 0.7633 (mtmt) REVERT: E 369 LYS cc_start: 0.7854 (mttt) cc_final: 0.7397 (mtpt) REVERT: F 369 LYS cc_start: 0.8061 (mttt) cc_final: 0.7668 (mtpt) outliers start: 11 outliers final: 8 residues processed: 61 average time/residue: 0.1599 time to fit residues: 10.7089 Evaluate side-chains 58 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 50 time to evaluate : 0.099 ------------------------------------------------------------------------------- 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 D residue 324 SER Chi-restraints excluded: chain E residue 324 SER Chi-restraints excluded: chain F residue 324 SER Chi-restraints excluded: chain F residue 363 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 21 optimal weight: 3.9990 chunk 28 optimal weight: 10.0000 chunk 9 optimal weight: 6.9990 chunk 7 optimal weight: 0.9980 chunk 6 optimal weight: 10.0000 chunk 11 optimal weight: 6.9990 chunk 40 optimal weight: 0.7980 chunk 26 optimal weight: 0.6980 chunk 8 optimal weight: 6.9990 chunk 3 optimal weight: 4.9990 chunk 15 optimal weight: 2.9990 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 362 HIS E 374 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 = 0.4330 r_free = 0.4330 target = 0.174186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.144485 restraints weight = 4117.793| |-----------------------------------------------------------------------------| r_work (start): 0.4040 rms_B_bonded: 2.11 r_work: 0.3934 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3846 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.4695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3498 Z= 0.141 Angle : 0.561 4.425 4680 Z= 0.302 Chirality : 0.050 0.141 528 Planarity : 0.003 0.028 594 Dihedral : 4.889 14.233 462 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 2.27 % Allowed : 24.24 % Favored : 73.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.96 (0.33), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.49 (0.25), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 379 TYR 0.020 0.004 TYR E 310 PHE 0.004 0.001 PHE F 346 HIS 0.005 0.001 HIS E 330 Details of bonding type rmsd covalent geometry : bond 0.00322 ( 3498) covalent geometry : angle 0.56115 ( 4680) hydrogen bonds : bond 0.01220 ( 67) hydrogen bonds : angle 5.04990 ( 201) *********************** 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 58 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 49 time to evaluate : 0.100 Fit side-chains REVERT: A 369 LYS cc_start: 0.7981 (mttt) cc_final: 0.7540 (mtpt) REVERT: B 349 ARG cc_start: 0.8159 (mtt180) cc_final: 0.7387 (mmm160) REVERT: B 369 LYS cc_start: 0.7946 (mttt) cc_final: 0.7516 (mtpt) REVERT: C 349 ARG cc_start: 0.8301 (mtt180) cc_final: 0.7525 (mmm160) REVERT: C 369 LYS cc_start: 0.8078 (mttt) cc_final: 0.7613 (mtpt) REVERT: D 369 LYS cc_start: 0.7998 (mttt) cc_final: 0.7632 (mtmt) REVERT: E 369 LYS cc_start: 0.7853 (mttt) cc_final: 0.7392 (mtpt) REVERT: F 331 LYS cc_start: 0.8871 (mtpp) cc_final: 0.8155 (tttp) REVERT: F 369 LYS cc_start: 0.8038 (mttt) cc_final: 0.7656 (mtpt) outliers start: 9 outliers final: 9 residues processed: 58 average time/residue: 0.1565 time to fit residues: 9.9941 Evaluate side-chains 56 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 47 time to evaluate : 0.093 ------------------------------------------------------------------------------- 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 374 HIS Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain E residue 324 SER Chi-restraints excluded: chain F residue 324 SER Chi-restraints excluded: chain F residue 363 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 13 optimal weight: 2.9990 chunk 39 optimal weight: 4.9990 chunk 34 optimal weight: 10.0000 chunk 19 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 37 optimal weight: 9.9990 chunk 15 optimal weight: 5.9990 chunk 11 optimal weight: 4.9990 chunk 25 optimal weight: 2.9990 chunk 4 optimal weight: 0.9990 chunk 18 optimal weight: 4.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- 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 = 0.4316 r_free = 0.4316 target = 0.173315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.143492 restraints weight = 4133.622| |-----------------------------------------------------------------------------| r_work (start): 0.4023 rms_B_bonded: 2.12 r_work: 0.3918 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3828 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.4874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 3498 Z= 0.168 Angle : 0.583 4.851 4680 Z= 0.313 Chirality : 0.051 0.145 528 Planarity : 0.004 0.026 594 Dihedral : 4.959 17.111 462 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 2.53 % Allowed : 23.48 % Favored : 73.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.98 (0.33), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.50 (0.25), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 379 TYR 0.019 0.004 TYR A 310 PHE 0.006 0.001 PHE F 346 HIS 0.007 0.001 HIS E 330 Details of bonding type rmsd covalent geometry : bond 0.00385 ( 3498) covalent geometry : angle 0.58313 ( 4680) hydrogen bonds : bond 0.01166 ( 67) hydrogen bonds : angle 4.92561 ( 201) *********************** 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 62 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 52 time to evaluate : 0.146 Fit side-chains REVERT: A 369 LYS cc_start: 0.7978 (mttt) cc_final: 0.7543 (mtpt) REVERT: B 349 ARG cc_start: 0.8186 (mtt180) cc_final: 0.7402 (mmm160) REVERT: B 369 LYS cc_start: 0.7961 (mttt) cc_final: 0.7529 (mtpt) REVERT: C 349 ARG cc_start: 0.8298 (mtt180) cc_final: 0.7506 (mmm160) REVERT: C 369 LYS cc_start: 0.8106 (mttt) cc_final: 0.7628 (mtpt) REVERT: D 369 LYS cc_start: 0.8007 (mttt) cc_final: 0.7651 (mtmt) REVERT: E 369 LYS cc_start: 0.7852 (mttt) cc_final: 0.7408 (mtpt) REVERT: F 331 LYS cc_start: 0.8874 (mtpp) cc_final: 0.8158 (tttp) REVERT: F 369 LYS cc_start: 0.8087 (mttt) cc_final: 0.7691 (mtpt) outliers start: 10 outliers final: 9 residues processed: 62 average time/residue: 0.1514 time to fit residues: 10.3656 Evaluate side-chains 61 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 52 time to evaluate : 0.152 ------------------------------------------------------------------------------- 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 374 HIS Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain E residue 324 SER Chi-restraints excluded: chain F residue 324 SER Chi-restraints excluded: chain F residue 363 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 33 optimal weight: 3.9990 chunk 37 optimal weight: 10.0000 chunk 10 optimal weight: 7.9990 chunk 39 optimal weight: 3.9990 chunk 26 optimal weight: 0.8980 chunk 20 optimal weight: 10.0000 chunk 7 optimal weight: 0.6980 chunk 17 optimal weight: 0.5980 chunk 18 optimal weight: 0.9990 chunk 31 optimal weight: 8.9990 chunk 32 optimal weight: 2.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 374 HIS ** F 330 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 = 0.4381 r_free = 0.4381 target = 0.178477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.147473 restraints weight = 3925.820| |-----------------------------------------------------------------------------| r_work (start): 0.4036 rms_B_bonded: 2.19 r_work: 0.3926 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3830 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.5029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 3498 Z= 0.109 Angle : 0.551 5.036 4680 Z= 0.296 Chirality : 0.050 0.140 528 Planarity : 0.003 0.026 594 Dihedral : 4.613 15.916 462 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 2.27 % Allowed : 23.74 % Favored : 73.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.85 (0.33), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.40 (0.25), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG C 349 TYR 0.015 0.003 TYR A 310 PHE 0.003 0.001 PHE E 378 HIS 0.004 0.001 HIS E 330 Details of bonding type rmsd covalent geometry : bond 0.00249 ( 3498) covalent geometry : angle 0.55149 ( 4680) hydrogen bonds : bond 0.01000 ( 67) hydrogen bonds : angle 4.70273 ( 201) *********************** 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 58 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 49 time to evaluate : 0.118 Fit side-chains REVERT: A 369 LYS cc_start: 0.7930 (mttt) cc_final: 0.7494 (mtpt) REVERT: B 349 ARG cc_start: 0.8244 (mtt180) cc_final: 0.7351 (mmm160) REVERT: B 369 LYS cc_start: 0.7947 (mttt) cc_final: 0.7546 (mtpt) REVERT: C 349 ARG cc_start: 0.8300 (mtt180) cc_final: 0.7503 (mmm160) REVERT: C 369 LYS cc_start: 0.8111 (mttt) cc_final: 0.7620 (mtpt) REVERT: D 369 LYS cc_start: 0.8006 (mttt) cc_final: 0.7630 (mtmt) REVERT: E 369 LYS cc_start: 0.7817 (mttt) cc_final: 0.7356 (mtpt) REVERT: F 331 LYS cc_start: 0.8828 (mtpp) cc_final: 0.8102 (tttt) REVERT: F 369 LYS cc_start: 0.8080 (mttt) cc_final: 0.7700 (mtpt) outliers start: 9 outliers final: 9 residues processed: 58 average time/residue: 0.1569 time to fit residues: 10.0736 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 : 0.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain A residue 374 HIS 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 374 HIS 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 34 optimal weight: 9.9990 chunk 37 optimal weight: 7.9990 chunk 21 optimal weight: 6.9990 chunk 29 optimal weight: 10.0000 chunk 30 optimal weight: 0.9990 chunk 16 optimal weight: 3.9990 chunk 7 optimal weight: 0.0000 chunk 28 optimal weight: 9.9990 chunk 22 optimal weight: 7.9990 chunk 35 optimal weight: 5.9990 chunk 32 optimal weight: 0.0980 overall best weight: 2.2190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 374 HIS ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4333 r_free = 0.4333 target = 0.173800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.143272 restraints weight = 4241.287| |-----------------------------------------------------------------------------| r_work (start): 0.4010 rms_B_bonded: 2.17 r_work: 0.3914 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3828 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.5048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 3498 Z= 0.158 Angle : 0.602 7.960 4680 Z= 0.319 Chirality : 0.050 0.145 528 Planarity : 0.003 0.027 594 Dihedral : 4.751 15.251 462 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 2.27 % Allowed : 24.49 % Favored : 73.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.83 (0.33), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.38 (0.25), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 379 TYR 0.014 0.003 TYR A 310 PHE 0.006 0.001 PHE F 346 HIS 0.006 0.001 HIS E 330 Details of bonding type rmsd covalent geometry : bond 0.00367 ( 3498) covalent geometry : angle 0.60201 ( 4680) hydrogen bonds : bond 0.01187 ( 67) hydrogen bonds : angle 4.68663 ( 201) ********************** 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 56 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 47 time to evaluate : 0.126 Fit side-chains REVERT: A 369 LYS cc_start: 0.7963 (mttt) cc_final: 0.7537 (mtpt) REVERT: B 349 ARG cc_start: 0.8292 (mtt180) cc_final: 0.7387 (mmm160) REVERT: B 369 LYS cc_start: 0.7922 (mttt) cc_final: 0.7529 (mtpt) REVERT: C 349 ARG cc_start: 0.8278 (mtt180) cc_final: 0.7461 (mmm160) REVERT: C 369 LYS cc_start: 0.8064 (mttt) cc_final: 0.7562 (mtpt) REVERT: D 369 LYS cc_start: 0.8002 (mttt) cc_final: 0.7597 (mtmt) REVERT: E 369 LYS cc_start: 0.7906 (mttt) cc_final: 0.7447 (mtpt) REVERT: F 331 LYS cc_start: 0.8848 (mtpp) cc_final: 0.8133 (tttt) REVERT: F 369 LYS cc_start: 0.8095 (mttt) cc_final: 0.7703 (mtpt) outliers start: 9 outliers final: 9 residues processed: 56 average time/residue: 0.1558 time to fit residues: 9.5950 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 : 0.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain A residue 374 HIS 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 374 HIS 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 1 optimal weight: 10.0000 chunk 4 optimal weight: 4.9990 chunk 3 optimal weight: 6.9990 chunk 8 optimal weight: 1.9990 chunk 24 optimal weight: 0.0470 chunk 33 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 35 optimal weight: 0.0270 chunk 29 optimal weight: 4.9990 chunk 25 optimal weight: 3.9990 chunk 37 optimal weight: 0.5980 overall best weight: 0.9340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 374 HIS ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4357 r_free = 0.4357 target = 0.176219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.146311 restraints weight = 4214.832| |-----------------------------------------------------------------------------| r_work (start): 0.4054 rms_B_bonded: 2.12 r_work: 0.3959 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3872 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.5142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 3498 Z= 0.100 Angle : 0.568 8.109 4680 Z= 0.300 Chirality : 0.049 0.137 528 Planarity : 0.003 0.030 594 Dihedral : 4.525 15.540 462 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 2.27 % Allowed : 24.49 % Favored : 73.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.74 (0.34), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.32 (0.26), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 379 TYR 0.015 0.002 TYR A 310 PHE 0.003 0.001 PHE E 378 HIS 0.004 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00233 ( 3498) covalent geometry : angle 0.56766 ( 4680) hydrogen bonds : bond 0.01027 ( 67) hydrogen bonds : angle 4.62195 ( 201) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1158.01 seconds wall clock time: 20 minutes 41.08 seconds (1241.08 seconds total)