Starting phenix.real_space_refine on Tue Aug 4 13:28:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/29os_57273/08_2026/29os_57273.cif Found real_map, /net/cci-nas-00/data/ceres_data/29os_57273/08_2026/29os_57273.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/29os_57273/08_2026/29os_57273.map" default_real_map = "/net/cci-nas-00/data/ceres_data/29os_57273/08_2026/29os_57273.map" model { file = "/net/cci-nas-00/data/ceres_data/29os_57273/08_2026/29os_57273.cif" } default_model = "/net/cci-nas-00/data/ceres_data/29os_57273/08_2026/29os_57273.cif" } resolution = 3.6 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= 0.001 sd= 0.004 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 2076 2.51 5 N 600 2.21 5 O 618 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 3300 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 550 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 550 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 3, 'TRANS': 68} Chain: "B" Number of atoms: 550 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 550 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 3, 'TRANS': 68} Chain: "C" Number of atoms: 550 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 550 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 3, 'TRANS': 68} Chain: "D" Number of atoms: 550 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 550 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 3, 'TRANS': 68} Chain: "E" Number of atoms: 550 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 550 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 3, 'TRANS': 68} Chain: "F" Number of atoms: 550 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 550 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 3, 'TRANS': 68} Time building chain proxies: 1.16, per 1000 atoms: 0.35 Number of scatterers: 3300 At special positions: 0 Unit cell: (135.408, 87.792, 35.712, 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 618 8.00 N 600 7.00 C 2076 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: 0.17 Conformation dependent library (CDL) restraints added in 77.4 milliseconds 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 756 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 18 sheets defined 0.0% alpha, 30.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.11 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 308 through 310 removed outlier: 6.588A pdb=" N VAL A 309 " --> pdb=" O TYR D 310 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 317 through 318 removed outlier: 6.738A pdb=" N LYS A 317 " --> pdb=" O VAL D 318 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N VAL B 318 " --> pdb=" O LYS D 317 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 321 through 322 removed outlier: 6.739A pdb=" N LYS A 321 " --> pdb=" O CYS D 322 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 326 through 330 removed outlier: 7.160A pdb=" N ASN A 327 " --> pdb=" O GLY D 326 " (cutoff:3.500A) removed outlier: 5.872A pdb=" N GLY B 326 " --> pdb=" O ASN D 327 " (cutoff:3.500A) removed outlier: 8.487A pdb=" N HIS D 329 " --> pdb=" O GLY B 326 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N ILE B 328 " --> pdb=" O HIS D 329 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 336 through 340 Processing sheet with id=AA6, first strand: chain 'A' and resid 343 through 346 removed outlier: 6.620A pdb=" N LYS A 343 " --> pdb=" O LEU D 344 " (cutoff:3.500A) removed outlier: 8.353A pdb=" N PHE D 346 " --> pdb=" O LYS A 343 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N ASP A 345 " --> pdb=" O PHE D 346 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 359 through 362 removed outlier: 6.321A pdb=" N LEU B 357 " --> pdb=" O ASP D 358 " (cutoff:3.500A) removed outlier: 7.995A pdb=" N ILE D 360 " --> pdb=" O LEU B 357 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N ASN B 359 " --> pdb=" O ILE D 360 " (cutoff:3.500A) removed outlier: 7.968A pdb=" N HIS D 362 " --> pdb=" O ASN B 359 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N THR B 361 " --> pdb=" O HIS D 362 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 369 through 370 removed outlier: 6.525A pdb=" N LYS A 369 " --> pdb=" O LYS D 370 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 374 through 375 removed outlier: 4.109A pdb=" N LYS A 375 " --> pdb=" O HIS D 374 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'B' and resid 351 through 354 removed outlier: 4.227A pdb=" N LYS D 353 " --> pdb=" O SER B 352 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 308 through 310 removed outlier: 6.745A pdb=" N ILE C 308 " --> pdb=" O VAL E 309 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 313 through 314 Processing sheet with id=AB4, first strand: chain 'C' and resid 325 through 330 removed outlier: 5.672A pdb=" N GLY C 326 " --> pdb=" O ASN E 327 " (cutoff:3.500A) removed outlier: 8.502A pdb=" N HIS E 329 " --> pdb=" O GLY C 326 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N ILE C 328 " --> pdb=" O HIS E 329 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N GLY E 326 " --> pdb=" O ASN F 327 " (cutoff:3.500A) removed outlier: 8.630A pdb=" N HIS F 329 " --> pdb=" O GLY E 326 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N ILE E 328 " --> pdb=" O HIS F 329 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'C' and resid 336 through 340 removed outlier: 6.352A pdb=" N VAL E 337 " --> pdb=" O GLU F 338 " (cutoff:3.500A) removed outlier: 8.317A pdb=" N LYS F 340 " --> pdb=" O VAL E 337 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N VAL E 339 " --> pdb=" O LYS F 340 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 369 through 370 Processing sheet with id=AB7, first strand: chain 'E' and resid 317 through 322 removed outlier: 6.297A pdb=" N VAL E 318 " --> pdb=" O THR F 319 " (cutoff:3.500A) removed outlier: 8.339A pdb=" N LYS F 321 " --> pdb=" O VAL E 318 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N SER E 320 " --> pdb=" O LYS F 321 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'E' and resid 343 through 346 Processing sheet with id=AB9, first strand: chain 'E' and resid 374 through 375 removed outlier: 6.446A pdb=" N HIS E 374 " --> pdb=" O LYS F 375 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 39 hydrogen bonds defined for protein. 117 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: 0.39 Time building geometry restraints manager: 0.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 874 1.33 - 1.45: 468 1.45 - 1.57: 2006 1.57 - 1.69: 0 1.69 - 1.81: 6 Bond restraints: 3354 Sorted by residual: bond pdb=" N PRO D 364 " pdb=" CD PRO D 364 " ideal model delta sigma weight residual 1.473 1.430 0.043 1.40e-02 5.10e+03 9.41e+00 bond pdb=" CA THR C 361 " pdb=" C THR C 361 " ideal model delta sigma weight residual 1.533 1.506 0.027 9.60e-03 1.09e+04 7.94e+00 bond pdb=" N PRO A 364 " pdb=" CD PRO A 364 " ideal model delta sigma weight residual 1.473 1.436 0.037 1.40e-02 5.10e+03 7.16e+00 bond pdb=" CZ ARG C 349 " pdb=" NH2 ARG C 349 " ideal model delta sigma weight residual 1.330 1.296 0.034 1.30e-02 5.92e+03 6.82e+00 bond pdb=" CZ ARG F 349 " pdb=" NH2 ARG F 349 " ideal model delta sigma weight residual 1.330 1.297 0.033 1.30e-02 5.92e+03 6.48e+00 ... (remaining 3349 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.73: 2670 1.73 - 3.46: 1348 3.46 - 5.20: 391 5.20 - 6.93: 72 6.93 - 8.66: 7 Bond angle restraints: 4488 Sorted by residual: angle pdb=" CA ASP E 358 " pdb=" CB ASP E 358 " pdb=" CG ASP E 358 " ideal model delta sigma weight residual 112.60 118.57 -5.97 1.00e+00 1.00e+00 3.57e+01 angle pdb=" CA ASP A 358 " pdb=" CB ASP A 358 " pdb=" CG ASP A 358 " ideal model delta sigma weight residual 112.60 118.02 -5.42 1.00e+00 1.00e+00 2.94e+01 angle pdb=" CB HIS A 362 " pdb=" CG HIS A 362 " pdb=" CD2 HIS A 362 " ideal model delta sigma weight residual 131.20 124.18 7.02 1.30e+00 5.92e-01 2.92e+01 angle pdb=" CA PHE D 346 " pdb=" CB PHE D 346 " pdb=" CG PHE D 346 " ideal model delta sigma weight residual 113.80 119.18 -5.38 1.00e+00 1.00e+00 2.90e+01 angle pdb=" N ASP E 358 " pdb=" CA ASP E 358 " pdb=" C ASP E 358 " ideal model delta sigma weight residual 110.24 118.04 -7.80 1.47e+00 4.63e-01 2.81e+01 ... (remaining 4483 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.52: 1817 15.52 - 31.04: 180 31.04 - 46.56: 32 46.56 - 62.08: 6 62.08 - 77.60: 5 Dihedral angle restraints: 2040 sinusoidal: 852 harmonic: 1188 Sorted by residual: dihedral pdb=" CA VAL F 318 " pdb=" C VAL F 318 " pdb=" N THR F 319 " pdb=" CA THR F 319 " ideal model delta harmonic sigma weight residual -180.00 -151.23 -28.77 0 5.00e+00 4.00e-02 3.31e+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 180.00 151.86 28.14 0 5.00e+00 4.00e-02 3.17e+01 dihedral pdb=" CA ASP B 358 " pdb=" C ASP B 358 " pdb=" N ASN B 359 " pdb=" CA ASN B 359 " ideal model delta harmonic sigma weight residual 180.00 152.15 27.85 0 5.00e+00 4.00e-02 3.10e+01 ... (remaining 2037 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.080: 309 0.080 - 0.160: 155 0.160 - 0.240: 31 0.240 - 0.319: 3 0.319 - 0.399: 6 Chirality restraints: 504 Sorted by residual: chirality pdb=" CA ARG F 349 " pdb=" N ARG F 349 " pdb=" C ARG F 349 " pdb=" CB ARG F 349 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 3.98e+00 chirality pdb=" CA ARG B 349 " pdb=" N ARG B 349 " pdb=" C ARG B 349 " pdb=" CB ARG B 349 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.45e+00 chirality pdb=" CA ARG D 349 " pdb=" N ARG D 349 " pdb=" C ARG D 349 " pdb=" CB ARG D 349 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.31e+00 ... (remaining 501 not shown) Planarity restraints: 570 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR F 310 " -0.135 2.00e-02 2.50e+03 7.26e-02 1.05e+02 pdb=" CG TYR F 310 " 0.044 2.00e-02 2.50e+03 pdb=" CD1 TYR F 310 " 0.062 2.00e-02 2.50e+03 pdb=" CD2 TYR F 310 " 0.062 2.00e-02 2.50e+03 pdb=" CE1 TYR F 310 " 0.036 2.00e-02 2.50e+03 pdb=" CE2 TYR F 310 " 0.041 2.00e-02 2.50e+03 pdb=" CZ TYR F 310 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR F 310 " -0.107 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR D 310 " 0.116 2.00e-02 2.50e+03 5.98e-02 7.15e+01 pdb=" CG TYR D 310 " -0.051 2.00e-02 2.50e+03 pdb=" CD1 TYR D 310 " -0.055 2.00e-02 2.50e+03 pdb=" CD2 TYR D 310 " -0.050 2.00e-02 2.50e+03 pdb=" CE1 TYR D 310 " -0.022 2.00e-02 2.50e+03 pdb=" CE2 TYR D 310 " -0.023 2.00e-02 2.50e+03 pdb=" CZ TYR D 310 " 0.008 2.00e-02 2.50e+03 pdb=" OH TYR D 310 " 0.077 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 310 " 0.088 2.00e-02 2.50e+03 4.69e-02 4.41e+01 pdb=" CG TYR B 310 " -0.031 2.00e-02 2.50e+03 pdb=" CD1 TYR B 310 " -0.042 2.00e-02 2.50e+03 pdb=" CD2 TYR B 310 " -0.039 2.00e-02 2.50e+03 pdb=" CE1 TYR B 310 " -0.022 2.00e-02 2.50e+03 pdb=" CE2 TYR B 310 " -0.026 2.00e-02 2.50e+03 pdb=" CZ TYR B 310 " 0.006 2.00e-02 2.50e+03 pdb=" OH TYR B 310 " 0.066 2.00e-02 2.50e+03 ... (remaining 567 not shown) Histogram of nonbonded interaction distances: 2.54 - 3.01: 1671 3.01 - 3.49: 2881 3.49 - 3.96: 4872 3.96 - 4.43: 4693 4.43 - 4.90: 9437 Nonbonded interactions: 23554 Sorted by model distance: nonbonded pdb=" OD1 ASP A 314 " pdb=" OG SER A 316 " model vdw 2.542 3.040 nonbonded pdb=" OD1 ASP F 314 " pdb=" OG SER F 316 " model vdw 2.546 3.040 nonbonded pdb=" OD1 ASP B 314 " pdb=" OG SER B 316 " model vdw 2.555 3.040 nonbonded pdb=" OD1 ASP C 314 " pdb=" OG SER C 316 " model vdw 2.559 3.040 nonbonded pdb=" OD1 ASP E 314 " pdb=" OG SER E 316 " model vdw 2.561 3.040 ... (remaining 23549 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' 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 group one per residue 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: 0.460 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.060 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.090 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 7.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7511 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 : 0.011 0.043 3354 Z= 0.726 Angle : 2.127 8.660 4488 Z= 1.393 Chirality : 0.096 0.399 504 Planarity : 0.012 0.073 570 Dihedral : 13.194 77.604 1284 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 0.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.57 % Favored : 86.43 % Rotamer: Outliers : 0.53 % Allowed : 4.50 % Favored : 94.97 % Cbeta Deviations : 0.53 % 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 are not related in a simple way. whole: -3.83 (0.26), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.91 (0.20), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 349 TYR 0.135 0.038 TYR F 310 PHE 0.051 0.014 PHE D 346 HIS 0.016 0.004 HIS E 362 Details of bonding type rmsd/Z covalent geometry : bond 0.01125 / 0.73 ( 3354) covalent geometry : angle 2.12732 / 1.39 ( 4488) hydrogen bonds : bond 0.22917 / 13.78 ( 39) hydrogen bonds : angle 6.89610 / 4.74 ( 117) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 120 time to evaluate : 0.132 Fit side-chains REVERT: A 348 ASP cc_start: 0.8458 (t0) cc_final: 0.8171 (t0) REVERT: A 349 ARG cc_start: 0.7617 (mtm180) cc_final: 0.7408 (mmp-170) REVERT: B 352 SER cc_start: 0.8638 (t) cc_final: 0.8108 (t) REVERT: C 321 LYS cc_start: 0.8606 (mttt) cc_final: 0.8352 (mttp) REVERT: D 321 LYS cc_start: 0.8734 (mttt) cc_final: 0.8401 (mttp) REVERT: D 342 GLU cc_start: 0.6530 (mm-30) cc_final: 0.6144 (mp0) REVERT: D 372 GLU cc_start: 0.8079 (mm-30) cc_final: 0.7449 (mm-30) outliers start: 2 outliers final: 0 residues processed: 122 average time/residue: 0.1256 time to fit residues: 17.0855 Evaluate side-chains 93 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 93 time to evaluate : 0.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 24 optimal weight: 4.9990 chunk 26 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 16 optimal weight: 0.7980 chunk 32 optimal weight: 1.9990 chunk 31 optimal weight: 5.9990 chunk 25 optimal weight: 2.9990 chunk 19 optimal weight: 10.0000 chunk 30 optimal weight: 5.9990 chunk 22 optimal weight: 8.9990 chunk 37 optimal weight: 0.6980 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 327 ASN A 351 GLN B 351 GLN C 327 ASN C 351 GLN D 351 GLN E 307 GLN E 351 GLN F 351 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5041 r_free = 0.5041 target = 0.290004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.5477 r_free = 0.5477 target = 0.223318 restraints weight = 5051.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.5514 r_free = 0.5514 target = 0.226566 restraints weight = 3292.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.5545 r_free = 0.5545 target = 0.228793 restraints weight = 2410.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.5549 r_free = 0.5549 target = 0.229928 restraints weight = 1905.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.5576 r_free = 0.5576 target = 0.231339 restraints weight = 1650.371| |-----------------------------------------------------------------------------| r_work (final): 0.4979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7409 moved from start: 0.3962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3354 Z= 0.149 Angle : 0.872 8.369 4488 Z= 0.434 Chirality : 0.051 0.147 504 Planarity : 0.004 0.032 570 Dihedral : 7.761 19.318 438 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 1.59 % Allowed : 11.90 % Favored : 86.51 % 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 are not related in a simple way. whole: -3.17 (0.28), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.41 (0.21), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 349 TYR 0.025 0.002 TYR D 310 PHE 0.010 0.002 PHE D 346 HIS 0.005 0.001 HIS D 362 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.15 ( 3354) covalent geometry : angle 0.87221 / 0.43 ( 4488) hydrogen bonds : bond 0.03419 / 2.00 ( 39) hydrogen bonds : angle 5.03067 / 3.53 ( 117) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 118 time to evaluate : 0.080 Fit side-chains REVERT: B 347 LYS cc_start: 0.7604 (mttm) cc_final: 0.7220 (pttp) REVERT: B 352 SER cc_start: 0.8724 (t) cc_final: 0.8272 (t) REVERT: B 363 VAL cc_start: 0.8750 (t) cc_final: 0.8523 (t) REVERT: C 317 LYS cc_start: 0.8409 (mptt) cc_final: 0.8153 (mtpt) REVERT: C 347 LYS cc_start: 0.4731 (pptt) cc_final: 0.4484 (pttm) REVERT: D 317 LYS cc_start: 0.7786 (mttp) cc_final: 0.6684 (tmtt) REVERT: D 327 ASN cc_start: 0.8800 (t0) cc_final: 0.8585 (t0) REVERT: D 342 GLU cc_start: 0.6909 (mm-30) cc_final: 0.6323 (mp0) REVERT: E 327 ASN cc_start: 0.8628 (t0) cc_final: 0.8415 (t0) REVERT: F 349 ARG cc_start: 0.7398 (mtt-85) cc_final: 0.6634 (mmp-170) REVERT: F 363 VAL cc_start: 0.8916 (t) cc_final: 0.8681 (t) outliers start: 6 outliers final: 2 residues processed: 121 average time/residue: 0.0825 time to fit residues: 11.2825 Evaluate side-chains 99 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 97 time to evaluate : 0.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 343 LYS Chi-restraints excluded: chain C residue 348 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 11 optimal weight: 9.9990 chunk 34 optimal weight: 20.0000 chunk 38 optimal weight: 7.9990 chunk 7 optimal weight: 20.0000 chunk 28 optimal weight: 6.9990 chunk 30 optimal weight: 4.9990 chunk 13 optimal weight: 9.9990 chunk 22 optimal weight: 20.0000 chunk 15 optimal weight: 9.9990 chunk 5 optimal weight: 8.9990 chunk 31 optimal weight: 5.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 307 GLN B 368 ASN C 327 ASN C 368 ASN E 307 GLN E 330 HIS F 330 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4915 r_free = 0.4915 target = 0.269304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.5325 r_free = 0.5325 target = 0.200825 restraints weight = 5113.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.5357 r_free = 0.5357 target = 0.203891 restraints weight = 3223.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.5369 r_free = 0.5369 target = 0.205905 restraints weight = 2362.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.5376 r_free = 0.5376 target = 0.207015 restraints weight = 1905.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.5417 r_free = 0.5417 target = 0.208297 restraints weight = 1668.662| |-----------------------------------------------------------------------------| r_work (final): 0.4855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7613 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 0.036 3354 Z= 0.278 Angle : 0.953 9.150 4488 Z= 0.487 Chirality : 0.054 0.169 504 Planarity : 0.005 0.038 570 Dihedral : 8.239 22.285 438 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.52 % Favored : 90.48 % Rotamer: Outliers : 4.23 % Allowed : 16.40 % Favored : 79.37 % 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 are not related in a simple way. whole: -3.46 (0.28), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.63 (0.21), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 349 TYR 0.024 0.004 TYR F 310 PHE 0.014 0.002 PHE F 346 HIS 0.010 0.002 HIS A 362 Details of bonding type rmsd/Z covalent geometry : bond 0.00620 / 0.28 ( 3354) covalent geometry : angle 0.95329 / 0.49 ( 4488) hydrogen bonds : bond 0.03764 / 2.24 ( 39) hydrogen bonds : angle 5.62512 / 3.80 ( 117) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 91 time to evaluate : 0.139 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 325 LEU cc_start: 0.5178 (OUTLIER) cc_final: 0.4963 (pp) REVERT: A 375 LYS cc_start: 0.8223 (mtpt) cc_final: 0.8013 (mtpt) REVERT: B 352 SER cc_start: 0.8842 (t) cc_final: 0.8513 (t) REVERT: C 317 LYS cc_start: 0.8469 (mptt) cc_final: 0.8185 (mtpt) REVERT: D 310 TYR cc_start: 0.8259 (t80) cc_final: 0.8007 (t80) REVERT: D 317 LYS cc_start: 0.7986 (mttp) cc_final: 0.6911 (tmtt) REVERT: D 342 GLU cc_start: 0.7163 (mm-30) cc_final: 0.6078 (mp0) REVERT: E 343 LYS cc_start: 0.8674 (tttm) cc_final: 0.8459 (tmtm) REVERT: E 372 GLU cc_start: 0.8524 (mm-30) cc_final: 0.8180 (mm-30) outliers start: 16 outliers final: 10 residues processed: 102 average time/residue: 0.1183 time to fit residues: 13.5713 Evaluate side-chains 96 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 85 time to evaluate : 0.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain C residue 343 LYS Chi-restraints excluded: chain C residue 348 ASP Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain D residue 328 ILE Chi-restraints excluded: chain D residue 343 LYS Chi-restraints excluded: chain D residue 373 THR Chi-restraints excluded: chain D residue 375 LYS Chi-restraints excluded: chain F residue 350 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 5 optimal weight: 10.0000 chunk 40 optimal weight: 7.9990 chunk 36 optimal weight: 0.6980 chunk 28 optimal weight: 7.9990 chunk 34 optimal weight: 5.9990 chunk 20 optimal weight: 9.9990 chunk 38 optimal weight: 10.0000 chunk 12 optimal weight: 2.9990 chunk 35 optimal weight: 20.0000 chunk 2 optimal weight: 9.9990 chunk 14 optimal weight: 5.9990 overall best weight: 4.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 307 GLN E 327 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4936 r_free = 0.4936 target = 0.273226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.5346 r_free = 0.5346 target = 0.206023 restraints weight = 5077.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.5388 r_free = 0.5388 target = 0.209235 restraints weight = 3165.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.5402 r_free = 0.5402 target = 0.211429 restraints weight = 2309.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.5407 r_free = 0.5407 target = 0.212233 restraints weight = 1837.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.5442 r_free = 0.5442 target = 0.213770 restraints weight = 1653.296| |-----------------------------------------------------------------------------| r_work (final): 0.4875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7573 moved from start: 0.4881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 3354 Z= 0.205 Angle : 0.835 6.776 4488 Z= 0.423 Chirality : 0.051 0.149 504 Planarity : 0.005 0.038 570 Dihedral : 7.546 21.733 438 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 2.91 % Allowed : 18.25 % Favored : 78.84 % 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 are not related in a simple way. whole: -3.31 (0.30), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.52 (0.23), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 349 TYR 0.017 0.003 TYR F 310 PHE 0.019 0.002 PHE F 346 HIS 0.006 0.001 HIS D 362 Details of bonding type rmsd/Z covalent geometry : bond 0.00458 / 0.20 ( 3354) covalent geometry : angle 0.83487 / 0.42 ( 4488) hydrogen bonds : bond 0.02754 / 1.66 ( 39) hydrogen bonds : angle 5.39096 / 3.63 ( 117) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 88 time to evaluate : 0.140 Fit side-chains REVERT: A 325 LEU cc_start: 0.4760 (OUTLIER) cc_final: 0.4545 (pp) REVERT: A 340 LYS cc_start: 0.5587 (tppt) cc_final: 0.4827 (tppt) REVERT: B 347 LYS cc_start: 0.7675 (mttm) cc_final: 0.7366 (pttp) REVERT: B 352 SER cc_start: 0.8751 (t) cc_final: 0.8399 (t) REVERT: C 317 LYS cc_start: 0.8475 (mptt) cc_final: 0.8154 (mttt) REVERT: D 317 LYS cc_start: 0.7958 (mttp) cc_final: 0.6895 (tmtt) REVERT: D 342 GLU cc_start: 0.7008 (mm-30) cc_final: 0.6097 (mp0) REVERT: E 342 GLU cc_start: 0.7559 (tp30) cc_final: 0.7292 (tp30) REVERT: E 343 LYS cc_start: 0.8649 (tttm) cc_final: 0.8352 (tttm) REVERT: E 372 GLU cc_start: 0.8456 (mm-30) cc_final: 0.8080 (mm-30) REVERT: F 317 LYS cc_start: 0.8007 (mttt) cc_final: 0.7724 (mttt) REVERT: F 372 GLU cc_start: 0.7816 (mm-30) cc_final: 0.7421 (tm-30) REVERT: F 378 PHE cc_start: 0.7308 (m-80) cc_final: 0.6685 (m-10) outliers start: 11 outliers final: 8 residues processed: 94 average time/residue: 0.1268 time to fit residues: 13.3099 Evaluate side-chains 91 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 82 time to evaluate : 0.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain C residue 319 THR Chi-restraints excluded: chain C residue 343 LYS Chi-restraints excluded: chain C residue 348 ASP Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain D residue 350 VAL Chi-restraints excluded: chain D residue 375 LYS Chi-restraints excluded: chain E residue 324 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 28 optimal weight: 10.0000 chunk 14 optimal weight: 9.9990 chunk 35 optimal weight: 5.9990 chunk 26 optimal weight: 5.9990 chunk 30 optimal weight: 30.0000 chunk 40 optimal weight: 4.9990 chunk 11 optimal weight: 0.7980 chunk 2 optimal weight: 9.9990 chunk 39 optimal weight: 0.0370 chunk 33 optimal weight: 2.9990 chunk 17 optimal weight: 5.9990 overall best weight: 2.9664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 327 ASN ** A 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 307 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4950 r_free = 0.4950 target = 0.275483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.5366 r_free = 0.5366 target = 0.209160 restraints weight = 5040.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.5399 r_free = 0.5399 target = 0.212096 restraints weight = 3276.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.5417 r_free = 0.5417 target = 0.214062 restraints weight = 2432.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.5454 r_free = 0.5454 target = 0.215527 restraints weight = 1957.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.5457 r_free = 0.5457 target = 0.216046 restraints weight = 1646.928| |-----------------------------------------------------------------------------| r_work (final): 0.4886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7520 moved from start: 0.5179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3354 Z= 0.151 Angle : 0.754 7.296 4488 Z= 0.380 Chirality : 0.049 0.136 504 Planarity : 0.005 0.044 570 Dihedral : 6.939 20.826 438 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.14 % Favored : 92.86 % Rotamer: Outliers : 5.56 % Allowed : 16.14 % Favored : 78.31 % 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 are not related in a simple way. whole: -3.11 (0.32), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.36 (0.24), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 349 TYR 0.012 0.003 TYR F 310 PHE 0.014 0.001 PHE F 346 HIS 0.004 0.001 HIS D 362 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.15 ( 3354) covalent geometry : angle 0.75429 / 0.38 ( 4488) hydrogen bonds : bond 0.02190 / 1.31 ( 39) hydrogen bonds : angle 5.18299 / 3.51 ( 117) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 87 time to evaluate : 0.140 Fit side-chains REVERT: A 325 LEU cc_start: 0.4657 (OUTLIER) cc_final: 0.4434 (pp) REVERT: A 340 LYS cc_start: 0.5179 (tppt) cc_final: 0.4758 (tppt) REVERT: A 347 LYS cc_start: 0.8389 (mmtm) cc_final: 0.7934 (mptt) REVERT: A 375 LYS cc_start: 0.8137 (mtpt) cc_final: 0.7859 (mttt) REVERT: B 347 LYS cc_start: 0.7615 (mttm) cc_final: 0.7330 (pttm) REVERT: B 352 SER cc_start: 0.8652 (t) cc_final: 0.8325 (t) REVERT: B 363 VAL cc_start: 0.8775 (OUTLIER) cc_final: 0.8492 (t) REVERT: C 317 LYS cc_start: 0.8338 (mptt) cc_final: 0.8067 (mttt) REVERT: C 357 LEU cc_start: 0.8470 (OUTLIER) cc_final: 0.8193 (tt) REVERT: C 378 PHE cc_start: 0.7612 (OUTLIER) cc_final: 0.6999 (t80) REVERT: D 342 GLU cc_start: 0.7070 (mm-30) cc_final: 0.6068 (mp0) REVERT: D 349 ARG cc_start: 0.7781 (mtm180) cc_final: 0.7429 (mtt180) REVERT: E 342 GLU cc_start: 0.7648 (tp30) cc_final: 0.7431 (tp30) REVERT: E 343 LYS cc_start: 0.8704 (tttm) cc_final: 0.8441 (tttm) REVERT: E 349 ARG cc_start: 0.7524 (OUTLIER) cc_final: 0.7126 (mpt-90) REVERT: E 357 LEU cc_start: 0.8864 (OUTLIER) cc_final: 0.8587 (tt) REVERT: F 317 LYS cc_start: 0.7916 (mttt) cc_final: 0.7633 (mttt) REVERT: F 378 PHE cc_start: 0.7234 (m-80) cc_final: 0.6616 (m-10) outliers start: 21 outliers final: 12 residues processed: 100 average time/residue: 0.1191 time to fit residues: 13.4020 Evaluate side-chains 96 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 78 time to evaluate : 0.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain C residue 319 THR Chi-restraints excluded: chain C residue 343 LYS Chi-restraints excluded: chain C residue 348 ASP Chi-restraints excluded: chain C residue 357 LEU Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 378 PHE Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain D residue 328 ILE Chi-restraints excluded: chain D residue 350 VAL Chi-restraints excluded: chain E residue 307 GLN Chi-restraints excluded: chain E residue 324 SER Chi-restraints excluded: chain E residue 349 ARG Chi-restraints excluded: chain E residue 357 LEU Chi-restraints excluded: chain F residue 350 VAL Chi-restraints excluded: chain F residue 363 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 25 optimal weight: 5.9990 chunk 38 optimal weight: 4.9990 chunk 21 optimal weight: 30.0000 chunk 12 optimal weight: 7.9990 chunk 22 optimal weight: 6.9990 chunk 34 optimal weight: 20.0000 chunk 26 optimal weight: 1.9990 chunk 30 optimal weight: 20.0000 chunk 13 optimal weight: 9.9990 chunk 29 optimal weight: 0.8980 chunk 41 optimal weight: 8.9990 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 307 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4954 r_free = 0.4954 target = 0.275237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.5369 r_free = 0.5369 target = 0.208152 restraints weight = 5050.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.5406 r_free = 0.5406 target = 0.211042 restraints weight = 3338.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.5434 r_free = 0.5434 target = 0.213107 restraints weight = 2461.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.5441 r_free = 0.5441 target = 0.214407 restraints weight = 1967.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.5465 r_free = 0.5465 target = 0.215514 restraints weight = 1680.928| |-----------------------------------------------------------------------------| r_work (final): 0.4894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7527 moved from start: 0.5304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 3354 Z= 0.186 Angle : 0.791 9.305 4488 Z= 0.396 Chirality : 0.049 0.140 504 Planarity : 0.006 0.041 570 Dihedral : 6.942 20.731 438 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % Rotamer: Outliers : 6.35 % Allowed : 17.46 % Favored : 76.19 % 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 are not related in a simple way. whole: -3.13 (0.32), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.38 (0.24), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 349 TYR 0.016 0.003 TYR D 310 PHE 0.015 0.001 PHE F 346 HIS 0.005 0.001 HIS A 362 Details of bonding type rmsd/Z covalent geometry : bond 0.00414 / 0.19 ( 3354) covalent geometry : angle 0.79115 / 0.40 ( 4488) hydrogen bonds : bond 0.02451 / 1.46 ( 39) hydrogen bonds : angle 5.31789 / 3.58 ( 117) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 84 time to evaluate : 0.106 Fit side-chains REVERT: A 325 LEU cc_start: 0.4281 (OUTLIER) cc_final: 0.3993 (pp) REVERT: A 340 LYS cc_start: 0.5303 (tppt) cc_final: 0.4846 (tppt) REVERT: A 347 LYS cc_start: 0.8435 (mmtm) cc_final: 0.8015 (mptt) REVERT: A 375 LYS cc_start: 0.8183 (mtpt) cc_final: 0.7888 (mttt) REVERT: B 347 LYS cc_start: 0.7691 (mttm) cc_final: 0.7378 (pttm) REVERT: B 349 ARG cc_start: 0.5250 (ptt90) cc_final: 0.4325 (mtt-85) REVERT: B 352 SER cc_start: 0.8692 (t) cc_final: 0.8366 (t) REVERT: C 317 LYS cc_start: 0.8308 (mptt) cc_final: 0.8069 (mttt) REVERT: C 378 PHE cc_start: 0.7636 (OUTLIER) cc_final: 0.7081 (t80) REVERT: D 349 ARG cc_start: 0.7773 (mtm180) cc_final: 0.7457 (mtt180) REVERT: E 342 GLU cc_start: 0.7674 (tp30) cc_final: 0.7472 (tp30) REVERT: E 343 LYS cc_start: 0.8723 (tttm) cc_final: 0.8445 (tttm) REVERT: E 349 ARG cc_start: 0.7300 (OUTLIER) cc_final: 0.7088 (mpt-90) REVERT: E 357 LEU cc_start: 0.8888 (OUTLIER) cc_final: 0.8641 (tt) REVERT: E 372 GLU cc_start: 0.8175 (tp30) cc_final: 0.7589 (tp30) REVERT: F 372 GLU cc_start: 0.7666 (mm-30) cc_final: 0.7313 (tm-30) REVERT: F 378 PHE cc_start: 0.7233 (m-80) cc_final: 0.6680 (m-10) outliers start: 24 outliers final: 17 residues processed: 97 average time/residue: 0.0769 time to fit residues: 8.4377 Evaluate side-chains 103 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 82 time to evaluate : 0.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain C residue 319 THR Chi-restraints excluded: chain C residue 343 LYS Chi-restraints excluded: chain C residue 348 ASP Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 378 PHE Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain D residue 328 ILE Chi-restraints excluded: chain D residue 347 LYS Chi-restraints excluded: chain D residue 350 VAL Chi-restraints excluded: chain D residue 373 THR Chi-restraints excluded: chain D residue 375 LYS Chi-restraints excluded: chain E residue 307 GLN Chi-restraints excluded: chain E residue 324 SER Chi-restraints excluded: chain E residue 349 ARG Chi-restraints excluded: chain E residue 357 LEU Chi-restraints excluded: chain F residue 350 VAL 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 35 optimal weight: 10.0000 chunk 29 optimal weight: 8.9990 chunk 5 optimal weight: 9.9990 chunk 6 optimal weight: 7.9990 chunk 3 optimal weight: 2.9990 chunk 10 optimal weight: 0.0770 chunk 20 optimal weight: 8.9990 chunk 33 optimal weight: 10.0000 chunk 30 optimal weight: 5.9990 chunk 27 optimal weight: 7.9990 chunk 9 optimal weight: 20.0000 overall best weight: 5.0146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 327 ASN ** D 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 = 0.4933 r_free = 0.4933 target = 0.272876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.5348 r_free = 0.5348 target = 0.205746 restraints weight = 5121.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.5372 r_free = 0.5372 target = 0.208533 restraints weight = 3338.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.5409 r_free = 0.5409 target = 0.210616 restraints weight = 2499.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.5415 r_free = 0.5415 target = 0.211814 restraints weight = 1999.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.5418 r_free = 0.5418 target = 0.212243 restraints weight = 1716.221| |-----------------------------------------------------------------------------| r_work (final): 0.4868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 moved from start: 0.5406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.026 3354 Z= 0.211 Angle : 0.813 7.839 4488 Z= 0.408 Chirality : 0.050 0.144 504 Planarity : 0.006 0.041 570 Dihedral : 7.032 21.173 438 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.62 % Favored : 92.38 % Rotamer: Outliers : 6.35 % Allowed : 17.46 % Favored : 76.19 % 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 are not related in a simple way. whole: -3.21 (0.32), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.43 (0.24), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 349 TYR 0.017 0.004 TYR F 310 PHE 0.015 0.001 PHE F 346 HIS 0.006 0.001 HIS A 362 Details of bonding type rmsd/Z covalent geometry : bond 0.00469 / 0.21 ( 3354) covalent geometry : angle 0.81317 / 0.41 ( 4488) hydrogen bonds : bond 0.02630 / 1.55 ( 39) hydrogen bonds : angle 5.46782 / 3.67 ( 117) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 88 time to evaluate : 0.131 Fit side-chains REVERT: A 325 LEU cc_start: 0.4293 (OUTLIER) cc_final: 0.3977 (pp) REVERT: A 340 LYS cc_start: 0.5126 (tppt) cc_final: 0.4563 (tppt) REVERT: A 347 LYS cc_start: 0.8433 (mmtm) cc_final: 0.8070 (mptt) REVERT: A 375 LYS cc_start: 0.8198 (mtpt) cc_final: 0.7901 (mttt) REVERT: B 347 LYS cc_start: 0.7747 (mttm) cc_final: 0.7435 (pttm) REVERT: B 352 SER cc_start: 0.8722 (t) cc_final: 0.8400 (t) REVERT: C 317 LYS cc_start: 0.8347 (mptt) cc_final: 0.8111 (mttt) REVERT: C 321 LYS cc_start: 0.8789 (OUTLIER) cc_final: 0.8285 (mtmm) REVERT: C 378 PHE cc_start: 0.7665 (OUTLIER) cc_final: 0.7098 (t80) REVERT: E 321 LYS cc_start: 0.8481 (mttt) cc_final: 0.8273 (mttp) REVERT: E 342 GLU cc_start: 0.7644 (tp30) cc_final: 0.7439 (tp30) REVERT: E 343 LYS cc_start: 0.8746 (tttm) cc_final: 0.8472 (tttm) REVERT: E 349 ARG cc_start: 0.7125 (OUTLIER) cc_final: 0.6875 (mpt-90) REVERT: E 357 LEU cc_start: 0.8915 (OUTLIER) cc_final: 0.8680 (tt) REVERT: E 369 LYS cc_start: 0.8358 (mtpt) cc_final: 0.7935 (mttt) REVERT: F 372 GLU cc_start: 0.7696 (mm-30) cc_final: 0.7331 (tm-30) REVERT: F 378 PHE cc_start: 0.7265 (m-80) cc_final: 0.6741 (m-10) outliers start: 24 outliers final: 18 residues processed: 99 average time/residue: 0.1027 time to fit residues: 11.4177 Evaluate side-chains 105 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 82 time to evaluate : 0.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain C residue 319 THR Chi-restraints excluded: chain C residue 321 LYS Chi-restraints excluded: chain C residue 340 LYS Chi-restraints excluded: chain C residue 343 LYS Chi-restraints excluded: chain C residue 348 ASP Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 378 PHE Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain D residue 328 ILE Chi-restraints excluded: chain D residue 343 LYS Chi-restraints excluded: chain D residue 347 LYS Chi-restraints excluded: chain D residue 350 VAL Chi-restraints excluded: chain D residue 373 THR Chi-restraints excluded: chain D residue 375 LYS Chi-restraints excluded: chain E residue 324 SER Chi-restraints excluded: chain E residue 349 ARG Chi-restraints excluded: chain E residue 357 LEU Chi-restraints excluded: chain F residue 350 VAL 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 8 optimal weight: 4.9990 chunk 37 optimal weight: 20.0000 chunk 4 optimal weight: 9.9990 chunk 24 optimal weight: 9.9990 chunk 17 optimal weight: 0.5980 chunk 18 optimal weight: 9.9990 chunk 9 optimal weight: 20.0000 chunk 31 optimal weight: 5.9990 chunk 28 optimal weight: 9.9990 chunk 22 optimal weight: 8.9990 chunk 36 optimal weight: 10.0000 overall best weight: 6.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 307 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4920 r_free = 0.4920 target = 0.271576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.5332 r_free = 0.5332 target = 0.203726 restraints weight = 5198.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.5346 r_free = 0.5346 target = 0.206486 restraints weight = 3339.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.5390 r_free = 0.5390 target = 0.208490 restraints weight = 2482.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.5395 r_free = 0.5395 target = 0.209430 restraints weight = 2005.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.5416 r_free = 0.5416 target = 0.210653 restraints weight = 1770.130| |-----------------------------------------------------------------------------| r_work (final): 0.4848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7595 moved from start: 0.5575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.032 3354 Z= 0.249 Angle : 0.857 7.842 4488 Z= 0.436 Chirality : 0.051 0.152 504 Planarity : 0.006 0.041 570 Dihedral : 7.314 21.622 438 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.81 % Favored : 91.19 % Rotamer: Outliers : 7.14 % Allowed : 18.52 % Favored : 74.34 % 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 are not related in a simple way. whole: -3.35 (0.32), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.55 (0.24), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 349 TYR 0.025 0.005 TYR F 310 PHE 0.021 0.002 PHE F 346 HIS 0.008 0.002 HIS A 362 Details of bonding type rmsd/Z covalent geometry : bond 0.00551 / 0.25 ( 3354) covalent geometry : angle 0.85724 / 0.44 ( 4488) hydrogen bonds : bond 0.02877 / 1.71 ( 39) hydrogen bonds : angle 5.70906 / 3.82 ( 117) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 88 time to evaluate : 0.107 Fit side-chains REVERT: A 325 LEU cc_start: 0.4367 (OUTLIER) cc_final: 0.4035 (pp) REVERT: A 340 LYS cc_start: 0.5320 (tppt) cc_final: 0.4416 (tppt) REVERT: A 347 LYS cc_start: 0.8481 (mmtm) cc_final: 0.8026 (mptt) REVERT: A 375 LYS cc_start: 0.8210 (mtpt) cc_final: 0.7900 (mttt) REVERT: B 347 LYS cc_start: 0.7863 (mttm) cc_final: 0.7513 (pttp) REVERT: B 352 SER cc_start: 0.8765 (t) cc_final: 0.8423 (t) REVERT: C 317 LYS cc_start: 0.8349 (mptt) cc_final: 0.8099 (mttt) REVERT: C 321 LYS cc_start: 0.8817 (OUTLIER) cc_final: 0.8330 (mtmm) REVERT: C 343 LYS cc_start: 0.7268 (OUTLIER) cc_final: 0.7060 (pttp) REVERT: C 378 PHE cc_start: 0.7698 (OUTLIER) cc_final: 0.7128 (t80) REVERT: D 317 LYS cc_start: 0.8134 (mttp) cc_final: 0.7126 (tmtt) REVERT: D 342 GLU cc_start: 0.7266 (tp30) cc_final: 0.6319 (mp0) REVERT: D 372 GLU cc_start: 0.8381 (mt-10) cc_final: 0.8130 (mt-10) REVERT: E 343 LYS cc_start: 0.8757 (tttm) cc_final: 0.8442 (tmtm) REVERT: E 349 ARG cc_start: 0.7218 (OUTLIER) cc_final: 0.6837 (mpt-90) REVERT: E 357 LEU cc_start: 0.8964 (OUTLIER) cc_final: 0.8716 (tt) REVERT: E 372 GLU cc_start: 0.8154 (tp30) cc_final: 0.7641 (tp30) REVERT: F 372 GLU cc_start: 0.8048 (OUTLIER) cc_final: 0.7629 (tm-30) REVERT: F 378 PHE cc_start: 0.7315 (m-80) cc_final: 0.6754 (m-10) outliers start: 27 outliers final: 16 residues processed: 103 average time/residue: 0.0893 time to fit residues: 10.3461 Evaluate side-chains 108 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 85 time to evaluate : 0.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain C residue 319 THR Chi-restraints excluded: chain C residue 321 LYS Chi-restraints excluded: chain C residue 343 LYS Chi-restraints excluded: chain C residue 348 ASP Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 378 PHE Chi-restraints excluded: chain D residue 316 SER Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain D residue 328 ILE Chi-restraints excluded: chain D residue 343 LYS Chi-restraints excluded: chain D residue 347 LYS Chi-restraints excluded: chain D residue 350 VAL Chi-restraints excluded: chain D residue 373 THR Chi-restraints excluded: chain D residue 375 LYS Chi-restraints excluded: chain E residue 324 SER Chi-restraints excluded: chain E residue 349 ARG Chi-restraints excluded: chain E residue 357 LEU Chi-restraints excluded: chain F residue 325 LEU Chi-restraints excluded: chain F residue 350 VAL Chi-restraints excluded: chain F residue 372 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 9 optimal weight: 3.9990 chunk 32 optimal weight: 10.0000 chunk 30 optimal weight: 30.0000 chunk 28 optimal weight: 9.9990 chunk 15 optimal weight: 10.0000 chunk 25 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 36 optimal weight: 0.4980 chunk 12 optimal weight: 0.0870 chunk 14 optimal weight: 5.9990 chunk 19 optimal weight: 0.4980 overall best weight: 0.8160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 307 GLN F 330 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5259 r_free = 0.5259 target = 0.352988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 95)----------------| | r_work = 0.5850 r_free = 0.5850 target = 0.266214 restraints weight = 5644.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.5881 r_free = 0.5881 target = 0.269547 restraints weight = 3450.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.5906 r_free = 0.5906 target = 0.271783 restraints weight = 2453.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.5909 r_free = 0.5909 target = 0.272783 restraints weight = 1920.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.5937 r_free = 0.5937 target = 0.274167 restraints weight = 1679.733| |-----------------------------------------------------------------------------| r_work (final): 0.4966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7399 moved from start: 0.5962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3354 Z= 0.116 Angle : 0.723 8.168 4488 Z= 0.358 Chirality : 0.049 0.128 504 Planarity : 0.005 0.048 570 Dihedral : 5.980 18.272 438 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 4.23 % Allowed : 20.90 % Favored : 74.87 % 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 are not related in a simple way. whole: -2.92 (0.33), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.21 (0.25), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 349 TYR 0.013 0.002 TYR C 310 PHE 0.014 0.001 PHE F 346 HIS 0.004 0.001 HIS F 330 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.12 ( 3354) covalent geometry : angle 0.72306 / 0.36 ( 4488) hydrogen bonds : bond 0.01454 / 0.84 ( 39) hydrogen bonds : angle 4.98090 / 3.38 ( 117) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 88 time to evaluate : 0.081 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 310 TYR cc_start: 0.7793 (t80) cc_final: 0.7581 (t80) REVERT: A 325 LEU cc_start: 0.4164 (OUTLIER) cc_final: 0.3854 (pp) REVERT: A 347 LYS cc_start: 0.8240 (mmtm) cc_final: 0.7941 (mptt) REVERT: B 319 THR cc_start: 0.8593 (m) cc_final: 0.8167 (m) REVERT: B 347 LYS cc_start: 0.7368 (mttm) cc_final: 0.7119 (pttm) REVERT: B 352 SER cc_start: 0.8572 (t) cc_final: 0.8256 (t) REVERT: C 317 LYS cc_start: 0.7975 (mptt) cc_final: 0.7773 (mttt) REVERT: C 321 LYS cc_start: 0.8611 (OUTLIER) cc_final: 0.8070 (mtmm) REVERT: C 327 ASN cc_start: 0.8453 (t0) cc_final: 0.7596 (p0) REVERT: C 357 LEU cc_start: 0.8307 (OUTLIER) cc_final: 0.7984 (tt) REVERT: C 378 PHE cc_start: 0.7509 (OUTLIER) cc_final: 0.7189 (t80) REVERT: D 327 ASN cc_start: 0.8801 (t0) cc_final: 0.8580 (t0) REVERT: D 342 GLU cc_start: 0.7269 (tp30) cc_final: 0.6513 (mp0) REVERT: D 349 ARG cc_start: 0.7325 (mtm180) cc_final: 0.7035 (mtt180) REVERT: E 357 LEU cc_start: 0.8663 (OUTLIER) cc_final: 0.8340 (tt) REVERT: F 363 VAL cc_start: 0.8795 (t) cc_final: 0.8494 (t) REVERT: F 378 PHE cc_start: 0.7050 (m-80) cc_final: 0.6568 (m-10) outliers start: 16 outliers final: 6 residues processed: 96 average time/residue: 0.0894 time to fit residues: 9.7804 Evaluate side-chains 89 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 78 time to evaluate : 0.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain C residue 319 THR Chi-restraints excluded: chain C residue 321 LYS Chi-restraints excluded: chain C residue 348 ASP Chi-restraints excluded: chain C residue 357 LEU Chi-restraints excluded: chain C residue 378 PHE Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain D residue 347 LYS Chi-restraints excluded: chain E residue 324 SER Chi-restraints excluded: chain E residue 357 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 9 optimal weight: 30.0000 chunk 32 optimal weight: 9.9990 chunk 27 optimal weight: 9.9990 chunk 11 optimal weight: 0.9990 chunk 23 optimal weight: 10.0000 chunk 41 optimal weight: 6.9990 chunk 24 optimal weight: 9.9990 chunk 22 optimal weight: 7.9990 chunk 13 optimal weight: 10.0000 chunk 31 optimal weight: 7.9990 chunk 14 optimal weight: 20.0000 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 307 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 = 0.4884 r_free = 0.4884 target = 0.270227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.5317 r_free = 0.5317 target = 0.201177 restraints weight = 5211.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.5351 r_free = 0.5351 target = 0.204290 restraints weight = 3146.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.5375 r_free = 0.5375 target = 0.206376 restraints weight = 2251.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.5380 r_free = 0.5380 target = 0.207387 restraints weight = 1787.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.5385 r_free = 0.5385 target = 0.208366 restraints weight = 1557.351| |-----------------------------------------------------------------------------| r_work (final): 0.4812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 moved from start: 0.5902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 3354 Z= 0.281 Angle : 0.887 7.792 4488 Z= 0.454 Chirality : 0.052 0.187 504 Planarity : 0.008 0.099 570 Dihedral : 7.219 21.912 438 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.29 % Favored : 90.71 % Rotamer: Outliers : 3.17 % Allowed : 23.02 % Favored : 73.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.24 (0.33), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.46 (0.25), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.002 ARG B 349 TYR 0.025 0.005 TYR F 310 PHE 0.013 0.002 PHE F 346 HIS 0.015 0.002 HIS F 330 Details of bonding type rmsd/Z covalent geometry : bond 0.00627 / 0.28 ( 3354) covalent geometry : angle 0.88685 / 0.45 ( 4488) hydrogen bonds : bond 0.02851 / 1.71 ( 39) hydrogen bonds : angle 5.73867 / 3.83 ( 117) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 90 time to evaluate : 0.129 Fit side-chains revert: symmetry clash REVERT: A 325 LEU cc_start: 0.4559 (OUTLIER) cc_final: 0.4210 (pp) REVERT: A 347 LYS cc_start: 0.8399 (mmtm) cc_final: 0.7887 (mptt) REVERT: A 375 LYS cc_start: 0.8188 (mtpt) cc_final: 0.7863 (mttt) REVERT: B 347 LYS cc_start: 0.7826 (mttm) cc_final: 0.7553 (pttp) REVERT: B 352 SER cc_start: 0.8761 (t) cc_final: 0.8457 (t) REVERT: C 321 LYS cc_start: 0.8776 (OUTLIER) cc_final: 0.8288 (mtmm) REVERT: C 378 PHE cc_start: 0.7689 (m-80) cc_final: 0.7248 (t80) REVERT: D 317 LYS cc_start: 0.8141 (mttp) cc_final: 0.7916 (ttmt) REVERT: E 343 LYS cc_start: 0.8673 (tttm) cc_final: 0.8376 (tttm) REVERT: E 349 ARG cc_start: 0.7236 (mpt-90) cc_final: 0.6742 (mpt-90) REVERT: E 357 LEU cc_start: 0.8997 (OUTLIER) cc_final: 0.8764 (tt) REVERT: E 369 LYS cc_start: 0.8526 (mtpt) cc_final: 0.8143 (mttt) REVERT: E 372 GLU cc_start: 0.8071 (tp30) cc_final: 0.7614 (tp30) REVERT: F 372 GLU cc_start: 0.7930 (mm-30) cc_final: 0.7507 (tm-30) REVERT: F 378 PHE cc_start: 0.7296 (m-80) cc_final: 0.6726 (m-10) outliers start: 12 outliers final: 8 residues processed: 94 average time/residue: 0.1184 time to fit residues: 12.4339 Evaluate side-chains 99 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 88 time to evaluate : 0.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain C residue 319 THR Chi-restraints excluded: chain C residue 321 LYS Chi-restraints excluded: chain C residue 348 ASP Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain D residue 347 LYS Chi-restraints excluded: chain D residue 373 THR Chi-restraints excluded: chain E residue 324 SER Chi-restraints excluded: chain E residue 357 LEU Chi-restraints excluded: chain F residue 307 GLN Chi-restraints excluded: chain F residue 328 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 10 optimal weight: 2.9990 chunk 26 optimal weight: 4.9990 chunk 11 optimal weight: 5.9990 chunk 18 optimal weight: 0.0270 chunk 13 optimal weight: 10.0000 chunk 3 optimal weight: 0.8980 chunk 20 optimal weight: 6.9990 chunk 27 optimal weight: 5.9990 chunk 2 optimal weight: 7.9990 chunk 30 optimal weight: 0.9990 chunk 7 optimal weight: 20.0000 overall best weight: 1.9844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 307 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4955 r_free = 0.4955 target = 0.281293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.5410 r_free = 0.5410 target = 0.214207 restraints weight = 5169.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.5440 r_free = 0.5440 target = 0.217170 restraints weight = 3236.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.5453 r_free = 0.5453 target = 0.219132 restraints weight = 2345.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.5481 r_free = 0.5481 target = 0.220596 restraints weight = 1865.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.5486 r_free = 0.5486 target = 0.221443 restraints weight = 1576.351| |-----------------------------------------------------------------------------| r_work (final): 0.4889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7492 moved from start: 0.6103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 3354 Z= 0.144 Angle : 0.774 7.911 4488 Z= 0.387 Chirality : 0.049 0.185 504 Planarity : 0.007 0.093 570 Dihedral : 6.442 18.397 438 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.14 % Favored : 92.86 % Rotamer: Outliers : 3.17 % Allowed : 23.28 % Favored : 73.54 % 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 are not related in a simple way. whole: -3.04 (0.33), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.31 (0.26), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 349 TYR 0.013 0.002 TYR C 310 PHE 0.014 0.001 PHE F 346 HIS 0.009 0.001 HIS F 330 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.14 ( 3354) covalent geometry : angle 0.77426 / 0.39 ( 4488) hydrogen bonds : bond 0.02041 / 1.23 ( 39) hydrogen bonds : angle 5.31500 / 3.53 ( 117) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 747.79 seconds wall clock time: 13 minutes 36.58 seconds (816.58 seconds total)