Starting phenix.real_space_refine on Fri Aug 2 15:49:16 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q9i_18282/08_2024/8q9i_18282.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q9i_18282/08_2024/8q9i_18282.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.56 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q9i_18282/08_2024/8q9i_18282.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q9i_18282/08_2024/8q9i_18282.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q9i_18282/08_2024/8q9i_18282.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q9i_18282/08_2024/8q9i_18282.cif" } resolution = 2.56 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 1053 2.51 5 N 303 2.21 5 O 312 1.98 5 H 1740 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 338": "OE1" <-> "OE2" Residue "A ASP 345": "OD1" <-> "OD2" Residue "A ASP 348": "OD1" <-> "OD2" Residue "A ARG 349": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ASP 358": "OD1" <-> "OD2" Residue "A GLU 372": "OE1" <-> "OE2" Residue "C GLU 338": "OE1" <-> "OE2" Residue "C ASP 348": "OD1" <-> "OD2" Residue "C ARG 349": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ASP 358": "OD1" <-> "OD2" Residue "C GLU 372": "OE1" <-> "OE2" Residue "C PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 338": "OE1" <-> "OE2" Residue "E GLU 342": "OE1" <-> "OE2" Residue "E PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ARG 349": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ASP 358": "OD1" <-> "OD2" Residue "E GLU 372": "OE1" <-> "OE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 3411 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 1137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1137 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 3, 'TRANS': 69} Chain: "C" Number of atoms: 1137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1137 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 3, 'TRANS': 69} Chain: "E" Number of atoms: 1137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1137 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 3, 'TRANS': 69} Time building chain proxies: 2.91, per 1000 atoms: 0.85 Number of scatterers: 3411 At special positions: 0 Unit cell: (69.065, 98.145, 39.258, 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 312 8.00 N 303 7.00 C 1053 6.00 H 1740 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: 2.45 Conformation dependent library (CDL) restraints added in 500.2 milliseconds 426 Ramachandran restraints generated. 213 Oldfield, 0 Emsley, 213 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 384 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 9 sheets defined 0.0% alpha, 50.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.39 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'C' and resid 307 through 310 removed outlier: 6.785A pdb=" N ILE A 308 " --> pdb=" O VAL C 309 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 313 through 314 removed outlier: 6.851A pdb=" N VAL A 313 " --> pdb=" O ASP E 314 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 317 through 322 removed outlier: 6.396A pdb=" N VAL A 318 " --> pdb=" O THR C 319 " (cutoff:3.500A) removed outlier: 8.278A pdb=" N LYS C 321 " --> pdb=" O VAL A 318 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N SER A 320 " --> pdb=" O LYS C 321 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 325 through 330 removed outlier: 5.991A pdb=" N GLY A 326 " --> pdb=" O ASN C 327 " (cutoff:3.500A) removed outlier: 8.359A pdb=" N HIS C 329 " --> pdb=" O GLY A 326 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N ILE A 328 " --> pdb=" O HIS C 329 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N GLY E 326 " --> pdb=" O LEU A 325 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N ASN A 327 " --> pdb=" O GLY E 326 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 337 through 342 removed outlier: 6.857A pdb=" N GLU A 338 " --> pdb=" O VAL E 339 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N SER E 341 " --> pdb=" O GLU A 338 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N LYS A 340 " --> pdb=" O SER E 341 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 345 through 346 removed outlier: 6.672A pdb=" N ASP A 345 " --> pdb=" O PHE E 346 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 350 through 357 removed outlier: 6.354A pdb=" N VAL A 350 " --> pdb=" O GLN C 351 " (cutoff:3.500A) removed outlier: 8.137A pdb=" N LYS C 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N SER A 352 " --> pdb=" O LYS C 353 " (cutoff:3.500A) removed outlier: 8.286A pdb=" N GLY C 355 " --> pdb=" O SER A 352 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N ILE A 354 " --> pdb=" O GLY C 355 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N LEU C 357 " --> pdb=" O ILE A 354 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N SER A 356 " --> pdb=" O LEU C 357 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 360 through 362 removed outlier: 6.381A pdb=" N THR A 361 " --> pdb=" O HIS C 362 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N ILE A 360 " --> pdb=" O THR E 361 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'C' and resid 369 through 377 removed outlier: 6.741A pdb=" N LYS A 369 " --> pdb=" O LYS E 370 " (cutoff:3.500A) removed outlier: 8.088A pdb=" N GLU E 372 " --> pdb=" O LYS A 369 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N ILE A 371 " --> pdb=" O GLU E 372 " (cutoff:3.500A) removed outlier: 7.864A pdb=" N HIS E 374 " --> pdb=" O ILE A 371 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N THR A 373 " --> pdb=" O HIS E 374 " (cutoff:3.500A) removed outlier: 8.120A pdb=" N LEU E 376 " --> pdb=" O THR A 373 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N LYS A 375 " --> pdb=" O LEU E 376 " (cutoff:3.500A) 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: 1.07 Time building geometry restraints manager: 2.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.94 - 1.12: 1737 1.12 - 1.29: 279 1.29 - 1.46: 486 1.46 - 1.64: 933 1.64 - 1.81: 3 Bond restraints: 3438 Sorted by residual: bond pdb=" CE1 PHE C 346 " pdb=" HE1 PHE C 346 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.70e+01 bond pdb=" NE2 GLN E 336 " pdb="HE21 GLN E 336 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.69e+01 bond pdb=" CE1 PHE A 346 " pdb=" HE1 PHE A 346 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.68e+01 bond pdb=" ND2 ASN A 327 " pdb="HD22 ASN A 327 " 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 A 337 " pdb=" H VAL A 337 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.68e+01 ... (remaining 3433 not shown) Histogram of bond angle deviations from ideal: 97.01 - 103.41: 15 103.41 - 109.82: 2961 109.82 - 116.22: 1542 116.22 - 122.62: 1416 122.62 - 129.02: 339 Bond angle restraints: 6273 Sorted by residual: angle pdb=" CB HIS E 374 " pdb=" CG HIS E 374 " pdb=" CD2 HIS E 374 " ideal model delta sigma weight residual 131.20 125.10 6.10 1.30e+00 5.92e-01 2.20e+01 angle pdb=" CB HIS E 329 " pdb=" CG HIS E 329 " pdb=" CD2 HIS E 329 " ideal model delta sigma weight residual 131.20 125.13 6.07 1.30e+00 5.92e-01 2.18e+01 angle pdb=" C GLY C 334 " pdb=" N GLY C 335 " pdb=" CA GLY C 335 " ideal model delta sigma weight residual 120.60 125.21 -4.61 1.01e+00 9.80e-01 2.08e+01 angle pdb=" N GLY A 326 " pdb=" CA GLY A 326 " pdb=" C GLY A 326 " ideal model delta sigma weight residual 110.69 116.62 -5.93 1.33e+00 5.65e-01 1.99e+01 angle pdb=" CB HIS C 329 " pdb=" CG HIS C 329 " pdb=" CD2 HIS C 329 " ideal model delta sigma weight residual 131.20 125.41 5.79 1.30e+00 5.92e-01 1.98e+01 ... (remaining 6268 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.51: 1406 15.51 - 31.01: 85 31.01 - 46.51: 32 46.51 - 62.01: 44 62.01 - 77.51: 17 Dihedral angle restraints: 1584 sinusoidal: 903 harmonic: 681 Sorted by residual: dihedral pdb=" CA SER C 316 " pdb=" C SER C 316 " pdb=" N LYS C 317 " pdb=" CA LYS C 317 " ideal model delta harmonic sigma weight residual 180.00 152.00 28.00 0 5.00e+00 4.00e-02 3.14e+01 dihedral pdb=" CA LYS E 347 " pdb=" C LYS E 347 " pdb=" N ASP E 348 " pdb=" CA ASP E 348 " ideal model delta harmonic sigma weight residual -180.00 -158.00 -22.00 0 5.00e+00 4.00e-02 1.94e+01 dihedral pdb=" CA ILE C 360 " pdb=" C ILE C 360 " pdb=" N THR C 361 " pdb=" CA THR C 361 " ideal model delta harmonic sigma weight residual 180.00 159.18 20.82 0 5.00e+00 4.00e-02 1.73e+01 ... (remaining 1581 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.062: 154 0.062 - 0.122: 68 0.122 - 0.183: 24 0.183 - 0.243: 8 0.243 - 0.304: 4 Chirality restraints: 258 Sorted by residual: chirality pdb=" CA LYS A 317 " pdb=" N LYS A 317 " pdb=" C LYS A 317 " pdb=" CB LYS A 317 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.31e+00 chirality pdb=" CA ASP E 348 " pdb=" N ASP E 348 " pdb=" C ASP E 348 " pdb=" CB ASP E 348 " both_signs ideal model delta sigma weight residual False 2.51 2.77 -0.26 2.00e-01 2.50e+01 1.69e+00 chirality pdb=" CA LYS C 317 " pdb=" N LYS C 317 " pdb=" C LYS C 317 " pdb=" CB LYS C 317 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.55e+00 ... (remaining 255 not shown) Planarity restraints: 495 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG E 349 " 0.307 9.50e-02 1.11e+02 1.19e-01 9.29e+01 pdb=" NE ARG E 349 " 0.032 2.00e-02 2.50e+03 pdb=" CZ ARG E 349 " 0.028 2.00e-02 2.50e+03 pdb=" NH1 ARG E 349 " 0.080 2.00e-02 2.50e+03 pdb=" NH2 ARG E 349 " -0.013 2.00e-02 2.50e+03 pdb="HH11 ARG E 349 " -0.140 2.00e-02 2.50e+03 pdb="HH12 ARG E 349 " 0.057 2.00e-02 2.50e+03 pdb="HH21 ARG E 349 " -0.040 2.00e-02 2.50e+03 pdb="HH22 ARG E 349 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 310 " -0.108 2.00e-02 2.50e+03 4.95e-02 7.34e+01 pdb=" CG TYR C 310 " 0.007 2.00e-02 2.50e+03 pdb=" CD1 TYR C 310 " 0.033 2.00e-02 2.50e+03 pdb=" CD2 TYR C 310 " 0.036 2.00e-02 2.50e+03 pdb=" CE1 TYR C 310 " 0.033 2.00e-02 2.50e+03 pdb=" CE2 TYR C 310 " 0.025 2.00e-02 2.50e+03 pdb=" CZ TYR C 310 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR C 310 " -0.107 2.00e-02 2.50e+03 pdb=" HD1 TYR C 310 " 0.010 2.00e-02 2.50e+03 pdb=" HD2 TYR C 310 " 0.033 2.00e-02 2.50e+03 pdb=" HE1 TYR C 310 " 0.028 2.00e-02 2.50e+03 pdb=" HE2 TYR C 310 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 310 " -0.089 2.00e-02 2.50e+03 4.44e-02 5.91e+01 pdb=" CG TYR A 310 " 0.004 2.00e-02 2.50e+03 pdb=" CD1 TYR A 310 " 0.026 2.00e-02 2.50e+03 pdb=" CD2 TYR A 310 " 0.030 2.00e-02 2.50e+03 pdb=" CE1 TYR A 310 " 0.038 2.00e-02 2.50e+03 pdb=" CE2 TYR A 310 " 0.020 2.00e-02 2.50e+03 pdb=" CZ TYR A 310 " 0.006 2.00e-02 2.50e+03 pdb=" OH TYR A 310 " -0.101 2.00e-02 2.50e+03 pdb=" HD1 TYR A 310 " -0.003 2.00e-02 2.50e+03 pdb=" HD2 TYR A 310 " 0.031 2.00e-02 2.50e+03 pdb=" HE1 TYR A 310 " 0.032 2.00e-02 2.50e+03 pdb=" HE2 TYR A 310 " 0.007 2.00e-02 2.50e+03 ... (remaining 492 not shown) Histogram of nonbonded interaction distances: 1.58 - 2.18: 270 2.18 - 2.79: 5939 2.79 - 3.39: 8984 3.39 - 4.00: 12050 4.00 - 4.60: 16883 Nonbonded interactions: 44126 Sorted by model distance: nonbonded pdb=" OD1 ASP C 314 " pdb=" HG SER C 316 " model vdw 1.577 2.450 nonbonded pdb=" OD1 ASP A 314 " pdb=" HG SER A 316 " model vdw 1.607 2.450 nonbonded pdb=" OD1 ASP E 314 " pdb=" HG SER E 316 " model vdw 1.609 2.450 nonbonded pdb=" OD2 ASP A 314 " pdb=" HZ1 LYS A 370 " model vdw 1.673 2.450 nonbonded pdb=" OD2 ASP E 314 " pdb=" HZ3 LYS E 370 " model vdw 1.717 2.450 ... (remaining 44121 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: 2.210 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: 0.060 Extract box with map and model: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 16.850 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 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:13.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7317 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 1698 Z= 0.745 Angle : 1.796 6.814 2274 Z= 1.195 Chirality : 0.085 0.304 258 Planarity : 0.011 0.092 288 Dihedral : 11.444 77.511 648 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % 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: -1.34 (0.48), residues: 213 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.01 (0.37), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.014 0.004 HIS A 330 PHE 0.047 0.014 PHE E 346 TYR 0.098 0.033 TYR C 310 ARG 0.004 0.001 ARG E 349 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 426 Ramachandran restraints generated. 213 Oldfield, 0 Emsley, 213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 426 Ramachandran restraints generated. 213 Oldfield, 0 Emsley, 213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 75 time to evaluate : 0.292 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 321 LYS cc_start: 0.7081 (ttpt) cc_final: 0.6613 (mtmm) REVERT: A 338 GLU cc_start: 0.7593 (tt0) cc_final: 0.7362 (mt-10) REVERT: A 342 GLU cc_start: 0.8031 (mt-10) cc_final: 0.7683 (mt-10) REVERT: C 321 LYS cc_start: 0.7235 (ttpt) cc_final: 0.6692 (mttp) REVERT: E 311 LYS cc_start: 0.6678 (ttpt) cc_final: 0.6345 (tmtt) REVERT: E 320 SER cc_start: 0.8128 (t) cc_final: 0.7827 (p) REVERT: E 321 LYS cc_start: 0.7912 (ttpt) cc_final: 0.7258 (mttp) REVERT: E 336 GLN cc_start: 0.8340 (tt0) cc_final: 0.8109 (tt0) REVERT: E 342 GLU cc_start: 0.8292 (tt0) cc_final: 0.7751 (mt-10) REVERT: E 345 ASP cc_start: 0.7908 (m-30) cc_final: 0.7614 (t70) outliers start: 0 outliers final: 0 residues processed: 75 average time/residue: 2.7910 time to fit residues: 211.9828 Evaluate side-chains 47 residues out of total 192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 47 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 21 random chunks: chunk 17 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 chunk 8 optimal weight: 4.9990 chunk 5 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 16 optimal weight: 0.9980 chunk 6 optimal weight: 2.9990 chunk 12 optimal weight: 0.8980 chunk 19 optimal weight: 0.8980 chunk 20 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7452 moved from start: 0.3204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 1698 Z= 0.204 Angle : 0.619 4.167 2274 Z= 0.330 Chirality : 0.051 0.160 258 Planarity : 0.003 0.019 288 Dihedral : 6.450 18.133 222 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 0.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Rotamer: Outliers : 1.04 % Allowed : 15.10 % Favored : 83.85 % 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: -1.44 (0.47), residues: 213 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.09 (0.36), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS E 330 PHE 0.009 0.001 PHE A 346 TYR 0.005 0.001 TYR E 310 ARG 0.002 0.001 ARG A 349 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 426 Ramachandran restraints generated. 213 Oldfield, 0 Emsley, 213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 426 Ramachandran restraints generated. 213 Oldfield, 0 Emsley, 213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 48 time to evaluate : 0.308 Fit side-chains revert: symmetry clash REVERT: A 321 LYS cc_start: 0.7046 (ttpt) cc_final: 0.6511 (mtmm) REVERT: A 338 GLU cc_start: 0.7602 (tt0) cc_final: 0.7376 (mt-10) REVERT: A 342 GLU cc_start: 0.8038 (mt-10) cc_final: 0.7697 (mt-10) REVERT: C 321 LYS cc_start: 0.7260 (ttpt) cc_final: 0.6736 (mttm) REVERT: C 342 GLU cc_start: 0.8409 (OUTLIER) cc_final: 0.8154 (mt-10) REVERT: E 311 LYS cc_start: 0.6697 (ttpt) cc_final: 0.6257 (ptmt) REVERT: E 320 SER cc_start: 0.8062 (t) cc_final: 0.7596 (p) REVERT: E 321 LYS cc_start: 0.7886 (ttpt) cc_final: 0.7331 (mttm) REVERT: E 342 GLU cc_start: 0.8279 (tt0) cc_final: 0.7685 (mt-10) REVERT: E 345 ASP cc_start: 0.7961 (m-30) cc_final: 0.7579 (t70) REVERT: E 347 LYS cc_start: 0.7957 (tttt) cc_final: 0.7604 (mptt) REVERT: E 349 ARG cc_start: 0.4770 (pmt-80) cc_final: 0.4177 (mtp180) outliers start: 2 outliers final: 0 residues processed: 48 average time/residue: 2.9620 time to fit residues: 144.1604 Evaluate side-chains 45 residues out of total 192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 44 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 342 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 21 random chunks: chunk 6 optimal weight: 7.9990 chunk 15 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 chunk 14 optimal weight: 0.4980 chunk 9 optimal weight: 3.9990 chunk 2 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 10 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7456 moved from start: 0.3696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 1698 Z= 0.192 Angle : 0.538 4.169 2274 Z= 0.279 Chirality : 0.051 0.148 258 Planarity : 0.002 0.012 288 Dihedral : 5.341 13.555 222 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 0.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 1.04 % Allowed : 15.10 % Favored : 83.85 % 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: -1.53 (0.47), residues: 213 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.15 (0.36), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS E 329 PHE 0.007 0.002 PHE A 346 TYR 0.009 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) ************************************************ 426 Ramachandran restraints generated. 213 Oldfield, 0 Emsley, 213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 426 Ramachandran restraints generated. 213 Oldfield, 0 Emsley, 213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 49 time to evaluate : 0.305 Fit side-chains revert: symmetry clash REVERT: A 321 LYS cc_start: 0.7070 (ttpt) cc_final: 0.6567 (mtmm) REVERT: A 342 GLU cc_start: 0.8076 (mt-10) cc_final: 0.7781 (mt-10) REVERT: A 347 LYS cc_start: 0.8082 (mttt) cc_final: 0.7868 (mptp) REVERT: C 311 LYS cc_start: 0.5783 (ttpt) cc_final: 0.5431 (ttmt) REVERT: C 321 LYS cc_start: 0.7212 (ttpt) cc_final: 0.6685 (mttm) REVERT: C 345 ASP cc_start: 0.7538 (m-30) cc_final: 0.7114 (t70) REVERT: E 311 LYS cc_start: 0.6714 (ttpt) cc_final: 0.6278 (ptmt) REVERT: E 320 SER cc_start: 0.8059 (t) cc_final: 0.7534 (p) REVERT: E 321 LYS cc_start: 0.7894 (ttpt) cc_final: 0.7338 (mttm) REVERT: E 342 GLU cc_start: 0.8296 (tt0) cc_final: 0.7732 (mt-10) REVERT: E 345 ASP cc_start: 0.7935 (m-30) cc_final: 0.7543 (t70) REVERT: E 347 LYS cc_start: 0.7941 (tttt) cc_final: 0.7586 (mptt) REVERT: E 349 ARG cc_start: 0.4838 (pmt-80) cc_final: 0.4250 (mtp85) outliers start: 2 outliers final: 0 residues processed: 50 average time/residue: 2.7367 time to fit residues: 138.7721 Evaluate side-chains 46 residues out of total 192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 46 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 21 random chunks: chunk 16 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 15 optimal weight: 6.9990 chunk 8 optimal weight: 5.9990 chunk 17 optimal weight: 5.9990 chunk 14 optimal weight: 0.9990 chunk 10 optimal weight: 5.9990 chunk 18 optimal weight: 3.9990 chunk 5 optimal weight: 4.9990 chunk 6 optimal weight: 0.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7478 moved from start: 0.3878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 1698 Z= 0.266 Angle : 0.566 4.132 2274 Z= 0.298 Chirality : 0.050 0.149 258 Planarity : 0.002 0.013 288 Dihedral : 5.207 13.209 222 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 0.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 0.00 % Allowed : 15.62 % Favored : 84.38 % 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: -1.61 (0.46), residues: 213 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.22 (0.35), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 329 PHE 0.008 0.002 PHE A 346 TYR 0.010 0.002 TYR A 310 ARG 0.003 0.001 ARG E 349 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 426 Ramachandran restraints generated. 213 Oldfield, 0 Emsley, 213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 426 Ramachandran restraints generated. 213 Oldfield, 0 Emsley, 213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 47 time to evaluate : 0.355 Fit side-chains REVERT: A 321 LYS cc_start: 0.7123 (ttpt) cc_final: 0.6625 (mtmm) REVERT: A 342 GLU cc_start: 0.8113 (mt-10) cc_final: 0.7768 (mt-10) REVERT: A 347 LYS cc_start: 0.8012 (mttt) cc_final: 0.7811 (mptp) REVERT: C 311 LYS cc_start: 0.5545 (ttpt) cc_final: 0.5236 (ttmt) REVERT: C 321 LYS cc_start: 0.7189 (ttpt) cc_final: 0.6636 (mttm) REVERT: C 345 ASP cc_start: 0.7546 (m-30) cc_final: 0.7147 (t70) REVERT: E 311 LYS cc_start: 0.6741 (ttpt) cc_final: 0.6353 (ptmt) REVERT: E 321 LYS cc_start: 0.7930 (ttpt) cc_final: 0.7324 (mttm) REVERT: E 342 GLU cc_start: 0.8353 (tt0) cc_final: 0.7828 (mt-10) REVERT: E 345 ASP cc_start: 0.7987 (m-30) cc_final: 0.7619 (t70) REVERT: E 347 LYS cc_start: 0.8131 (tttt) cc_final: 0.7720 (mptt) REVERT: E 349 ARG cc_start: 0.4857 (pmt-80) cc_final: 0.4208 (mtp85) outliers start: 0 outliers final: 0 residues processed: 47 average time/residue: 2.6835 time to fit residues: 128.0058 Evaluate side-chains 47 residues out of total 192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 47 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 21 random chunks: chunk 18 optimal weight: 0.8980 chunk 4 optimal weight: 0.9990 chunk 11 optimal weight: 0.8980 chunk 5 optimal weight: 3.9990 chunk 20 optimal weight: 0.9980 chunk 16 optimal weight: 0.5980 chunk 9 optimal weight: 3.9990 chunk 1 optimal weight: 4.9990 chunk 6 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 19 optimal weight: 0.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7466 moved from start: 0.4047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 1698 Z= 0.148 Angle : 0.489 3.862 2274 Z= 0.251 Chirality : 0.050 0.142 258 Planarity : 0.002 0.013 288 Dihedral : 4.813 12.004 222 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 0.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Rotamer: Outliers : 0.00 % Allowed : 15.62 % Favored : 84.38 % 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: -1.65 (0.46), residues: 213 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.25 (0.35), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS E 330 PHE 0.005 0.001 PHE E 346 TYR 0.006 0.001 TYR E 310 ARG 0.001 0.001 ARG A 349 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 426 Ramachandran restraints generated. 213 Oldfield, 0 Emsley, 213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 426 Ramachandran restraints generated. 213 Oldfield, 0 Emsley, 213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 47 time to evaluate : 0.310 Fit side-chains REVERT: A 321 LYS cc_start: 0.7085 (ttpt) cc_final: 0.6636 (mttm) REVERT: A 342 GLU cc_start: 0.8141 (mt-10) cc_final: 0.7792 (mt-10) REVERT: C 311 LYS cc_start: 0.5728 (ttpt) cc_final: 0.5388 (ttmt) REVERT: C 321 LYS cc_start: 0.7198 (ttpt) cc_final: 0.6677 (mttm) REVERT: C 345 ASP cc_start: 0.7586 (m-30) cc_final: 0.7166 (t70) REVERT: E 311 LYS cc_start: 0.6672 (ttpt) cc_final: 0.6247 (pttt) REVERT: E 320 SER cc_start: 0.8076 (t) cc_final: 0.7487 (p) REVERT: E 321 LYS cc_start: 0.7922 (ttpt) cc_final: 0.7334 (mttm) REVERT: E 342 GLU cc_start: 0.8342 (tt0) cc_final: 0.7840 (mt-10) REVERT: E 345 ASP cc_start: 0.7943 (m-30) cc_final: 0.7554 (t70) REVERT: E 347 LYS cc_start: 0.8090 (tttt) cc_final: 0.7676 (mptt) REVERT: E 349 ARG cc_start: 0.4714 (pmt-80) cc_final: 0.4130 (mtp85) outliers start: 0 outliers final: 0 residues processed: 47 average time/residue: 2.6456 time to fit residues: 126.1779 Evaluate side-chains 46 residues out of total 192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 46 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 21 random chunks: chunk 2 optimal weight: 3.9990 chunk 11 optimal weight: 4.9990 chunk 14 optimal weight: 3.9990 chunk 17 optimal weight: 5.9990 chunk 20 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 8 optimal weight: 5.9990 chunk 6 optimal weight: 0.7980 chunk 3 optimal weight: 0.9980 chunk 13 optimal weight: 0.9980 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7475 moved from start: 0.4179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 1698 Z= 0.205 Angle : 0.514 4.122 2274 Z= 0.267 Chirality : 0.050 0.144 258 Planarity : 0.002 0.015 288 Dihedral : 4.791 12.197 222 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 0.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.47 % Favored : 99.53 % Rotamer: Outliers : 0.52 % Allowed : 14.58 % Favored : 84.90 % 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: -1.67 (0.46), residues: 213 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.26 (0.35), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 374 PHE 0.007 0.002 PHE A 346 TYR 0.009 0.002 TYR E 310 ARG 0.001 0.001 ARG C 349 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 426 Ramachandran restraints generated. 213 Oldfield, 0 Emsley, 213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 426 Ramachandran restraints generated. 213 Oldfield, 0 Emsley, 213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 47 time to evaluate : 0.335 Fit side-chains REVERT: A 321 LYS cc_start: 0.7168 (ttpt) cc_final: 0.6669 (mtmm) REVERT: A 342 GLU cc_start: 0.8092 (mt-10) cc_final: 0.7741 (mt-10) REVERT: C 311 LYS cc_start: 0.5586 (ttpt) cc_final: 0.5252 (tttt) REVERT: C 321 LYS cc_start: 0.7215 (ttpt) cc_final: 0.6676 (mttm) REVERT: C 345 ASP cc_start: 0.7555 (m-30) cc_final: 0.7151 (t70) REVERT: C 347 LYS cc_start: 0.7983 (OUTLIER) cc_final: 0.7687 (mptt) REVERT: E 311 LYS cc_start: 0.6727 (ttpt) cc_final: 0.6324 (pttt) REVERT: E 321 LYS cc_start: 0.7937 (ttpt) cc_final: 0.7297 (mttm) REVERT: E 342 GLU cc_start: 0.8340 (tt0) cc_final: 0.7857 (mt-10) REVERT: E 345 ASP cc_start: 0.7968 (m-30) cc_final: 0.7601 (t70) REVERT: E 347 LYS cc_start: 0.8170 (tttt) cc_final: 0.7678 (mptt) REVERT: E 348 ASP cc_start: 0.6307 (t0) cc_final: 0.5926 (t0) REVERT: E 349 ARG cc_start: 0.4689 (pmt-80) cc_final: 0.4021 (mtt-85) outliers start: 1 outliers final: 0 residues processed: 47 average time/residue: 2.6103 time to fit residues: 124.5013 Evaluate side-chains 48 residues out of total 192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 47 time to evaluate : 0.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 347 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 21 random chunks: chunk 10 optimal weight: 5.9990 chunk 1 optimal weight: 4.9990 chunk 15 optimal weight: 0.9980 chunk 18 optimal weight: 2.9990 chunk 19 optimal weight: 0.8980 chunk 17 optimal weight: 4.9990 chunk 11 optimal weight: 0.9990 chunk 8 optimal weight: 0.8980 chunk 14 optimal weight: 2.9990 chunk 5 optimal weight: 0.8980 chunk 12 optimal weight: 0.8980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7464 moved from start: 0.4291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 1698 Z= 0.141 Angle : 0.473 3.763 2274 Z= 0.243 Chirality : 0.050 0.141 258 Planarity : 0.002 0.013 288 Dihedral : 4.593 12.155 222 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 0.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.47 % Favored : 99.53 % Rotamer: Outliers : 0.52 % Allowed : 14.06 % Favored : 85.42 % 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: -1.66 (0.46), residues: 213 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.26 (0.35), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 362 PHE 0.004 0.001 PHE A 346 TYR 0.006 0.001 TYR E 310 ARG 0.001 0.001 ARG A 349 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 426 Ramachandran restraints generated. 213 Oldfield, 0 Emsley, 213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 426 Ramachandran restraints generated. 213 Oldfield, 0 Emsley, 213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 50 time to evaluate : 0.306 Fit side-chains REVERT: A 321 LYS cc_start: 0.7116 (ttpt) cc_final: 0.6630 (mtmm) REVERT: A 342 GLU cc_start: 0.8136 (mt-10) cc_final: 0.7783 (mt-10) REVERT: C 311 LYS cc_start: 0.5687 (ttpt) cc_final: 0.5350 (ttmt) REVERT: C 321 LYS cc_start: 0.7165 (ttpt) cc_final: 0.6673 (mttm) REVERT: C 345 ASP cc_start: 0.7551 (m-30) cc_final: 0.7155 (t70) REVERT: C 347 LYS cc_start: 0.7974 (OUTLIER) cc_final: 0.7670 (mptt) REVERT: E 311 LYS cc_start: 0.6704 (ttpt) cc_final: 0.6310 (pttt) REVERT: E 320 SER cc_start: 0.8074 (t) cc_final: 0.7472 (p) REVERT: E 321 LYS cc_start: 0.7921 (ttpt) cc_final: 0.7319 (mttm) REVERT: E 342 GLU cc_start: 0.8363 (tt0) cc_final: 0.7878 (mt-10) REVERT: E 345 ASP cc_start: 0.7958 (m-30) cc_final: 0.7578 (t70) REVERT: E 347 LYS cc_start: 0.8136 (tttt) cc_final: 0.7699 (mptt) REVERT: E 349 ARG cc_start: 0.4661 (pmt-80) cc_final: 0.4015 (mtt180) outliers start: 1 outliers final: 0 residues processed: 50 average time/residue: 2.5163 time to fit residues: 127.8538 Evaluate side-chains 48 residues out of total 192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 47 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 347 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 21 random chunks: chunk 19 optimal weight: 1.9990 chunk 12 optimal weight: 0.0870 chunk 9 optimal weight: 0.6980 chunk 13 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 chunk 16 optimal weight: 0.7980 chunk 1 optimal weight: 2.9990 chunk 10 optimal weight: 5.9990 chunk 17 optimal weight: 5.9990 chunk 5 optimal weight: 0.7980 chunk 15 optimal weight: 0.9980 overall best weight: 0.6758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7456 moved from start: 0.4384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 1698 Z= 0.136 Angle : 0.468 3.716 2274 Z= 0.237 Chirality : 0.050 0.140 258 Planarity : 0.002 0.014 288 Dihedral : 4.359 11.780 222 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 0.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.47 % Favored : 99.53 % Rotamer: Outliers : 0.52 % Allowed : 14.58 % Favored : 84.90 % 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: -1.66 (0.46), residues: 213 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.26 (0.35), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 362 PHE 0.004 0.001 PHE A 346 TYR 0.005 0.001 TYR E 310 ARG 0.001 0.001 ARG C 349 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 426 Ramachandran restraints generated. 213 Oldfield, 0 Emsley, 213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 426 Ramachandran restraints generated. 213 Oldfield, 0 Emsley, 213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 48 time to evaluate : 0.325 Fit side-chains REVERT: A 321 LYS cc_start: 0.7132 (ttpt) cc_final: 0.6638 (mtmm) REVERT: A 342 GLU cc_start: 0.8116 (mt-10) cc_final: 0.7766 (mt-10) REVERT: C 311 LYS cc_start: 0.5632 (ttpt) cc_final: 0.5298 (ttmt) REVERT: C 321 LYS cc_start: 0.7174 (ttpt) cc_final: 0.6702 (mttm) REVERT: C 345 ASP cc_start: 0.7585 (m-30) cc_final: 0.7168 (t70) REVERT: C 347 LYS cc_start: 0.7955 (OUTLIER) cc_final: 0.7674 (mptt) REVERT: E 311 LYS cc_start: 0.6690 (ttpt) cc_final: 0.6301 (pttt) REVERT: E 320 SER cc_start: 0.8070 (t) cc_final: 0.7501 (p) REVERT: E 321 LYS cc_start: 0.7915 (ttpt) cc_final: 0.7320 (mttm) REVERT: E 338 GLU cc_start: 0.8028 (mt-10) cc_final: 0.7792 (mt-10) REVERT: E 342 GLU cc_start: 0.8376 (tt0) cc_final: 0.7875 (mt-10) REVERT: E 345 ASP cc_start: 0.7961 (m-30) cc_final: 0.7565 (t70) REVERT: E 347 LYS cc_start: 0.8127 (tttt) cc_final: 0.7695 (mptt) REVERT: E 349 ARG cc_start: 0.4690 (pmt-80) cc_final: 0.4038 (mtt180) REVERT: E 372 GLU cc_start: 0.7067 (mm-30) cc_final: 0.6787 (tt0) outliers start: 1 outliers final: 0 residues processed: 48 average time/residue: 2.5714 time to fit residues: 125.2710 Evaluate side-chains 49 residues out of total 192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 48 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 347 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 21 random chunks: chunk 2 optimal weight: 3.9990 chunk 4 optimal weight: 6.9990 chunk 16 optimal weight: 0.7980 chunk 6 optimal weight: 5.9990 chunk 17 optimal weight: 5.9990 chunk 3 optimal weight: 0.9990 chunk 14 optimal weight: 3.9990 chunk 0 optimal weight: 2.9990 chunk 12 optimal weight: 0.7980 chunk 19 optimal weight: 0.8980 chunk 11 optimal weight: 0.7980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7457 moved from start: 0.4433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 1698 Z= 0.141 Angle : 0.466 3.709 2274 Z= 0.238 Chirality : 0.050 0.140 258 Planarity : 0.002 0.013 288 Dihedral : 4.316 11.373 222 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Rotamer: Outliers : 0.52 % Allowed : 14.06 % Favored : 85.42 % 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: -1.69 (0.46), residues: 213 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.28 (0.35), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 362 PHE 0.004 0.001 PHE E 346 TYR 0.006 0.001 TYR E 310 ARG 0.001 0.000 ARG A 349 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 426 Ramachandran restraints generated. 213 Oldfield, 0 Emsley, 213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 426 Ramachandran restraints generated. 213 Oldfield, 0 Emsley, 213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 49 time to evaluate : 0.301 Fit side-chains REVERT: A 321 LYS cc_start: 0.7165 (ttpt) cc_final: 0.6697 (mtmm) REVERT: A 342 GLU cc_start: 0.8105 (mt-10) cc_final: 0.7757 (mt-10) REVERT: C 311 LYS cc_start: 0.5427 (ttpt) cc_final: 0.5110 (ttmt) REVERT: C 321 LYS cc_start: 0.7157 (ttpt) cc_final: 0.6685 (mttm) REVERT: C 345 ASP cc_start: 0.7603 (m-30) cc_final: 0.7173 (t70) REVERT: C 347 LYS cc_start: 0.7969 (OUTLIER) cc_final: 0.7688 (mptt) REVERT: E 311 LYS cc_start: 0.6679 (ttpt) cc_final: 0.6298 (pttt) REVERT: E 321 LYS cc_start: 0.7923 (ttpt) cc_final: 0.7286 (mttm) REVERT: E 338 GLU cc_start: 0.8040 (mt-10) cc_final: 0.7803 (mt-10) REVERT: E 342 GLU cc_start: 0.8371 (tt0) cc_final: 0.7886 (mt-10) REVERT: E 345 ASP cc_start: 0.7946 (m-30) cc_final: 0.7554 (t70) REVERT: E 347 LYS cc_start: 0.8143 (tttt) cc_final: 0.7644 (mptt) REVERT: E 349 ARG cc_start: 0.4731 (pmt-80) cc_final: 0.4103 (mtt180) outliers start: 1 outliers final: 0 residues processed: 49 average time/residue: 2.5111 time to fit residues: 124.8978 Evaluate side-chains 48 residues out of total 192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 47 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 347 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 21 random chunks: chunk 14 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 13 optimal weight: 4.9990 chunk 12 optimal weight: 0.0060 chunk 8 optimal weight: 0.9990 chunk 7 optimal weight: 0.9990 chunk 20 optimal weight: 3.9990 chunk 3 optimal weight: 5.9990 chunk 2 optimal weight: 3.9990 chunk 4 optimal weight: 4.9990 chunk 16 optimal weight: 0.6980 overall best weight: 1.1402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7461 moved from start: 0.4431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 1698 Z= 0.157 Angle : 0.480 3.717 2274 Z= 0.246 Chirality : 0.050 0.140 258 Planarity : 0.002 0.014 288 Dihedral : 4.359 11.284 222 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.47 % Favored : 99.53 % Rotamer: Outliers : 0.52 % Allowed : 15.10 % Favored : 84.38 % 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: -1.67 (0.46), residues: 213 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.26 (0.35), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 374 PHE 0.006 0.001 PHE A 346 TYR 0.006 0.002 TYR E 310 ARG 0.001 0.001 ARG C 349 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 426 Ramachandran restraints generated. 213 Oldfield, 0 Emsley, 213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 426 Ramachandran restraints generated. 213 Oldfield, 0 Emsley, 213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 47 time to evaluate : 0.318 Fit side-chains revert: symmetry clash REVERT: A 321 LYS cc_start: 0.7174 (ttpt) cc_final: 0.6705 (mtmm) REVERT: A 342 GLU cc_start: 0.8092 (mt-10) cc_final: 0.7750 (mt-10) REVERT: C 311 LYS cc_start: 0.5415 (ttpt) cc_final: 0.5106 (tttt) REVERT: C 321 LYS cc_start: 0.7154 (ttpt) cc_final: 0.6689 (mttm) REVERT: C 345 ASP cc_start: 0.7599 (m-30) cc_final: 0.7175 (t70) REVERT: E 311 LYS cc_start: 0.6670 (ttpt) cc_final: 0.6287 (pttt) REVERT: E 321 LYS cc_start: 0.7918 (ttpt) cc_final: 0.7294 (mttm) REVERT: E 342 GLU cc_start: 0.8361 (tt0) cc_final: 0.7893 (mt-10) REVERT: E 345 ASP cc_start: 0.7903 (m-30) cc_final: 0.7542 (t70) REVERT: E 347 LYS cc_start: 0.8093 (tttt) cc_final: 0.7681 (mptt) REVERT: E 349 ARG cc_start: 0.4854 (pmt-80) cc_final: 0.4104 (mtt180) outliers start: 1 outliers final: 1 residues processed: 47 average time/residue: 2.6542 time to fit residues: 126.6154 Evaluate side-chains 48 residues out of total 192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 47 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 347 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 21 random chunks: chunk 19 optimal weight: 0.8980 chunk 0 optimal weight: 5.9990 chunk 8 optimal weight: 5.9990 chunk 2 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 4 optimal weight: 5.9990 chunk 13 optimal weight: 0.9980 chunk 7 optimal weight: 0.8980 chunk 3 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.133651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.123098 restraints weight = 6219.706| |-----------------------------------------------------------------------------| r_work (start): 0.3929 rms_B_bonded: 1.55 r_work: 0.3854 rms_B_bonded: 1.66 restraints_weight: 0.5000 r_work: 0.3775 rms_B_bonded: 2.91 restraints_weight: 0.2500 r_work (final): 0.3775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.4444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 1698 Z= 0.170 Angle : 0.495 3.737 2274 Z= 0.254 Chirality : 0.050 0.141 258 Planarity : 0.002 0.013 288 Dihedral : 4.438 11.230 222 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 0.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 0.52 % Allowed : 15.10 % Favored : 84.38 % 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: -1.69 (0.46), residues: 213 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.28 (0.35), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 374 PHE 0.006 0.001 PHE A 346 TYR 0.007 0.002 TYR E 310 ARG 0.001 0.001 ARG C 349 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3476.80 seconds wall clock time: 60 minutes 23.69 seconds (3623.69 seconds total)