Starting phenix.real_space_refine on Fri May 9 19:00:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8otc_17174/05_2025/8otc_17174.cif Found real_map, /net/cci-nas-00/data/ceres_data/8otc_17174/05_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_17174/05_2025/8otc_17174.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8otc_17174/05_2025/8otc_17174.map" model { file = "/net/cci-nas-00/data/ceres_data/8otc_17174/05_2025/8otc_17174.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8otc_17174/05_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-5687/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: 2.68, per 1000 atoms: 0.78 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: 0.81 Conformation dependent library (CDL) restraints added in 409.4 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: 0.44 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: 0.73 Time building geometry restraints manager: 0.95 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: 0.03 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: 2.720 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: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 12.650 Find NCS groups from input model: 0.070 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:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.440 ------------------------------------------------------------------------------- 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 (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 Details of bonding type rmsd hydrogen bonds : bond 0.14302 ( 67) hydrogen bonds : angle 8.19157 ( 201) covalent geometry : bond 0.00854 ( 3498) covalent geometry : angle 1.33614 ( 4680) *********************** 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 : 0.381 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: 0.3319 time to fit residues: 20.3727 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 : 0.415 ------------------------------------------------------------------------------- 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 = 43)----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.148403 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: 0.3833 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3833 ------------------------------------------------------------------------------- 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= 0.145 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 Details of bonding type rmsd hydrogen bonds : bond 0.01392 ( 67) hydrogen bonds : angle 5.58672 ( 201) covalent geometry : bond 0.00340 ( 3498) covalent geometry : angle 0.53255 ( 4680) *********************** 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 : 0.402 Fit side-chains REVERT: A 369 LYS cc_start: 0.7664 (mttt) cc_final: 0.7162 (mtmt) REVERT: B 349 ARG cc_start: 0.8040 (mtt180) cc_final: 0.7373 (mmm160) REVERT: B 369 LYS cc_start: 0.7644 (mttt) cc_final: 0.7194 (mtpt) REVERT: C 325 LEU cc_start: 0.7824 (OUTLIER) cc_final: 0.7592 (tt) REVERT: C 348 ASP cc_start: 0.7443 (t0) cc_final: 0.7220 (t0) REVERT: C 349 ARG cc_start: 0.8158 (mtt180) cc_final: 0.7332 (mmm160) REVERT: C 369 LYS cc_start: 0.7727 (mttt) cc_final: 0.7220 (mtpt) REVERT: D 369 LYS cc_start: 0.7992 (mttt) cc_final: 0.7494 (mtmt) REVERT: E 369 LYS cc_start: 0.7664 (mttt) cc_final: 0.7240 (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: 0.2791 time to fit residues: 17.7766 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 : 0.399 ------------------------------------------------------------------------------- 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: 7.9990 chunk 1 optimal weight: 0.0270 chunk 3 optimal weight: 9.9990 chunk 16 optimal weight: 7.9990 chunk 25 optimal weight: 3.9990 overall best weight: 4.0046 ------------------------------------------------------------------------------- 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 = 0.4339 r_free = 0.4339 target = 0.178251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.142611 restraints weight = 3812.796| |-----------------------------------------------------------------------------| r_work (start): 0.3950 rms_B_bonded: 2.27 r_work: 0.3853 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3756 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.2917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 3498 Z= 0.259 Angle : 0.616 4.652 4680 Z= 0.328 Chirality : 0.052 0.147 528 Planarity : 0.005 0.033 594 Dihedral : 5.735 32.496 466 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 1.77 % Allowed : 15.15 % Favored : 83.08 % 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: -2.24 (0.33), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.70 (0.25), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS C 330 PHE 0.012 0.002 PHE C 378 TYR 0.011 0.003 TYR E 310 ARG 0.005 0.001 ARG A 349 Details of bonding type rmsd hydrogen bonds : bond 0.01688 ( 67) hydrogen bonds : angle 5.60920 ( 201) covalent geometry : bond 0.00589 ( 3498) covalent geometry : angle 0.61567 ( 4680) *********************** 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 57 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 50 time to evaluate : 0.383 Fit side-chains REVERT: A 369 LYS cc_start: 0.7885 (mttt) cc_final: 0.7412 (mtmt) REVERT: B 349 ARG cc_start: 0.8016 (mtt180) cc_final: 0.7466 (mmm160) REVERT: B 369 LYS cc_start: 0.7796 (mttt) cc_final: 0.7355 (mtpt) REVERT: C 349 ARG cc_start: 0.8186 (mtt180) cc_final: 0.7415 (mmm160) REVERT: C 369 LYS cc_start: 0.7899 (mttt) cc_final: 0.7454 (mtpt) REVERT: D 369 LYS cc_start: 0.8083 (mttt) cc_final: 0.7622 (mtmt) REVERT: E 369 LYS cc_start: 0.7713 (mttt) cc_final: 0.7320 (mtmt) REVERT: F 369 LYS cc_start: 0.8110 (mttt) cc_final: 0.7686 (mtpt) outliers start: 7 outliers final: 6 residues processed: 56 average time/residue: 0.3232 time to fit residues: 20.3091 Evaluate side-chains 51 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 45 time to evaluate : 0.379 ------------------------------------------------------------------------------- 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 26 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 chunk 7 optimal weight: 7.9990 chunk 33 optimal weight: 0.9990 chunk 29 optimal weight: 5.9990 chunk 22 optimal weight: 0.0050 chunk 25 optimal weight: 2.9990 chunk 18 optimal weight: 0.8980 chunk 21 optimal weight: 1.9990 chunk 14 optimal weight: 0.8980 chunk 11 optimal weight: 3.9990 overall best weight: 0.7598 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4396 r_free = 0.4396 target = 0.182026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.148735 restraints weight = 4029.165| |-----------------------------------------------------------------------------| r_work (start): 0.4058 rms_B_bonded: 2.18 r_work: 0.3974 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3883 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.3342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 3498 Z= 0.086 Angle : 0.493 3.923 4680 Z= 0.262 Chirality : 0.048 0.131 528 Planarity : 0.003 0.028 594 Dihedral : 4.531 13.822 462 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.01 % Allowed : 18.18 % 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: -1.88 (0.34), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.42 (0.26), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS E 330 PHE 0.004 0.001 PHE C 378 TYR 0.009 0.002 TYR E 310 ARG 0.002 0.000 ARG C 349 Details of bonding type rmsd hydrogen bonds : bond 0.01060 ( 67) hydrogen bonds : angle 5.12369 ( 201) covalent geometry : bond 0.00193 ( 3498) covalent geometry : angle 0.49311 ( 4680) *********************** 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 52 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 48 time to evaluate : 0.419 Fit side-chains REVERT: A 369 LYS cc_start: 0.7844 (mttt) cc_final: 0.7411 (mtpt) REVERT: B 349 ARG cc_start: 0.8123 (mtt180) cc_final: 0.7462 (mmm160) REVERT: B 369 LYS cc_start: 0.7791 (mttt) cc_final: 0.7372 (mtpt) REVERT: C 349 ARG cc_start: 0.8181 (mtt180) cc_final: 0.7354 (mmm160) REVERT: C 369 LYS cc_start: 0.7896 (mttt) cc_final: 0.7450 (mtpt) REVERT: D 369 LYS cc_start: 0.8075 (mttt) cc_final: 0.7589 (mtmt) REVERT: E 369 LYS cc_start: 0.7746 (mttt) cc_final: 0.7325 (mtmt) REVERT: F 369 LYS cc_start: 0.8087 (mttt) cc_final: 0.7684 (mtpt) outliers start: 4 outliers final: 3 residues processed: 52 average time/residue: 0.3683 time to fit residues: 21.2260 Evaluate side-chains 49 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 46 time to evaluate : 0.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 8.9990 chunk 7 optimal weight: 10.0000 chunk 15 optimal weight: 8.9990 chunk 30 optimal weight: 8.9990 chunk 25 optimal weight: 0.9990 chunk 6 optimal weight: 0.6980 chunk 22 optimal weight: 3.9990 chunk 3 optimal weight: 10.0000 chunk 32 optimal weight: 1.9990 chunk 1 optimal weight: 5.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- 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 = 0.4319 r_free = 0.4319 target = 0.172920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.142447 restraints weight = 4072.570| |-----------------------------------------------------------------------------| r_work (start): 0.4009 rms_B_bonded: 2.09 r_work: 0.3906 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3818 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.3839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 3498 Z= 0.185 Angle : 0.556 4.379 4680 Z= 0.294 Chirality : 0.050 0.144 528 Planarity : 0.004 0.029 594 Dihedral : 4.766 12.783 462 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 1.77 % Allowed : 18.69 % Favored : 79.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.87 (0.34), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.41 (0.26), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 330 PHE 0.008 0.002 PHE A 378 TYR 0.014 0.003 TYR E 310 ARG 0.002 0.000 ARG B 379 Details of bonding type rmsd hydrogen bonds : bond 0.01240 ( 67) hydrogen bonds : angle 5.03763 ( 201) covalent geometry : bond 0.00425 ( 3498) covalent geometry : angle 0.55624 ( 4680) *********************** 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 55 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 48 time to evaluate : 0.420 Fit side-chains REVERT: A 369 LYS cc_start: 0.7947 (mttt) cc_final: 0.7521 (mtpt) REVERT: B 349 ARG cc_start: 0.8232 (mtt180) cc_final: 0.7558 (mmm160) REVERT: B 369 LYS cc_start: 0.7861 (mttt) cc_final: 0.7470 (mtpt) REVERT: C 349 ARG cc_start: 0.8191 (mtt180) cc_final: 0.7449 (mmm160) REVERT: C 369 LYS cc_start: 0.7986 (mttt) cc_final: 0.7532 (mtmt) REVERT: D 369 LYS cc_start: 0.8146 (mttt) cc_final: 0.7731 (mtmt) REVERT: E 369 LYS cc_start: 0.7826 (mttt) cc_final: 0.7411 (mtmt) REVERT: F 369 LYS cc_start: 0.8162 (mttt) cc_final: 0.7774 (mtpt) outliers start: 7 outliers final: 7 residues processed: 55 average time/residue: 0.3447 time to fit residues: 21.1863 Evaluate side-chains 52 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 45 time to evaluate : 0.430 ------------------------------------------------------------------------------- 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 25 optimal weight: 3.9990 chunk 24 optimal weight: 3.9990 chunk 6 optimal weight: 0.9990 chunk 21 optimal weight: 0.0170 chunk 7 optimal weight: 7.9990 chunk 27 optimal weight: 9.9990 chunk 2 optimal weight: 1.9990 chunk 15 optimal weight: 10.0000 chunk 40 optimal weight: 0.9990 chunk 4 optimal weight: 2.9990 chunk 16 optimal weight: 7.9990 overall best weight: 1.4026 ------------------------------------------------------------------------------- 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 = 0.4394 r_free = 0.4394 target = 0.179808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.150259 restraints weight = 4189.733| |-----------------------------------------------------------------------------| r_work (start): 0.4038 rms_B_bonded: 2.11 r_work: 0.3921 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3828 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.4148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3498 Z= 0.112 Angle : 0.514 3.964 4680 Z= 0.274 Chirality : 0.049 0.140 528 Planarity : 0.003 0.030 594 Dihedral : 4.499 14.557 462 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 1.77 % Allowed : 20.45 % Favored : 77.78 % 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: -1.70 (0.35), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.29 (0.26), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 330 PHE 0.008 0.001 PHE C 378 TYR 0.014 0.003 TYR F 310 ARG 0.003 0.000 ARG C 379 Details of bonding type rmsd hydrogen bonds : bond 0.01069 ( 67) hydrogen bonds : angle 4.84510 ( 201) covalent geometry : bond 0.00257 ( 3498) covalent geometry : angle 0.51395 ( 4680) *********************** 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 53 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 46 time to evaluate : 0.392 Fit side-chains REVERT: A 369 LYS cc_start: 0.7902 (mttt) cc_final: 0.7479 (mtpt) REVERT: B 349 ARG cc_start: 0.8144 (mtt180) cc_final: 0.7433 (mmm160) REVERT: B 369 LYS cc_start: 0.7865 (mttt) cc_final: 0.7463 (mtpt) REVERT: C 349 ARG cc_start: 0.8268 (mtt180) cc_final: 0.7459 (mmm160) REVERT: C 369 LYS cc_start: 0.7979 (mttt) cc_final: 0.7523 (mtmt) REVERT: D 369 LYS cc_start: 0.8074 (mttt) cc_final: 0.7672 (mtmt) REVERT: E 349 ARG cc_start: 0.8160 (mtt180) cc_final: 0.7853 (mtt90) REVERT: E 369 LYS cc_start: 0.7771 (mttt) cc_final: 0.7365 (mtmt) REVERT: F 331 LYS cc_start: 0.8798 (mtpp) cc_final: 0.8091 (tttp) REVERT: F 369 LYS cc_start: 0.8054 (mttt) cc_final: 0.7688 (mtpt) outliers start: 7 outliers final: 6 residues processed: 53 average time/residue: 0.3354 time to fit residues: 19.8503 Evaluate side-chains 51 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 45 time to evaluate : 0.414 ------------------------------------------------------------------------------- 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 36 optimal weight: 0.0770 chunk 15 optimal weight: 0.9980 chunk 26 optimal weight: 0.8980 chunk 16 optimal weight: 0.0980 chunk 2 optimal weight: 3.9990 chunk 9 optimal weight: 0.9980 chunk 20 optimal weight: 0.8980 chunk 3 optimal weight: 7.9990 chunk 37 optimal weight: 0.0970 chunk 24 optimal weight: 9.9990 chunk 39 optimal weight: 4.9990 overall best weight: 0.4136 ------------------------------------------------------------------------------- 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 = 0.4455 r_free = 0.4455 target = 0.184405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.156206 restraints weight = 4163.056| |-----------------------------------------------------------------------------| r_work (start): 0.4119 rms_B_bonded: 2.05 r_work: 0.4025 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3942 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.4498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 3498 Z= 0.078 Angle : 0.470 4.169 4680 Z= 0.252 Chirality : 0.048 0.132 528 Planarity : 0.003 0.029 594 Dihedral : 4.054 12.656 462 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 1.26 % Allowed : 21.46 % Favored : 77.27 % 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: -1.49 (0.36), 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 0.000 HIS E 330 PHE 0.002 0.001 PHE B 346 TYR 0.011 0.002 TYR F 310 ARG 0.002 0.000 ARG E 379 Details of bonding type rmsd hydrogen bonds : bond 0.00845 ( 67) hydrogen bonds : angle 4.41571 ( 201) covalent geometry : bond 0.00176 ( 3498) covalent geometry : angle 0.46980 ( 4680) *********************** 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 52 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 47 time to evaluate : 0.419 Fit side-chains REVERT: A 369 LYS cc_start: 0.7818 (mttt) cc_final: 0.7385 (mtpt) REVERT: B 349 ARG cc_start: 0.8192 (mtt180) cc_final: 0.7433 (mmm160) REVERT: B 369 LYS cc_start: 0.7812 (mttt) cc_final: 0.7410 (mtpt) REVERT: C 349 ARG cc_start: 0.8310 (mtt180) cc_final: 0.7472 (mmm160) REVERT: C 369 LYS cc_start: 0.8055 (mttt) cc_final: 0.7574 (mtpt) REVERT: D 369 LYS cc_start: 0.7956 (mttt) cc_final: 0.7570 (mtmt) REVERT: E 369 LYS cc_start: 0.7676 (mttt) cc_final: 0.7266 (mtmt) REVERT: F 331 LYS cc_start: 0.8740 (mtpp) cc_final: 0.7982 (tttt) REVERT: F 369 LYS cc_start: 0.7957 (mttt) cc_final: 0.7605 (mtpt) outliers start: 5 outliers final: 5 residues processed: 52 average time/residue: 0.3264 time to fit residues: 19.1125 Evaluate side-chains 50 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 45 time to evaluate : 0.404 ------------------------------------------------------------------------------- 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 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: 5.9990 chunk 10 optimal weight: 8.9990 chunk 3 optimal weight: 4.9990 chunk 31 optimal weight: 8.9990 chunk 23 optimal weight: 0.9980 chunk 39 optimal weight: 2.9990 chunk 24 optimal weight: 10.0000 chunk 18 optimal weight: 1.9990 chunk 25 optimal weight: 0.1980 chunk 6 optimal weight: 10.0000 chunk 41 optimal weight: 5.9990 overall best weight: 2.2386 ------------------------------------------------------------------------------- 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** ** 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 = 0.4341 r_free = 0.4341 target = 0.174405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.143160 restraints weight = 4171.924| |-----------------------------------------------------------------------------| r_work (start): 0.4014 rms_B_bonded: 2.17 r_work: 0.3916 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3828 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.4396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 3498 Z= 0.157 Angle : 0.538 5.006 4680 Z= 0.286 Chirality : 0.049 0.138 528 Planarity : 0.004 0.030 594 Dihedral : 4.396 11.546 462 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 1.77 % Allowed : 20.20 % 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 (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 : -1.16 (0.27), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 330 PHE 0.006 0.001 PHE F 346 TYR 0.011 0.002 TYR F 310 ARG 0.001 0.000 ARG F 379 Details of bonding type rmsd hydrogen bonds : bond 0.01017 ( 67) hydrogen bonds : angle 4.55375 ( 201) covalent geometry : bond 0.00362 ( 3498) covalent geometry : angle 0.53753 ( 4680) *********************** 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 52 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 45 time to evaluate : 0.367 Fit side-chains REVERT: A 369 LYS cc_start: 0.7926 (mttt) cc_final: 0.7510 (mtpt) REVERT: B 349 ARG cc_start: 0.8288 (mtt180) cc_final: 0.7532 (mmm160) REVERT: B 369 LYS cc_start: 0.7868 (mttt) cc_final: 0.7478 (mtpt) REVERT: C 349 ARG cc_start: 0.8252 (mtt180) cc_final: 0.7449 (mmm160) REVERT: C 369 LYS cc_start: 0.8004 (mttt) cc_final: 0.7567 (mtpt) REVERT: D 369 LYS cc_start: 0.8025 (mttt) cc_final: 0.7634 (mtmt) REVERT: E 349 ARG cc_start: 0.8105 (mtt180) cc_final: 0.7839 (mtt90) REVERT: E 369 LYS cc_start: 0.7875 (mttt) cc_final: 0.7417 (mtpt) REVERT: F 331 LYS cc_start: 0.8814 (mtpp) cc_final: 0.8131 (tttt) REVERT: F 369 LYS cc_start: 0.8040 (mttt) cc_final: 0.7704 (mtpt) outliers start: 7 outliers final: 7 residues processed: 52 average time/residue: 0.3539 time to fit residues: 20.4447 Evaluate side-chains 52 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 45 time to evaluate : 0.409 ------------------------------------------------------------------------------- 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 22 optimal weight: 10.0000 chunk 8 optimal weight: 9.9990 chunk 27 optimal weight: 3.9990 chunk 37 optimal weight: 6.9990 chunk 39 optimal weight: 4.9990 chunk 17 optimal weight: 8.9990 chunk 14 optimal weight: 10.0000 chunk 13 optimal weight: 3.9990 chunk 3 optimal weight: 7.9990 chunk 40 optimal weight: 0.9980 chunk 21 optimal weight: 2.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- 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 = 0.4303 r_free = 0.4303 target = 0.171964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.141276 restraints weight = 4166.151| |-----------------------------------------------------------------------------| r_work (start): 0.3978 rms_B_bonded: 2.16 r_work: 0.3883 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3796 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.4598 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= 0.223 Angle : 0.613 5.211 4680 Z= 0.328 Chirality : 0.051 0.146 528 Planarity : 0.004 0.028 594 Dihedral : 5.053 13.339 462 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % 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: -1.70 (0.34), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.28 (0.26), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS A 330 PHE 0.009 0.002 PHE F 346 TYR 0.009 0.003 TYR C 310 ARG 0.002 0.000 ARG D 379 Details of bonding type rmsd hydrogen bonds : bond 0.01342 ( 67) hydrogen bonds : angle 4.90542 ( 201) covalent geometry : bond 0.00514 ( 3498) covalent geometry : angle 0.61260 ( 4680) *********************** 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 55 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 48 time to evaluate : 0.367 Fit side-chains REVERT: A 369 LYS cc_start: 0.7919 (mttt) cc_final: 0.7511 (mtpt) REVERT: B 349 ARG cc_start: 0.8224 (mtt180) cc_final: 0.7463 (mmm160) REVERT: B 369 LYS cc_start: 0.7884 (mttt) cc_final: 0.7457 (mtpt) REVERT: C 349 ARG cc_start: 0.8222 (mtt180) cc_final: 0.7423 (mmm160) REVERT: C 369 LYS cc_start: 0.8037 (mttt) cc_final: 0.7560 (mtmt) REVERT: D 369 LYS cc_start: 0.8006 (mttt) cc_final: 0.7618 (mtmt) REVERT: E 349 ARG cc_start: 0.8164 (mtt180) cc_final: 0.7844 (mtt90) REVERT: E 369 LYS cc_start: 0.7883 (mttt) cc_final: 0.7430 (mtpt) REVERT: F 369 LYS cc_start: 0.8147 (mttt) cc_final: 0.7760 (mtpt) outliers start: 7 outliers final: 7 residues processed: 55 average time/residue: 0.3617 time to fit residues: 21.9482 Evaluate side-chains 54 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 47 time to evaluate : 0.422 ------------------------------------------------------------------------------- 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 24 optimal weight: 3.9990 chunk 8 optimal weight: 9.9990 chunk 32 optimal weight: 5.9990 chunk 23 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 27 optimal weight: 5.9990 chunk 18 optimal weight: 2.9990 chunk 38 optimal weight: 5.9990 chunk 15 optimal weight: 1.9990 chunk 1 optimal weight: 6.9990 chunk 19 optimal weight: 1.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- 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 = 0.4337 r_free = 0.4337 target = 0.174158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.143350 restraints weight = 4201.930| |-----------------------------------------------------------------------------| r_work (start): 0.4010 rms_B_bonded: 2.17 r_work: 0.3917 rms_B_bonded: 2.24 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: 0.7852 moved from start: 0.4764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3498 Z= 0.144 Angle : 0.562 4.961 4680 Z= 0.301 Chirality : 0.049 0.139 528 Planarity : 0.003 0.028 594 Dihedral : 4.698 13.391 462 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 1.77 % Allowed : 21.21 % Favored : 77.02 % 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 (0.34), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.24 (0.26), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 330 PHE 0.005 0.001 PHE F 346 TYR 0.008 0.002 TYR E 310 ARG 0.001 0.000 ARG E 379 Details of bonding type rmsd hydrogen bonds : bond 0.01128 ( 67) hydrogen bonds : angle 4.72339 ( 201) covalent geometry : bond 0.00332 ( 3498) covalent geometry : angle 0.56206 ( 4680) ********************** 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 53 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 46 time to evaluate : 0.370 Fit side-chains REVERT: A 369 LYS cc_start: 0.8007 (mttt) cc_final: 0.7554 (mtpt) REVERT: B 349 ARG cc_start: 0.8314 (mtt180) cc_final: 0.7518 (mmm160) REVERT: B 369 LYS cc_start: 0.7859 (mttt) cc_final: 0.7433 (mtpt) REVERT: C 349 ARG cc_start: 0.8279 (mtt180) cc_final: 0.7457 (mmm160) REVERT: C 369 LYS cc_start: 0.7970 (mttt) cc_final: 0.7515 (mtpt) REVERT: D 369 LYS cc_start: 0.7980 (mttt) cc_final: 0.7596 (mtmt) REVERT: E 349 ARG cc_start: 0.8104 (mtt180) cc_final: 0.7814 (mtt90) REVERT: E 369 LYS cc_start: 0.7837 (mttt) cc_final: 0.7394 (mtpt) REVERT: F 331 LYS cc_start: 0.8836 (mtpp) cc_final: 0.8136 (tttp) REVERT: F 369 LYS cc_start: 0.8091 (mttt) cc_final: 0.7704 (mtpt) outliers start: 7 outliers final: 7 residues processed: 53 average time/residue: 0.3433 time to fit residues: 20.1612 Evaluate side-chains 53 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 46 time to evaluate : 0.369 ------------------------------------------------------------------------------- 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 30 optimal weight: 6.9990 chunk 35 optimal weight: 10.0000 chunk 21 optimal weight: 0.5980 chunk 7 optimal weight: 0.9980 chunk 29 optimal weight: 9.9990 chunk 16 optimal weight: 7.9990 chunk 22 optimal weight: 4.9990 chunk 40 optimal weight: 3.9990 chunk 23 optimal weight: 0.0370 chunk 15 optimal weight: 1.9990 chunk 10 optimal weight: 7.9990 overall best weight: 1.5262 ------------------------------------------------------------------------------- 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 = 0.4358 r_free = 0.4358 target = 0.176703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.145884 restraints weight = 4183.139| |-----------------------------------------------------------------------------| r_work (start): 0.4044 rms_B_bonded: 2.11 r_work: 0.3950 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3863 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.4872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3498 Z= 0.122 Angle : 0.558 5.486 4680 Z= 0.297 Chirality : 0.049 0.136 528 Planarity : 0.003 0.028 594 Dihedral : 4.506 13.539 462 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 1.77 % Allowed : 21.21 % Favored : 77.02 % 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 (0.34), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.23 (0.26), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 330 PHE 0.004 0.001 PHE F 346 TYR 0.007 0.002 TYR E 310 ARG 0.002 0.000 ARG C 379 Details of bonding type rmsd hydrogen bonds : bond 0.00988 ( 67) hydrogen bonds : angle 4.60205 ( 201) covalent geometry : bond 0.00281 ( 3498) covalent geometry : angle 0.55803 ( 4680) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2459.57 seconds wall clock time: 43 minutes 32.14 seconds (2612.14 seconds total)