Starting phenix.real_space_refine on Wed Jan 17 12:18:46 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qcr_18333/01_2024/8qcr_18333.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qcr_18333/01_2024/8qcr_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qcr_18333/01_2024/8qcr_18333.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qcr_18333/01_2024/8qcr_18333.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qcr_18333/01_2024/8qcr_18333.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qcr_18333/01_2024/8qcr_18333.pdb" } 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 Residue "A TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 342": "OE1" <-> "OE2" Residue "C TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 358": "OD1" <-> "OD2" Residue "C GLU 372": "OE1" <-> "OE2" Residue "E TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ASP 358": "OD1" <-> "OD2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/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: 1.90, per 1000 atoms: 0.60 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 - 3.50 Amino acid : False - 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: 2.34 Conformation dependent library (CDL) restraints added in 327.5 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: 0.33 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: 1.01 Time building geometry restraints manager: 2.46 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: 96.83 - 103.28: 17 103.28 - 109.72: 2633 109.72 - 116.16: 1563 116.16 - 122.61: 1271 122.61 - 129.05: 318 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: 1265 13.36 - 26.71: 77 26.71 - 40.07: 24 40.07 - 53.42: 8 53.42 - 66.78: 33 Dihedral angle restraints: 1407 sinusoidal: 786 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 1404 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 1.850 nonbonded pdb=" OD1 ASP E 314 " pdb=" HG SER E 316 " model vdw 1.575 1.850 nonbonded pdb=" OD1 ASP A 314 " pdb=" HG SER A 316 " model vdw 1.576 1.850 nonbonded pdb=" HG SER A 320 " pdb=" O GLY A 366 " model vdw 1.644 1.850 nonbonded pdb=" HG SER C 320 " pdb=" O GLY C 366 " model vdw 1.669 1.850 ... (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 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: 2.280 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.050 Extract box with map and model: 11.240 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 15.030 Find NCS groups from input model: 0.140 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:12.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.110 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 0 poor density : 72 time to evaluate : 0.291 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: 2.7815 time to fit residues: 202.6843 Evaluate side-chains 49 residues out of total 177 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 49 time to evaluate : 0.282 ------------------------------------------------------------------------------- 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: 0.9990 chunk 9 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 chunk 5 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 overall best weight: 0.9988 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.3753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 1569 Z= 0.197 Angle : 0.593 3.967 2097 Z= 0.300 Chirality : 0.051 0.132 234 Planarity : 0.003 0.031 267 Dihedral : 6.126 16.018 207 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 1.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 2.26 % Allowed : 11.86 % 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: -1.12 (0.52), residues: 198 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.84 (0.40), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS E 362 PHE 0.004 0.001 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 55 residues out of total 177 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 51 time to evaluate : 0.296 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 347 LYS cc_start: 0.8502 (mttt) cc_final: 0.7647 (pmtt) REVERT: A 369 LYS cc_start: 0.8248 (ttmt) cc_final: 0.7883 (ttpt) REVERT: C 338 GLU cc_start: 0.7629 (tt0) cc_final: 0.7350 (tt0) REVERT: C 340 LYS cc_start: 0.7432 (mttt) cc_final: 0.7223 (ttmm) REVERT: C 345 ASP cc_start: 0.7477 (m-30) cc_final: 0.6975 (t0) REVERT: C 347 LYS cc_start: 0.8439 (mttt) cc_final: 0.8174 (mtpt) REVERT: C 349 ARG cc_start: 0.7642 (mtt180) cc_final: 0.6532 (mtt-85) REVERT: C 375 LYS cc_start: 0.5908 (OUTLIER) cc_final: 0.4675 (tmmt) REVERT: E 347 LYS cc_start: 0.8358 (mttt) cc_final: 0.8037 (mptp) REVERT: E 369 LYS cc_start: 0.7605 (ttmt) cc_final: 0.7385 (ttpt) REVERT: E 372 GLU cc_start: 0.7906 (tt0) cc_final: 0.7645 (tt0) outliers start: 4 outliers final: 1 residues processed: 52 average time/residue: 3.5376 time to fit residues: 185.8798 Evaluate side-chains 45 residues out of total 177 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 43 time to evaluate : 0.292 ------------------------------------------------------------------------------- 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 4 optimal weight: 3.9990 chunk 16 optimal weight: 0.8980 chunk 17 optimal weight: 2.9990 chunk 14 optimal weight: 0.0980 chunk 5 optimal weight: 0.6980 chunk 13 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 1 optimal weight: 0.9980 chunk 7 optimal weight: 0.9990 chunk 10 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.4821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 1569 Z= 0.145 Angle : 0.505 4.029 2097 Z= 0.252 Chirality : 0.051 0.129 234 Planarity : 0.004 0.043 267 Dihedral : 5.305 14.910 207 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 1.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 2.26 % Allowed : 18.08 % 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: -0.83 (0.53), residues: 198 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.62 (0.41), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS E 362 PHE 0.004 0.001 PHE E 346 TYR 0.009 0.002 TYR E 310 ARG 0.006 0.001 ARG A 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 51 residues out of total 177 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 47 time to evaluate : 0.302 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 347 LYS cc_start: 0.8485 (mttt) cc_final: 0.7626 (pmtt) REVERT: A 349 ARG cc_start: 0.6079 (ptt-90) cc_final: 0.5849 (mtt180) REVERT: A 369 LYS cc_start: 0.8205 (ttmt) cc_final: 0.7603 (tttt) REVERT: C 338 GLU cc_start: 0.7536 (tt0) cc_final: 0.7287 (tt0) REVERT: C 340 LYS cc_start: 0.7387 (mttt) cc_final: 0.7147 (ttmm) REVERT: C 345 ASP cc_start: 0.7404 (m-30) cc_final: 0.6955 (t70) REVERT: C 347 LYS cc_start: 0.8451 (mttt) cc_final: 0.8197 (mtpt) REVERT: C 349 ARG cc_start: 0.7708 (mtt180) cc_final: 0.6619 (mtt-85) REVERT: C 375 LYS cc_start: 0.5865 (OUTLIER) cc_final: 0.4657 (tmmt) REVERT: E 345 ASP cc_start: 0.7410 (m-30) cc_final: 0.6980 (OUTLIER) REVERT: E 349 ARG cc_start: 0.7312 (mtm180) cc_final: 0.6781 (mtt180) REVERT: E 369 LYS cc_start: 0.7601 (ttmt) cc_final: 0.7271 (ttpt) REVERT: E 372 GLU cc_start: 0.7910 (tt0) cc_final: 0.7684 (tt0) outliers start: 4 outliers final: 4 residues processed: 49 average time/residue: 3.4824 time to fit residues: 172.4451 Evaluate side-chains 49 residues out of total 177 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 45 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 348 ASP 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 16 optimal weight: 5.9990 chunk 17 optimal weight: 2.9990 chunk 8 optimal weight: 0.8980 chunk 15 optimal weight: 2.9990 chunk 4 optimal weight: 0.9990 chunk 14 optimal weight: 0.6980 chunk 9 optimal weight: 0.9980 chunk 0 optimal weight: 3.9990 chunk 12 optimal weight: 0.9980 chunk 7 optimal weight: 2.9990 chunk 5 optimal weight: 0.6980 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.4972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 1569 Z= 0.150 Angle : 0.476 4.016 2097 Z= 0.235 Chirality : 0.051 0.125 234 Planarity : 0.003 0.026 267 Dihedral : 4.977 14.078 207 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 2.26 % Allowed : 19.21 % 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 : -0.50 (0.41), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 362 PHE 0.004 0.001 PHE E 346 TYR 0.008 0.002 TYR E 310 ARG 0.004 0.001 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 50 residues out of total 177 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 46 time to evaluate : 0.286 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 347 LYS cc_start: 0.8471 (mttt) cc_final: 0.7478 (pmtt) REVERT: A 349 ARG cc_start: 0.6098 (ptt-90) cc_final: 0.5875 (mtt180) REVERT: A 369 LYS cc_start: 0.8210 (ttmt) cc_final: 0.7602 (tttt) REVERT: C 338 GLU cc_start: 0.7544 (tt0) cc_final: 0.7278 (tt0) REVERT: C 340 LYS cc_start: 0.7358 (mttt) cc_final: 0.7121 (ttmm) REVERT: C 345 ASP cc_start: 0.7378 (m-30) cc_final: 0.6970 (t70) REVERT: C 347 LYS cc_start: 0.8444 (mttt) cc_final: 0.8195 (mtpt) REVERT: C 349 ARG cc_start: 0.7747 (mtt180) cc_final: 0.6670 (mtt-85) REVERT: C 375 LYS cc_start: 0.5857 (OUTLIER) cc_final: 0.4757 (tmmt) REVERT: E 345 ASP cc_start: 0.7367 (m-30) cc_final: 0.6958 (OUTLIER) REVERT: E 349 ARG cc_start: 0.7374 (mtm180) cc_final: 0.6966 (mtt180) REVERT: E 369 LYS cc_start: 0.7602 (ttmt) cc_final: 0.7314 (ttpt) REVERT: E 372 GLU cc_start: 0.7902 (tt0) cc_final: 0.7689 (tt0) outliers start: 4 outliers final: 3 residues processed: 47 average time/residue: 3.5098 time to fit residues: 166.6866 Evaluate side-chains 49 residues out of total 177 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 46 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 348 ASP Chi-restraints excluded: chain C residue 375 LYS Chi-restraints excluded: chain E residue 321 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 15 optimal weight: 4.9990 chunk 3 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 chunk 4 optimal weight: 0.9990 chunk 17 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 8 optimal weight: 0.9980 chunk 1 optimal weight: 3.9990 chunk 5 optimal weight: 0.9990 chunk 9 optimal weight: 0.9990 chunk 16 optimal weight: 0.9990 overall best weight: 0.9986 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.5123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 1569 Z= 0.160 Angle : 0.479 4.025 2097 Z= 0.235 Chirality : 0.051 0.124 234 Planarity : 0.003 0.022 267 Dihedral : 4.717 13.356 207 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % Rotamer: Outliers : 2.26 % Allowed : 19.21 % 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: -0.56 (0.55), residues: 198 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.42 (0.42), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 374 PHE 0.005 0.001 PHE E 346 TYR 0.009 0.002 TYR A 310 ARG 0.002 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 52 residues out of total 177 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 48 time to evaluate : 0.328 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 347 LYS cc_start: 0.8500 (mttt) cc_final: 0.7456 (pmtt) REVERT: A 349 ARG cc_start: 0.6119 (ptt-90) cc_final: 0.5822 (mtt180) REVERT: A 369 LYS cc_start: 0.8192 (ttmt) cc_final: 0.7712 (tttt) REVERT: C 340 LYS cc_start: 0.7352 (mttt) cc_final: 0.7100 (ttmm) REVERT: C 345 ASP cc_start: 0.7349 (m-30) cc_final: 0.6978 (t70) REVERT: C 347 LYS cc_start: 0.8394 (mttt) cc_final: 0.8166 (mtpt) REVERT: C 349 ARG cc_start: 0.7757 (mtt180) cc_final: 0.6760 (mtt-85) REVERT: C 375 LYS cc_start: 0.5928 (OUTLIER) cc_final: 0.4842 (tmmt) REVERT: E 345 ASP cc_start: 0.7393 (m-30) cc_final: 0.6985 (t0) REVERT: E 349 ARG cc_start: 0.7406 (mtm180) cc_final: 0.7032 (mtt180) REVERT: E 369 LYS cc_start: 0.7615 (ttmt) cc_final: 0.7368 (ttpt) outliers start: 4 outliers final: 2 residues processed: 49 average time/residue: 3.4469 time to fit residues: 170.6880 Evaluate side-chains 46 residues out of total 177 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 43 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 348 ASP Chi-restraints excluded: chain C residue 375 LYS 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 1 optimal weight: 3.9990 chunk 9 optimal weight: 4.9990 chunk 12 optimal weight: 1.9990 chunk 14 optimal weight: 5.9990 chunk 17 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 chunk 8 optimal weight: 0.9980 chunk 6 optimal weight: 0.5980 chunk 5 optimal weight: 0.8980 chunk 3 optimal weight: 0.9990 chunk 11 optimal weight: 0.4980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.5316 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= 0.141 Angle : 0.480 4.546 2097 Z= 0.233 Chirality : 0.051 0.124 234 Planarity : 0.002 0.019 267 Dihedral : 4.557 12.789 207 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 2.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 2.26 % Allowed : 19.21 % 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: -0.49 (0.55), residues: 198 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.36 (0.42), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 374 PHE 0.005 0.001 PHE E 346 TYR 0.007 0.002 TYR A 310 ARG 0.002 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 48 residues out of total 177 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 44 time to evaluate : 0.274 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 347 LYS cc_start: 0.8497 (mttt) cc_final: 0.7471 (pmtt) REVERT: A 349 ARG cc_start: 0.6097 (ptt-90) cc_final: 0.5847 (mtt180) REVERT: A 369 LYS cc_start: 0.8191 (ttmt) cc_final: 0.7775 (ttpt) REVERT: C 340 LYS cc_start: 0.7364 (mttt) cc_final: 0.7105 (ttmm) REVERT: C 345 ASP cc_start: 0.7366 (m-30) cc_final: 0.6980 (t70) REVERT: C 347 LYS cc_start: 0.8394 (mttt) cc_final: 0.8152 (mtpt) REVERT: C 349 ARG cc_start: 0.7742 (mtt180) cc_final: 0.6765 (mtt-85) REVERT: E 345 ASP cc_start: 0.7377 (m-30) cc_final: 0.6970 (t0) REVERT: E 349 ARG cc_start: 0.7421 (OUTLIER) cc_final: 0.6945 (mtt180) outliers start: 4 outliers final: 2 residues processed: 45 average time/residue: 3.3892 time to fit residues: 154.1869 Evaluate side-chains 44 residues out of total 177 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 41 time to evaluate : 0.276 ------------------------------------------------------------------------------- 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 349 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 11 optimal weight: 2.9990 chunk 8 optimal weight: 0.1980 chunk 1 optimal weight: 2.9990 chunk 13 optimal weight: 0.7980 chunk 15 optimal weight: 4.9990 chunk 16 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 7 optimal weight: 0.4980 chunk 12 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 chunk 14 optimal weight: 2.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.5287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 1569 Z= 0.156 Angle : 0.475 4.120 2097 Z= 0.231 Chirality : 0.050 0.123 234 Planarity : 0.002 0.017 267 Dihedral : 4.524 12.678 207 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.13 % Allowed : 19.77 % 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: -0.51 (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 0.002 0.001 HIS C 374 PHE 0.005 0.001 PHE E 346 TYR 0.008 0.002 TYR A 310 ARG 0.001 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 45 residues out of total 177 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 43 time to evaluate : 0.284 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 347 LYS cc_start: 0.8514 (mttt) cc_final: 0.7486 (pmtt) REVERT: A 349 ARG cc_start: 0.6090 (ptt-90) cc_final: 0.5854 (mtt180) REVERT: A 369 LYS cc_start: 0.8226 (ttmt) cc_final: 0.7718 (tttt) REVERT: C 340 LYS cc_start: 0.7370 (mttt) cc_final: 0.7111 (ttmm) REVERT: C 345 ASP cc_start: 0.7358 (m-30) cc_final: 0.6980 (t70) REVERT: C 347 LYS cc_start: 0.8399 (mttt) cc_final: 0.8158 (mtpt) REVERT: C 349 ARG cc_start: 0.7748 (mtt180) cc_final: 0.6764 (mtt-85) REVERT: C 375 LYS cc_start: 0.7515 (mptt) cc_final: 0.7304 (mptt) REVERT: E 345 ASP cc_start: 0.7448 (m-30) cc_final: 0.6994 (t0) REVERT: E 349 ARG cc_start: 0.7435 (mtm180) cc_final: 0.6961 (mtt180) outliers start: 2 outliers final: 1 residues processed: 44 average time/residue: 3.3680 time to fit residues: 149.8008 Evaluate side-chains 44 residues out of total 177 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 43 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 321 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 15 optimal weight: 5.9990 chunk 16 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 chunk 8 optimal weight: 0.8980 chunk 11 optimal weight: 0.6980 chunk 14 optimal weight: 0.9980 chunk 1 optimal weight: 2.9990 chunk 4 optimal weight: 0.9980 chunk 13 optimal weight: 0.8980 chunk 2 optimal weight: 0.8980 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.5392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 1569 Z= 0.149 Angle : 0.470 4.328 2097 Z= 0.229 Chirality : 0.051 0.123 234 Planarity : 0.002 0.017 267 Dihedral : 4.423 12.074 207 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.56 % Allowed : 20.34 % 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: -0.49 (0.56), residues: 198 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.36 (0.42), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 374 PHE 0.003 0.001 PHE E 346 TYR 0.008 0.002 TYR C 310 ARG 0.001 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 42 residues out of total 177 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 41 time to evaluate : 0.301 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 347 LYS cc_start: 0.8549 (mttt) cc_final: 0.7477 (pmtt) REVERT: A 349 ARG cc_start: 0.6121 (ptt-90) cc_final: 0.5789 (mtt180) REVERT: A 369 LYS cc_start: 0.8230 (ttmt) cc_final: 0.7731 (tttt) REVERT: C 340 LYS cc_start: 0.7366 (mttt) cc_final: 0.7112 (ttmm) REVERT: C 345 ASP cc_start: 0.7350 (m-30) cc_final: 0.6971 (t70) REVERT: C 347 LYS cc_start: 0.8385 (mttt) cc_final: 0.8152 (mtpt) REVERT: C 349 ARG cc_start: 0.7733 (mtt180) cc_final: 0.6831 (mtt-85) REVERT: C 375 LYS cc_start: 0.7478 (mptt) cc_final: 0.7229 (mptt) REVERT: E 345 ASP cc_start: 0.7435 (m-30) cc_final: 0.7005 (t0) REVERT: E 349 ARG cc_start: 0.7452 (mtm180) cc_final: 0.6973 (mtt180) outliers start: 1 outliers final: 1 residues processed: 42 average time/residue: 3.2411 time to fit residues: 137.7054 Evaluate side-chains 41 residues out of total 177 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 40 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 321 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 3 optimal weight: 3.9990 chunk 14 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 1 optimal weight: 0.9980 chunk 2 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 0 optimal weight: 0.5980 chunk 10 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 chunk 9 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.5440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 1569 Z= 0.188 Angle : 0.484 4.202 2097 Z= 0.236 Chirality : 0.050 0.122 234 Planarity : 0.002 0.018 267 Dihedral : 4.482 12.586 207 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % Rotamer: Outliers : 0.56 % Allowed : 20.90 % 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: -0.49 (0.56), residues: 198 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.36 (0.42), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 374 PHE 0.004 0.001 PHE E 346 TYR 0.010 0.003 TYR E 310 ARG 0.000 0.000 ARG A 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 41 residues out of total 177 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 40 time to evaluate : 0.299 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 347 LYS cc_start: 0.8558 (mttt) cc_final: 0.7456 (pmtt) REVERT: A 349 ARG cc_start: 0.6147 (ptt-90) cc_final: 0.5803 (mtt180) REVERT: A 369 LYS cc_start: 0.8254 (ttmt) cc_final: 0.7757 (tttt) REVERT: C 340 LYS cc_start: 0.7388 (mttt) cc_final: 0.7127 (ttmm) REVERT: C 345 ASP cc_start: 0.7354 (m-30) cc_final: 0.6973 (t70) REVERT: C 347 LYS cc_start: 0.8340 (mttt) cc_final: 0.8098 (mtpt) REVERT: C 349 ARG cc_start: 0.7753 (mtt180) cc_final: 0.6903 (mtt-85) REVERT: E 345 ASP cc_start: 0.7439 (m-30) cc_final: 0.7009 (t0) REVERT: E 349 ARG cc_start: 0.7446 (mtm180) cc_final: 0.6963 (mtt180) outliers start: 1 outliers final: 1 residues processed: 41 average time/residue: 3.2045 time to fit residues: 132.8761 Evaluate side-chains 40 residues out of total 177 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 39 time to evaluate : 0.207 ------------------------------------------------------------------------------- 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 10 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 3 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 chunk 16 optimal weight: 0.9990 chunk 1 optimal weight: 0.9980 chunk 4 optimal weight: 2.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.5489 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= 0.196 Angle : 0.489 4.219 2097 Z= 0.240 Chirality : 0.050 0.122 234 Planarity : 0.003 0.018 267 Dihedral : 4.548 12.659 207 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.56 % Allowed : 20.90 % 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: -0.49 (0.56), residues: 198 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.36 (0.43), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS C 374 PHE 0.004 0.001 PHE E 346 TYR 0.010 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 41 residues out of total 177 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 40 time to evaluate : 0.261 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 347 LYS cc_start: 0.8567 (mttt) cc_final: 0.7396 (pmtt) REVERT: A 349 ARG cc_start: 0.6175 (ptt-90) cc_final: 0.5785 (mtt180) REVERT: A 369 LYS cc_start: 0.8269 (ttmt) cc_final: 0.7772 (tttt) REVERT: C 340 LYS cc_start: 0.7393 (mttt) cc_final: 0.7133 (ttmm) REVERT: C 345 ASP cc_start: 0.7357 (m-30) cc_final: 0.6989 (t70) REVERT: C 347 LYS cc_start: 0.8349 (mttt) cc_final: 0.8104 (mtpt) REVERT: C 349 ARG cc_start: 0.7751 (mtt180) cc_final: 0.6899 (mtt-85) REVERT: C 373 THR cc_start: 0.8445 (m) cc_final: 0.8044 (p) REVERT: E 345 ASP cc_start: 0.7440 (m-30) cc_final: 0.7008 (t0) REVERT: E 349 ARG cc_start: 0.7435 (mtm180) cc_final: 0.6963 (mtt180) outliers start: 1 outliers final: 1 residues processed: 41 average time/residue: 3.2676 time to fit residues: 135.5291 Evaluate side-chains 40 residues out of total 177 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 39 time to evaluate : 0.280 ------------------------------------------------------------------------------- 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 3 optimal weight: 0.8980 chunk 11 optimal weight: 2.9990 chunk 6 optimal weight: 3.9990 chunk 9 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 1 optimal weight: 0.0770 chunk 17 optimal weight: 0.8980 chunk 13 optimal weight: 0.6980 chunk 15 optimal weight: 0.9990 chunk 16 optimal weight: 0.9990 chunk 12 optimal weight: 0.9990 overall best weight: 0.7140 ------------------------------------------------------------------------------- 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 = 0.3964 r_free = 0.3964 target = 0.116950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 20)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.108191 restraints weight = 6531.113| |-----------------------------------------------------------------------------| r_work (start): 0.3860 rms_B_bonded: 1.86 r_work: 0.3768 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.3683 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.3683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8569 moved from start: 0.5509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 1569 Z= 0.140 Angle : 0.476 4.265 2097 Z= 0.231 Chirality : 0.050 0.123 234 Planarity : 0.002 0.017 267 Dihedral : 4.397 11.642 207 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.56 % Allowed : 20.90 % 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: -0.47 (0.56), residues: 198 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.35 (0.43), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.000 HIS C 374 PHE 0.002 0.001 PHE E 346 TYR 0.008 0.002 TYR E 310 ARG 0.001 0.000 ARG A 349 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3599.23 seconds wall clock time: 63 minutes 36.88 seconds (3816.88 seconds total)