Starting phenix.real_space_refine on Mon Feb 10 22:52:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qcr_18333/02_2025/8qcr_18333.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qcr_18333/02_2025/8qcr_18333.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.75 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8qcr_18333/02_2025/8qcr_18333.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qcr_18333/02_2025/8qcr_18333.map" model { file = "/net/cci-nas-00/data/ceres_data/8qcr_18333/02_2025/8qcr_18333.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qcr_18333/02_2025/8qcr_18333.cif" } resolution = 2.75 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= 0.001 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: 5 Type Number sf(0) Gaussians S 3 5.16 5 C 966 2.51 5 N 285 2.21 5 O 291 1.98 5 H 1608 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 3153 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 1051 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 1051 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 3, 'TRANS': 64} Chain: "C" Number of atoms: 1051 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 1051 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 3, 'TRANS': 64} Chain: "E" Number of atoms: 1051 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 1051 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 3, 'TRANS': 64} Time building chain proxies: 2.74, per 1000 atoms: 0.87 Number of scatterers: 3153 At special positions: 0 Unit cell: (99.704, 70.864, 37.08, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 3 16.00 O 291 8.00 N 285 7.00 C 966 6.00 H 1608 1.00 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: 0.70 Conformation dependent library (CDL) restraints added in 205.4 milliseconds 396 Ramachandran restraints generated. 198 Oldfield, 0 Emsley, 198 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 354 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 10 sheets defined 0.0% alpha, 64.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.37 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 309 through 310 removed outlier: 6.614A pdb=" N VAL C 309 " --> pdb=" O TYR E 310 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 313 through 314 removed outlier: 6.715A pdb=" N VAL C 313 " --> pdb=" O ASP E 314 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 317 through 325 removed outlier: 6.754A pdb=" N VAL A 318 " --> pdb=" O THR E 319 " (cutoff:3.500A) removed outlier: 8.060A pdb=" N LYS E 321 " --> pdb=" O VAL A 318 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N SER A 320 " --> pdb=" O LYS E 321 " (cutoff:3.500A) removed outlier: 7.892A pdb=" N GLY E 323 " --> pdb=" O SER A 320 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N CYS A 322 " --> pdb=" O GLY E 323 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N LEU E 325 " --> pdb=" O CYS A 322 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N SER A 324 " --> pdb=" O LEU E 325 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 328 through 330 removed outlier: 6.313A pdb=" N ILE C 328 " --> pdb=" O HIS E 329 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 337 through 342 removed outlier: 6.513A pdb=" N VAL A 337 " --> pdb=" O GLU E 338 " (cutoff:3.500A) removed outlier: 7.901A pdb=" N LYS E 340 " --> pdb=" O VAL A 337 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N VAL A 339 " --> pdb=" O LYS E 340 " (cutoff:3.500A) removed outlier: 7.883A pdb=" N GLU E 342 " --> pdb=" O VAL A 339 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N SER A 341 " --> pdb=" O GLU E 342 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 345 through 346 removed outlier: 6.529A pdb=" N ASP C 345 " --> pdb=" O PHE E 346 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 350 through 362 removed outlier: 8.920A pdb=" N GLN A 351 " --> pdb=" O SER E 352 " (cutoff:3.500A) removed outlier: 10.505A pdb=" N ILE E 354 " --> pdb=" O GLN A 351 " (cutoff:3.500A) removed outlier: 9.159A pdb=" N LYS A 353 " --> pdb=" O ILE E 354 " (cutoff:3.500A) removed outlier: 10.114A pdb=" N SER E 356 " --> pdb=" O LYS A 353 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N GLY A 355 " --> pdb=" O SER E 356 " (cutoff:3.500A) removed outlier: 8.093A pdb=" N ASP E 358 " --> pdb=" O GLY A 355 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N LEU A 357 " --> pdb=" O ASP E 358 " (cutoff:3.500A) removed outlier: 7.884A pdb=" N ILE E 360 " --> pdb=" O LEU A 357 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N ASN A 359 " --> pdb=" O ILE E 360 " (cutoff:3.500A) removed outlier: 7.989A pdb=" N HIS E 362 " --> pdb=" O ASN A 359 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N THR A 361 " --> pdb=" O HIS E 362 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 350 through 362 removed outlier: 8.920A pdb=" N GLN A 351 " --> pdb=" O SER E 352 " (cutoff:3.500A) removed outlier: 10.505A pdb=" N ILE E 354 " --> pdb=" O GLN A 351 " (cutoff:3.500A) removed outlier: 9.159A pdb=" N LYS A 353 " --> pdb=" O ILE E 354 " (cutoff:3.500A) removed outlier: 10.114A pdb=" N SER E 356 " --> pdb=" O LYS A 353 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N GLY A 355 " --> pdb=" O SER E 356 " (cutoff:3.500A) removed outlier: 8.093A pdb=" N ASP E 358 " --> pdb=" O GLY A 355 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N LEU A 357 " --> pdb=" O ASP E 358 " (cutoff:3.500A) removed outlier: 7.884A pdb=" N ILE E 360 " --> pdb=" O LEU A 357 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N ASN A 359 " --> pdb=" O ILE E 360 " (cutoff:3.500A) removed outlier: 7.989A pdb=" N HIS E 362 " --> pdb=" O ASN A 359 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N THR A 361 " --> pdb=" O HIS E 362 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 368 through 374 removed outlier: 6.370A pdb=" N LYS C 369 " --> pdb=" O LYS E 370 " (cutoff:3.500A) removed outlier: 8.064A pdb=" N GLU E 372 " --> pdb=" O LYS C 369 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N ILE C 371 " --> pdb=" O GLU E 372 " (cutoff:3.500A) removed outlier: 8.101A pdb=" N HIS E 374 " --> pdb=" O ILE C 371 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N THR C 373 " --> pdb=" O HIS E 374 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 333 through 334 removed outlier: 6.871A pdb=" N GLY C 333 " --> pdb=" O GLY E 334 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 33 hydrogen bonds defined for protein. 99 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: 0.92 Time building geometry restraints manager: 0.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.95 - 1.12: 1605 1.12 - 1.29: 261 1.29 - 1.47: 487 1.47 - 1.64: 821 1.64 - 1.81: 3 Bond restraints: 3177 Sorted by residual: bond pdb=" N ILE C 308 " pdb=" H ILE C 308 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.69e+01 bond pdb=" N SER A 324 " pdb=" H SER A 324 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.69e+01 bond pdb=" N GLY C 326 " pdb=" H GLY C 326 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.68e+01 bond pdb=" N VAL C 309 " pdb=" H VAL C 309 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.68e+01 bond pdb=" ND2 ASN E 359 " pdb="HD21 ASN E 359 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.68e+01 ... (remaining 3172 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.43: 4867 2.43 - 4.87: 722 4.87 - 7.30: 203 7.30 - 9.74: 7 9.74 - 12.17: 3 Bond angle restraints: 5802 Sorted by residual: angle pdb=" CA ASP E 345 " pdb=" CB ASP E 345 " pdb=" CG ASP E 345 " ideal model delta sigma weight residual 112.60 118.01 -5.41 1.00e+00 1.00e+00 2.92e+01 angle pdb=" CA ASP A 358 " pdb=" CB ASP A 358 " pdb=" CG ASP A 358 " ideal model delta sigma weight residual 112.60 117.08 -4.48 1.00e+00 1.00e+00 2.01e+01 angle pdb=" CA ASP A 345 " pdb=" CB ASP A 345 " pdb=" CG ASP A 345 " ideal model delta sigma weight residual 112.60 117.06 -4.46 1.00e+00 1.00e+00 1.99e+01 angle pdb=" CA GLY E 355 " pdb=" C GLY E 355 " pdb=" N SER E 356 " ideal model delta sigma weight residual 114.84 119.43 -4.59 1.06e+00 8.90e-01 1.87e+01 angle pdb=" CB HIS E 362 " pdb=" CG HIS E 362 " pdb=" CD2 HIS E 362 " ideal model delta sigma weight residual 131.20 125.68 5.52 1.30e+00 5.92e-01 1.80e+01 ... (remaining 5797 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.36: 1277 13.36 - 26.71: 88 26.71 - 40.07: 33 40.07 - 53.42: 22 53.42 - 66.78: 41 Dihedral angle restraints: 1461 sinusoidal: 840 harmonic: 621 Sorted by residual: dihedral pdb=" CA LYS E 321 " pdb=" C LYS E 321 " pdb=" N CYS E 322 " pdb=" CA CYS E 322 " ideal model delta harmonic sigma weight residual 180.00 -158.34 -21.66 0 5.00e+00 4.00e-02 1.88e+01 dihedral pdb=" CA VAL C 350 " pdb=" C VAL C 350 " pdb=" N GLN C 351 " pdb=" CA GLN C 351 " ideal model delta harmonic sigma weight residual 180.00 159.56 20.44 0 5.00e+00 4.00e-02 1.67e+01 dihedral pdb=" CA VAL E 350 " pdb=" C VAL E 350 " pdb=" N GLN E 351 " pdb=" CA GLN E 351 " ideal model delta harmonic sigma weight residual 180.00 161.41 18.59 0 5.00e+00 4.00e-02 1.38e+01 ... (remaining 1458 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 115 0.052 - 0.104: 77 0.104 - 0.157: 27 0.157 - 0.209: 12 0.209 - 0.261: 3 Chirality restraints: 234 Sorted by residual: chirality pdb=" CA LYS C 343 " pdb=" N LYS C 343 " pdb=" C LYS C 343 " pdb=" CB LYS C 343 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.70e+00 chirality pdb=" CA LYS C 347 " pdb=" N LYS C 347 " pdb=" C LYS C 347 " pdb=" CB LYS C 347 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.21e+00 chirality pdb=" CA VAL E 337 " pdb=" N VAL E 337 " pdb=" C VAL E 337 " pdb=" CB VAL E 337 " both_signs ideal model delta sigma weight residual False 2.44 2.22 0.22 2.00e-01 2.50e+01 1.17e+00 ... (remaining 231 not shown) Planarity restraints: 459 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN E 368 " -0.090 2.00e-02 2.50e+03 7.98e-02 9.55e+01 pdb=" CG ASN E 368 " 0.035 2.00e-02 2.50e+03 pdb=" OD1 ASN E 368 " 0.054 2.00e-02 2.50e+03 pdb=" ND2 ASN E 368 " 0.058 2.00e-02 2.50e+03 pdb="HD21 ASN E 368 " 0.074 2.00e-02 2.50e+03 pdb="HD22 ASN E 368 " -0.131 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS E 362 " 0.068 2.00e-02 2.50e+03 3.97e-02 3.55e+01 pdb=" CG HIS E 362 " -0.052 2.00e-02 2.50e+03 pdb=" ND1 HIS E 362 " -0.030 2.00e-02 2.50e+03 pdb=" CD2 HIS E 362 " -0.041 2.00e-02 2.50e+03 pdb=" CE1 HIS E 362 " -0.010 2.00e-02 2.50e+03 pdb=" NE2 HIS E 362 " -0.027 2.00e-02 2.50e+03 pdb=" HD2 HIS E 362 " 0.014 2.00e-02 2.50e+03 pdb=" HE1 HIS E 362 " 0.041 2.00e-02 2.50e+03 pdb=" HE2 HIS E 362 " 0.038 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS A 362 " 0.064 2.00e-02 2.50e+03 3.67e-02 3.03e+01 pdb=" CG HIS A 362 " -0.051 2.00e-02 2.50e+03 pdb=" ND1 HIS A 362 " -0.023 2.00e-02 2.50e+03 pdb=" CD2 HIS A 362 " -0.043 2.00e-02 2.50e+03 pdb=" CE1 HIS A 362 " -0.007 2.00e-02 2.50e+03 pdb=" NE2 HIS A 362 " -0.020 2.00e-02 2.50e+03 pdb=" HD2 HIS A 362 " 0.013 2.00e-02 2.50e+03 pdb=" HE1 HIS A 362 " 0.031 2.00e-02 2.50e+03 pdb=" HE2 HIS A 362 " 0.038 2.00e-02 2.50e+03 ... (remaining 456 not shown) Histogram of nonbonded interaction distances: 1.55 - 2.16: 196 2.16 - 2.77: 5228 2.77 - 3.38: 8238 3.38 - 3.99: 10907 3.99 - 4.60: 15415 Nonbonded interactions: 39984 Sorted by model distance: nonbonded pdb=" OD1 ASP C 314 " pdb=" HG SER C 316 " model vdw 1.546 2.450 nonbonded pdb=" OD1 ASP E 314 " pdb=" HG SER E 316 " model vdw 1.575 2.450 nonbonded pdb=" OD1 ASP A 314 " pdb=" HG SER A 316 " model vdw 1.576 2.450 nonbonded pdb=" HG SER A 320 " pdb=" O GLY A 366 " model vdw 1.644 2.450 nonbonded pdb=" HG SER C 320 " pdb=" O GLY C 366 " model vdw 1.669 2.450 ... (remaining 39979 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 'C' selection = chain 'E' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.250 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: 0.050 Extract box with map and model: 0.110 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.510 Find NCS groups from input model: 0.080 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:12.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7705 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 0.035 1569 Z= 0.720 Angle : 1.777 5.847 2097 Z= 1.194 Chirality : 0.079 0.261 234 Planarity : 0.009 0.038 267 Dihedral : 9.596 42.499 606 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % 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: -1.85 (0.50), residues: 198 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.40 (0.38), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS C 330 PHE 0.042 0.021 PHE A 346 TYR 0.068 0.019 TYR C 310 ARG 0.002 0.001 ARG E 349 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 396 Ramachandran restraints generated. 198 Oldfield, 0 Emsley, 198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 396 Ramachandran restraints generated. 198 Oldfield, 0 Emsley, 198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 0.280 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 321 LYS cc_start: 0.8115 (mttt) cc_final: 0.7912 (mtpt) REVERT: A 347 LYS cc_start: 0.8466 (mttt) cc_final: 0.7559 (pmtt) REVERT: A 369 LYS cc_start: 0.8309 (ttmt) cc_final: 0.7992 (ttpt) REVERT: A 375 LYS cc_start: 0.7146 (tptm) cc_final: 0.6860 (tptt) REVERT: C 340 LYS cc_start: 0.7413 (mttt) cc_final: 0.7164 (ttmm) REVERT: C 345 ASP cc_start: 0.7491 (m-30) cc_final: 0.7001 (t70) REVERT: C 347 LYS cc_start: 0.8400 (mttt) cc_final: 0.8141 (mtpt) REVERT: C 349 ARG cc_start: 0.7573 (mtt180) cc_final: 0.6532 (mtt-85) REVERT: E 320 SER cc_start: 0.8567 (m) cc_final: 0.8255 (p) REVERT: E 321 LYS cc_start: 0.7395 (tttt) cc_final: 0.7089 (ttmp) REVERT: E 340 LYS cc_start: 0.7549 (mttt) cc_final: 0.7296 (ttmm) REVERT: E 369 LYS cc_start: 0.7591 (ttmt) cc_final: 0.7330 (ttpt) outliers start: 0 outliers final: 0 residues processed: 72 average time/residue: 2.9335 time to fit residues: 213.5997 Evaluate side-chains 49 residues out of total 177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 49 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 15 optimal weight: 0.9980 chunk 13 optimal weight: 0.9990 chunk 7 optimal weight: 0.9990 chunk 4 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 chunk 10 optimal weight: 0.2980 chunk 16 optimal weight: 0.9990 chunk 11 optimal weight: 0.8980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 327 ASN C 336 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.120146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.111369 restraints weight = 6359.754| |-----------------------------------------------------------------------------| r_work (start): 0.3892 rms_B_bonded: 1.84 r_work: 0.3798 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3708 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.3708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8541 moved from start: 0.3756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 1569 Z= 0.192 Angle : 0.612 3.968 2097 Z= 0.313 Chirality : 0.053 0.138 234 Planarity : 0.004 0.029 267 Dihedral : 6.194 16.912 207 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 1.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % Rotamer: Outliers : 2.82 % Allowed : 11.30 % Favored : 85.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.28 (0.51), residues: 198 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.97 (0.39), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS E 362 PHE 0.007 0.002 PHE E 346 TYR 0.010 0.002 TYR E 310 ARG 0.001 0.000 ARG E 349 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 396 Ramachandran restraints generated. 198 Oldfield, 0 Emsley, 198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 396 Ramachandran restraints generated. 198 Oldfield, 0 Emsley, 198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 54 time to evaluate : 0.275 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 347 LYS cc_start: 0.8694 (mttt) cc_final: 0.7856 (pmtt) REVERT: C 345 ASP cc_start: 0.7946 (m-30) cc_final: 0.7544 (t0) REVERT: C 349 ARG cc_start: 0.8281 (mtt180) cc_final: 0.7029 (mtt-85) REVERT: C 375 LYS cc_start: 0.6512 (OUTLIER) cc_final: 0.5193 (tmmt) REVERT: E 340 LYS cc_start: 0.8213 (mttt) cc_final: 0.7965 (ttmm) REVERT: E 347 LYS cc_start: 0.8570 (mttt) cc_final: 0.8358 (mptp) outliers start: 5 outliers final: 1 residues processed: 56 average time/residue: 3.4317 time to fit residues: 194.1386 Evaluate side-chains 46 residues out of total 177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 44 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 370 LYS Chi-restraints excluded: chain C residue 375 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 0 optimal weight: 3.9990 chunk 9 optimal weight: 3.9990 chunk 11 optimal weight: 0.0060 chunk 15 optimal weight: 1.9990 chunk 5 optimal weight: 4.9990 chunk 14 optimal weight: 0.0970 chunk 4 optimal weight: 0.7980 chunk 8 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 10 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 overall best weight: 0.7796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.122101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.114104 restraints weight = 6211.592| |-----------------------------------------------------------------------------| r_work (start): 0.3907 rms_B_bonded: 1.67 r_work: 0.3824 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.3743 rms_B_bonded: 3.09 restraints_weight: 0.2500 r_work (final): 0.3743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8578 moved from start: 0.4830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 1569 Z= 0.165 Angle : 0.539 4.948 2097 Z= 0.266 Chirality : 0.052 0.136 234 Planarity : 0.003 0.022 267 Dihedral : 5.366 14.394 207 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 1.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % Rotamer: Outliers : 2.82 % Allowed : 17.51 % Favored : 79.66 % 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: -0.93 (0.52), residues: 198 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.70 (0.39), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS E 362 PHE 0.005 0.001 PHE C 346 TYR 0.010 0.002 TYR E 310 ARG 0.003 0.001 ARG E 349 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 396 Ramachandran restraints generated. 198 Oldfield, 0 Emsley, 198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 396 Ramachandran restraints generated. 198 Oldfield, 0 Emsley, 198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 45 time to evaluate : 0.273 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 347 LYS cc_start: 0.8681 (mttt) cc_final: 0.7787 (pmtt) REVERT: C 345 ASP cc_start: 0.7906 (m-30) cc_final: 0.7641 (t0) REVERT: C 349 ARG cc_start: 0.8326 (mtt180) cc_final: 0.7203 (mtt-85) REVERT: C 375 LYS cc_start: 0.6607 (OUTLIER) cc_final: 0.5310 (tmmt) REVERT: E 349 ARG cc_start: 0.7972 (mtm180) cc_final: 0.7377 (mtt180) outliers start: 5 outliers final: 2 residues processed: 47 average time/residue: 3.5389 time to fit residues: 168.0755 Evaluate side-chains 43 residues out of total 177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 40 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 370 LYS Chi-restraints excluded: chain C residue 375 LYS Chi-restraints excluded: chain E residue 321 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 8 optimal weight: 0.9980 chunk 9 optimal weight: 4.9990 chunk 14 optimal weight: 0.8980 chunk 5 optimal weight: 3.9990 chunk 1 optimal weight: 0.9990 chunk 16 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 327 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.119664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.111388 restraints weight = 6223.004| |-----------------------------------------------------------------------------| r_work (start): 0.3868 rms_B_bonded: 1.70 r_work: 0.3790 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.3711 rms_B_bonded: 3.07 restraints_weight: 0.2500 r_work (final): 0.3711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8602 moved from start: 0.5176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 1569 Z= 0.191 Angle : 0.528 4.651 2097 Z= 0.259 Chirality : 0.051 0.127 234 Planarity : 0.002 0.017 267 Dihedral : 5.065 14.742 207 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % Rotamer: Outliers : 2.82 % Allowed : 18.08 % Favored : 79.10 % 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: -0.74 (0.53), residues: 198 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.55 (0.41), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 362 PHE 0.007 0.001 PHE E 346 TYR 0.010 0.002 TYR E 310 ARG 0.001 0.000 ARG A 349 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 396 Ramachandran restraints generated. 198 Oldfield, 0 Emsley, 198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 396 Ramachandran restraints generated. 198 Oldfield, 0 Emsley, 198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 39 time to evaluate : 0.282 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 347 LYS cc_start: 0.8671 (mttt) cc_final: 0.7745 (pmtt) REVERT: C 345 ASP cc_start: 0.7890 (m-30) cc_final: 0.7665 (t0) REVERT: C 349 ARG cc_start: 0.8365 (mtt180) cc_final: 0.7188 (mtt-85) REVERT: C 375 LYS cc_start: 0.6632 (OUTLIER) cc_final: 0.5466 (tmmt) REVERT: E 347 LYS cc_start: 0.8596 (OUTLIER) cc_final: 0.8370 (mptp) REVERT: E 349 ARG cc_start: 0.8008 (mtm180) cc_final: 0.7405 (mtt180) REVERT: E 358 ASP cc_start: 0.8303 (t70) cc_final: 0.8028 (t0) outliers start: 5 outliers final: 1 residues processed: 40 average time/residue: 3.5881 time to fit residues: 145.1327 Evaluate side-chains 41 residues out of total 177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 38 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 375 LYS Chi-restraints excluded: chain E residue 321 LYS Chi-restraints excluded: chain E residue 347 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 5 optimal weight: 3.9990 chunk 8 optimal weight: 0.0070 chunk 9 optimal weight: 0.5980 chunk 7 optimal weight: 1.9990 chunk 3 optimal weight: 0.0070 chunk 6 optimal weight: 2.9990 chunk 2 optimal weight: 0.6980 chunk 4 optimal weight: 0.7980 chunk 15 optimal weight: 1.9990 chunk 12 optimal weight: 0.5980 chunk 17 optimal weight: 1.9990 overall best weight: 0.3816 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 336 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.123529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.115449 restraints weight = 6127.752| |-----------------------------------------------------------------------------| r_work (start): 0.3918 rms_B_bonded: 1.70 r_work: 0.3841 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.3764 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.3764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8585 moved from start: 0.5323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 1569 Z= 0.139 Angle : 0.509 5.021 2097 Z= 0.244 Chirality : 0.052 0.126 234 Planarity : 0.002 0.017 267 Dihedral : 4.676 12.542 207 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 1.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % Rotamer: Outliers : 2.82 % Allowed : 18.64 % Favored : 78.53 % 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: -0.68 (0.54), residues: 198 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.51 (0.41), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS C 362 PHE 0.001 0.000 PHE C 346 TYR 0.007 0.002 TYR E 310 ARG 0.001 0.000 ARG A 349 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 396 Ramachandran restraints generated. 198 Oldfield, 0 Emsley, 198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 396 Ramachandran restraints generated. 198 Oldfield, 0 Emsley, 198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 38 time to evaluate : 0.257 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 349 ARG cc_start: 0.8341 (mtt180) cc_final: 0.7197 (mtt-85) REVERT: E 349 ARG cc_start: 0.8016 (mtm180) cc_final: 0.7494 (mtt180) REVERT: E 358 ASP cc_start: 0.8240 (t70) cc_final: 0.8012 (t0) outliers start: 5 outliers final: 1 residues processed: 40 average time/residue: 3.5306 time to fit residues: 142.7596 Evaluate side-chains 35 residues out of total 177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 34 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 321 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 4 optimal weight: 0.8980 chunk 11 optimal weight: 3.9990 chunk 17 optimal weight: 0.9980 chunk 9 optimal weight: 4.9990 chunk 7 optimal weight: 1.9990 chunk 1 optimal weight: 3.9990 chunk 12 optimal weight: 3.9990 chunk 2 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 6 optimal weight: 0.5980 chunk 5 optimal weight: 0.8980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.119632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 23)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.110999 restraints weight = 6776.228| |-----------------------------------------------------------------------------| r_work (start): 0.3878 rms_B_bonded: 1.88 r_work: 0.3794 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3713 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.3713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8589 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 : 0.002 0.023 1569 Z= 0.165 Angle : 0.510 4.794 2097 Z= 0.244 Chirality : 0.051 0.125 234 Planarity : 0.002 0.018 267 Dihedral : 4.624 12.963 207 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 1.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % Rotamer: Outliers : 2.82 % Allowed : 18.64 % Favored : 78.53 % 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: -0.65 (0.54), residues: 198 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.49 (0.41), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 374 PHE 0.004 0.001 PHE E 346 TYR 0.008 0.002 TYR E 310 ARG 0.001 0.000 ARG A 349 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 396 Ramachandran restraints generated. 198 Oldfield, 0 Emsley, 198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 396 Ramachandran restraints generated. 198 Oldfield, 0 Emsley, 198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 35 time to evaluate : 0.253 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 349 ARG cc_start: 0.8346 (mtt180) cc_final: 0.7172 (mtt-85) REVERT: E 347 LYS cc_start: 0.8532 (OUTLIER) cc_final: 0.8277 (mmtm) REVERT: E 349 ARG cc_start: 0.7980 (mtm180) cc_final: 0.7493 (mtt180) outliers start: 5 outliers final: 2 residues processed: 38 average time/residue: 3.4409 time to fit residues: 132.2246 Evaluate side-chains 37 residues out of total 177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 34 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 348 ASP Chi-restraints excluded: chain E residue 321 LYS Chi-restraints excluded: chain E residue 347 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 9 optimal weight: 0.0870 chunk 0 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 15 optimal weight: 0.7980 chunk 8 optimal weight: 0.6980 chunk 7 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 chunk 4 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 11 optimal weight: 0.7980 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.120434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.111773 restraints weight = 6572.654| |-----------------------------------------------------------------------------| r_work (start): 0.3890 rms_B_bonded: 1.84 r_work: 0.3807 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3727 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.3727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8580 moved from start: 0.5478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 1569 Z= 0.151 Angle : 0.506 4.698 2097 Z= 0.242 Chirality : 0.051 0.124 234 Planarity : 0.003 0.021 267 Dihedral : 4.517 11.874 207 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 1.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % Rotamer: Outliers : 1.69 % Allowed : 18.64 % Favored : 79.66 % 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: -0.63 (0.54), residues: 198 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.47 (0.41), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 374 PHE 0.004 0.001 PHE E 346 TYR 0.008 0.002 TYR E 310 ARG 0.002 0.000 ARG A 349 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 396 Ramachandran restraints generated. 198 Oldfield, 0 Emsley, 198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 396 Ramachandran restraints generated. 198 Oldfield, 0 Emsley, 198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 34 time to evaluate : 0.299 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 349 ARG cc_start: 0.8316 (mtt180) cc_final: 0.7153 (mtt-85) REVERT: E 347 LYS cc_start: 0.8497 (OUTLIER) cc_final: 0.8240 (mmtm) REVERT: E 349 ARG cc_start: 0.7977 (mtm180) cc_final: 0.7525 (mtt180) REVERT: E 358 ASP cc_start: 0.8345 (t70) cc_final: 0.8080 (t0) outliers start: 3 outliers final: 2 residues processed: 36 average time/residue: 3.3800 time to fit residues: 123.1297 Evaluate side-chains 36 residues out of total 177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 33 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 348 ASP Chi-restraints excluded: chain E residue 321 LYS Chi-restraints excluded: chain E residue 347 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 0 optimal weight: 3.9990 chunk 7 optimal weight: 3.9990 chunk 15 optimal weight: 5.9990 chunk 14 optimal weight: 0.9980 chunk 10 optimal weight: 3.9990 chunk 11 optimal weight: 0.8980 chunk 1 optimal weight: 0.8980 chunk 9 optimal weight: 0.8980 chunk 12 optimal weight: 0.8980 chunk 3 optimal weight: 4.9990 chunk 4 optimal weight: 0.7980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.119473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.110858 restraints weight = 6500.696| |-----------------------------------------------------------------------------| r_work (start): 0.3881 rms_B_bonded: 1.84 r_work: 0.3796 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.3714 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.3714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8594 moved from start: 0.5577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 1569 Z= 0.169 Angle : 0.510 5.375 2097 Z= 0.244 Chirality : 0.051 0.125 234 Planarity : 0.003 0.021 267 Dihedral : 4.462 12.075 207 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 2.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % Rotamer: Outliers : 1.69 % Allowed : 18.08 % Favored : 80.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.54 (0.55), residues: 198 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.40 (0.42), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 374 PHE 0.004 0.001 PHE E 346 TYR 0.008 0.002 TYR E 310 ARG 0.002 0.000 ARG A 349 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 396 Ramachandran restraints generated. 198 Oldfield, 0 Emsley, 198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 396 Ramachandran restraints generated. 198 Oldfield, 0 Emsley, 198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 32 time to evaluate : 0.418 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 349 ARG cc_start: 0.8323 (mtt180) cc_final: 0.7165 (mtt-85) REVERT: E 347 LYS cc_start: 0.8497 (OUTLIER) cc_final: 0.8246 (mmtm) REVERT: E 349 ARG cc_start: 0.8008 (mtm180) cc_final: 0.7527 (mtt180) outliers start: 3 outliers final: 2 residues processed: 34 average time/residue: 3.5152 time to fit residues: 120.9712 Evaluate side-chains 35 residues out of total 177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 32 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 348 ASP Chi-restraints excluded: chain E residue 321 LYS Chi-restraints excluded: chain E residue 347 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 7 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 12 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 14 optimal weight: 0.6980 chunk 3 optimal weight: 4.9990 chunk 6 optimal weight: 0.5980 chunk 17 optimal weight: 0.5980 chunk 0 optimal weight: 0.5980 chunk 11 optimal weight: 0.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.120802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.112073 restraints weight = 6556.995| |-----------------------------------------------------------------------------| r_work (start): 0.3897 rms_B_bonded: 1.87 r_work: 0.3810 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3729 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.3729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8583 moved from start: 0.5655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 1569 Z= 0.150 Angle : 0.505 5.806 2097 Z= 0.240 Chirality : 0.051 0.122 234 Planarity : 0.003 0.023 267 Dihedral : 4.312 11.235 207 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 1.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % Rotamer: Outliers : 1.69 % Allowed : 18.64 % Favored : 79.66 % 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: -0.52 (0.55), residues: 198 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.38 (0.42), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS E 362 PHE 0.002 0.001 PHE E 346 TYR 0.006 0.002 TYR E 310 ARG 0.000 0.000 ARG C 349 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 396 Ramachandran restraints generated. 198 Oldfield, 0 Emsley, 198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 396 Ramachandran restraints generated. 198 Oldfield, 0 Emsley, 198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 30 time to evaluate : 0.281 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 349 ARG cc_start: 0.8283 (mtt180) cc_final: 0.7140 (mtt-85) REVERT: E 321 LYS cc_start: 0.8177 (OUTLIER) cc_final: 0.7887 (mtpt) REVERT: E 349 ARG cc_start: 0.8011 (mtm180) cc_final: 0.7518 (mtt180) outliers start: 3 outliers final: 1 residues processed: 32 average time/residue: 3.4598 time to fit residues: 112.0571 Evaluate side-chains 32 residues out of total 177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 30 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 348 ASP Chi-restraints excluded: chain E residue 321 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 0 optimal weight: 3.9990 chunk 12 optimal weight: 0.8980 chunk 5 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 3 optimal weight: 0.0170 chunk 9 optimal weight: 4.9990 chunk 10 optimal weight: 0.5980 chunk 11 optimal weight: 2.9990 chunk 1 optimal weight: 0.9990 chunk 8 optimal weight: 2.9990 chunk 13 optimal weight: 0.8980 overall best weight: 0.6820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.120690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.112023 restraints weight = 6463.692| |-----------------------------------------------------------------------------| r_work (start): 0.3897 rms_B_bonded: 1.85 r_work: 0.3812 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3731 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.3731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8589 moved from start: 0.5702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 1569 Z= 0.156 Angle : 0.500 5.299 2097 Z= 0.238 Chirality : 0.051 0.122 234 Planarity : 0.003 0.023 267 Dihedral : 4.259 11.423 207 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 1.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % Rotamer: Outliers : 1.13 % Allowed : 18.64 % Favored : 80.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.51 (0.56), residues: 198 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.38 (0.42), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS C 374 PHE 0.002 0.001 PHE C 346 TYR 0.007 0.002 TYR E 310 ARG 0.000 0.000 ARG E 349 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 396 Ramachandran restraints generated. 198 Oldfield, 0 Emsley, 198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 396 Ramachandran restraints generated. 198 Oldfield, 0 Emsley, 198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 32 time to evaluate : 0.254 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 349 ARG cc_start: 0.8286 (mtt180) cc_final: 0.7142 (mtt-85) REVERT: E 321 LYS cc_start: 0.8217 (OUTLIER) cc_final: 0.7938 (mtpt) REVERT: E 349 ARG cc_start: 0.7996 (mtm180) cc_final: 0.7511 (mtt180) outliers start: 2 outliers final: 0 residues processed: 33 average time/residue: 3.3769 time to fit residues: 112.7677 Evaluate side-chains 32 residues out of total 177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 31 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 321 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 15 optimal weight: 5.9990 chunk 13 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 chunk 8 optimal weight: 0.4980 chunk 10 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 5 optimal weight: 0.6980 chunk 7 optimal weight: 0.9990 chunk 1 optimal weight: 0.9990 overall best weight: 1.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.120371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.112305 restraints weight = 6356.391| |-----------------------------------------------------------------------------| r_work (start): 0.3876 rms_B_bonded: 1.74 r_work: 0.3796 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.3716 rms_B_bonded: 3.09 restraints_weight: 0.2500 r_work (final): 0.3716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8618 moved from start: 0.5698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 1569 Z= 0.177 Angle : 0.503 5.218 2097 Z= 0.241 Chirality : 0.051 0.122 234 Planarity : 0.003 0.021 267 Dihedral : 4.308 11.416 207 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 2.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % Rotamer: Outliers : 0.56 % Allowed : 19.77 % Favored : 79.66 % 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: -0.50 (0.56), residues: 198 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.37 (0.43), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 374 PHE 0.003 0.001 PHE E 346 TYR 0.008 0.002 TYR A 310 ARG 0.000 0.000 ARG C 349 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4266.54 seconds wall clock time: 75 minutes 26.46 seconds (4526.46 seconds total)