Starting phenix.real_space_refine on Sun Mar 10 17:06:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q9i_18282/03_2024/8q9i_18282.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q9i_18282/03_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_18282/03_2024/8q9i_18282.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q9i_18282/03_2024/8q9i_18282.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q9i_18282/03_2024/8q9i_18282.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q9i_18282/03_2024/8q9i_18282.pdb" } 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-5265/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: 1.88, per 1000 atoms: 0.55 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: 2.43 Conformation dependent library (CDL) restraints added in 347.6 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: 0.31 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: 1.12 Time building geometry restraints manager: 2.54 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 1.850 nonbonded pdb=" OD1 ASP A 314 " pdb=" HG SER A 316 " model vdw 1.607 1.850 nonbonded pdb=" OD1 ASP E 314 " pdb=" HG SER E 316 " model vdw 1.609 1.850 nonbonded pdb=" OD2 ASP A 314 " pdb=" HZ1 LYS A 370 " model vdw 1.673 1.850 nonbonded pdb=" OD2 ASP E 314 " pdb=" HZ3 LYS E 370 " model vdw 1.717 1.850 ... (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 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: 2.370 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: 0.040 Extract box with map and model: 11.460 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 15.200 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: 0.000 Load rotamer database and sin/cos tables:11.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.880 ------------------------------------------------------------------------------- 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 : 0.275 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: 2.7443 time to fit residues: 208.5151 Evaluate side-chains 47 residues out of total 192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 47 time to evaluate : 0.271 ------------------------------------------------------------------------------- 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: 1.9990 chunk 15 optimal weight: 3.9990 chunk 8 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 16 optimal weight: 0.7980 chunk 6 optimal weight: 3.9990 chunk 12 optimal weight: 0.9980 chunk 19 optimal weight: 0.7980 chunk 20 optimal weight: 0.9990 chunk 18 optimal weight: 0.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- 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: 0.7433 moved from start: 0.3226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 1698 Z= 0.199 Angle : 0.591 4.205 2274 Z= 0.308 Chirality : 0.050 0.153 258 Planarity : 0.002 0.019 288 Dihedral : 6.345 16.895 222 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 1.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.47 % Favored : 99.53 % Rotamer: Outliers : 1.56 % Allowed : 15.10 % Favored : 83.33 % 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: -1.36 (0.48), residues: 213 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.03 (0.36), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS E 330 PHE 0.007 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 53 residues out of total 192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 50 time to evaluate : 0.285 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 321 LYS cc_start: 0.7079 (ttpt) cc_final: 0.6547 (mtmm) REVERT: A 338 GLU cc_start: 0.7539 (tt0) cc_final: 0.7327 (mt-10) REVERT: A 342 GLU cc_start: 0.8028 (mt-10) cc_final: 0.7679 (mt-10) REVERT: C 321 LYS cc_start: 0.7092 (ttpt) cc_final: 0.6586 (mttm) REVERT: C 342 GLU cc_start: 0.8402 (OUTLIER) cc_final: 0.8147 (mt-10) REVERT: E 311 LYS cc_start: 0.6751 (ttpt) cc_final: 0.6373 (ptmt) REVERT: E 320 SER cc_start: 0.8043 (t) cc_final: 0.7571 (p) REVERT: E 321 LYS cc_start: 0.7897 (ttpt) cc_final: 0.7346 (mttm) REVERT: E 342 GLU cc_start: 0.8232 (tt0) cc_final: 0.7644 (mt-10) REVERT: E 345 ASP cc_start: 0.8033 (m-30) cc_final: 0.7648 (t70) REVERT: E 347 LYS cc_start: 0.8013 (tttt) cc_final: 0.7664 (mptt) REVERT: E 349 ARG cc_start: 0.4784 (pmt-80) cc_final: 0.4160 (mtp180) outliers start: 3 outliers final: 1 residues processed: 51 average time/residue: 2.8301 time to fit residues: 146.3194 Evaluate side-chains 49 residues out of total 192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 47 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 342 GLU Chi-restraints excluded: chain E residue 317 LYS 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: 5.9990 chunk 18 optimal weight: 0.0270 chunk 14 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 12 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 10 optimal weight: 5.9990 chunk 5 optimal weight: 0.6980 overall best weight: 1.1444 ------------------------------------------------------------------------------- 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: 0.7439 moved from start: 0.3766 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= 0.155 Angle : 0.513 3.921 2274 Z= 0.265 Chirality : 0.050 0.143 258 Planarity : 0.002 0.011 288 Dihedral : 5.092 13.008 222 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 1.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Rotamer: Outliers : 1.56 % Allowed : 15.62 % Favored : 82.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (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 0.002 0.001 HIS E 329 PHE 0.007 0.002 PHE A 346 TYR 0.008 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 54 residues out of total 192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 51 time to evaluate : 0.353 Fit side-chains revert: symmetry clash REVERT: A 321 LYS cc_start: 0.7186 (ttpt) cc_final: 0.6667 (mtmm) REVERT: A 342 GLU cc_start: 0.8042 (mt-10) cc_final: 0.7806 (mt-10) REVERT: C 321 LYS cc_start: 0.7095 (ttpt) cc_final: 0.6571 (mttm) REVERT: C 345 ASP cc_start: 0.7513 (m-30) cc_final: 0.7066 (t70) REVERT: E 311 LYS cc_start: 0.6685 (ttpt) cc_final: 0.6338 (ptmt) REVERT: E 320 SER cc_start: 0.8061 (t) cc_final: 0.7525 (p) REVERT: E 321 LYS cc_start: 0.7891 (ttpt) cc_final: 0.7333 (mttm) REVERT: E 342 GLU cc_start: 0.8273 (tt0) cc_final: 0.7723 (mt-10) REVERT: E 345 ASP cc_start: 0.7972 (m-30) cc_final: 0.7619 (t70) REVERT: E 347 LYS cc_start: 0.7974 (tttt) cc_final: 0.7587 (mptp) REVERT: E 349 ARG cc_start: 0.4897 (pmt-80) cc_final: 0.4263 (mtt180) outliers start: 3 outliers final: 1 residues processed: 52 average time/residue: 2.7546 time to fit residues: 145.2443 Evaluate side-chains 48 residues out of total 192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 47 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 315 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 21 random chunks: chunk 16 optimal weight: 0.9990 chunk 11 optimal weight: 0.9990 chunk 0 optimal weight: 5.9990 chunk 15 optimal weight: 6.9990 chunk 8 optimal weight: 3.9990 chunk 17 optimal weight: 5.9990 chunk 14 optimal weight: 2.9990 chunk 10 optimal weight: 4.9990 chunk 18 optimal weight: 4.9990 chunk 5 optimal weight: 4.9990 chunk 6 optimal weight: 2.9990 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: 0.7464 moved from start: 0.4037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 1698 Z= 0.261 Angle : 0.573 4.440 2274 Z= 0.300 Chirality : 0.050 0.145 258 Planarity : 0.002 0.014 288 Dihedral : 5.184 13.967 222 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 2.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Rotamer: Outliers : 0.00 % Allowed : 16.67 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.49 (0.47), residues: 213 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.13 (0.36), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 329 PHE 0.007 0.002 PHE A 346 TYR 0.011 0.003 TYR E 310 ARG 0.002 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 45 residues out of total 192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 45 time to evaluate : 0.295 Fit side-chains REVERT: A 321 LYS cc_start: 0.7194 (ttpt) cc_final: 0.6692 (mtmm) REVERT: A 342 GLU cc_start: 0.8068 (mt-10) cc_final: 0.7669 (mt-10) REVERT: C 321 LYS cc_start: 0.7078 (ttpt) cc_final: 0.6526 (mttm) REVERT: C 345 ASP cc_start: 0.7509 (m-30) cc_final: 0.7138 (t70) REVERT: E 311 LYS cc_start: 0.6675 (ttpt) cc_final: 0.6351 (ptmt) REVERT: E 321 LYS cc_start: 0.7909 (ttpt) cc_final: 0.7309 (mttm) REVERT: E 342 GLU cc_start: 0.8325 (tt0) cc_final: 0.7742 (mt-10) REVERT: E 345 ASP cc_start: 0.7981 (m-30) cc_final: 0.7581 (t70) REVERT: E 347 LYS cc_start: 0.8143 (tttt) cc_final: 0.7705 (mptp) REVERT: E 349 ARG cc_start: 0.4869 (pmt-80) cc_final: 0.4184 (mtp85) outliers start: 0 outliers final: 0 residues processed: 45 average time/residue: 2.8844 time to fit residues: 131.7320 Evaluate side-chains 43 residues out of total 192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 43 time to evaluate : 0.295 ------------------------------------------------------------------------------- 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: 0.7980 chunk 4 optimal weight: 1.9990 chunk 11 optimal weight: 0.7980 chunk 5 optimal weight: 4.9990 chunk 20 optimal weight: 4.9990 chunk 16 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 1 optimal weight: 5.9990 chunk 6 optimal weight: 0.8980 chunk 10 optimal weight: 4.9990 chunk 19 optimal weight: 0.8980 overall best weight: 1.0782 ------------------------------------------------------------------------------- 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: 0.4248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 1698 Z= 0.151 Angle : 0.498 4.987 2274 Z= 0.253 Chirality : 0.049 0.138 258 Planarity : 0.002 0.014 288 Dihedral : 4.852 12.620 222 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 1.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.47 % Favored : 99.53 % Rotamer: Outliers : 0.00 % Allowed : 17.19 % Favored : 82.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.54 (0.47), residues: 213 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.17 (0.36), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 374 PHE 0.007 0.001 PHE A 346 TYR 0.006 0.001 TYR E 310 ARG 0.002 0.001 ARG C 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 45 residues out of total 192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 45 time to evaluate : 0.295 Fit side-chains REVERT: A 315 LEU cc_start: 0.5763 (mm) cc_final: 0.5509 (mm) REVERT: A 321 LYS cc_start: 0.7216 (ttpt) cc_final: 0.6736 (mtmm) REVERT: A 342 GLU cc_start: 0.8074 (mt-10) cc_final: 0.7783 (mt-10) REVERT: C 321 LYS cc_start: 0.7038 (ttpt) cc_final: 0.6525 (mttm) REVERT: C 345 ASP cc_start: 0.7537 (m-30) cc_final: 0.7134 (t70) REVERT: E 311 LYS cc_start: 0.6695 (ttpt) cc_final: 0.6334 (ptmt) REVERT: E 321 LYS cc_start: 0.7922 (ttpt) cc_final: 0.7312 (mttm) REVERT: E 342 GLU cc_start: 0.8342 (tt0) cc_final: 0.7805 (mt-10) REVERT: E 345 ASP cc_start: 0.7973 (m-30) cc_final: 0.7563 (t70) REVERT: E 347 LYS cc_start: 0.8116 (tttt) cc_final: 0.7688 (mptt) REVERT: E 349 ARG cc_start: 0.4763 (pmt-80) cc_final: 0.4118 (mtp85) outliers start: 0 outliers final: 0 residues processed: 45 average time/residue: 2.8018 time to fit residues: 127.9581 Evaluate side-chains 44 residues out of total 192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 44 time to evaluate : 0.267 ------------------------------------------------------------------------------- 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: 5.9990 chunk 14 optimal weight: 3.9990 chunk 17 optimal weight: 6.9990 chunk 20 optimal weight: 4.9990 chunk 12 optimal weight: 0.6980 chunk 9 optimal weight: 0.9990 chunk 8 optimal weight: 6.9990 chunk 6 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- 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: 0.7454 moved from start: 0.4298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 1698 Z= 0.158 Angle : 0.487 3.857 2274 Z= 0.248 Chirality : 0.049 0.139 258 Planarity : 0.002 0.014 288 Dihedral : 4.676 12.962 222 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 0.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.47 % Favored : 99.53 % Rotamer: Outliers : 0.52 % Allowed : 17.19 % Favored : 82.29 % 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: -1.51 (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 0.001 0.001 HIS A 374 PHE 0.005 0.001 PHE A 346 TYR 0.007 0.001 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 : 0.223 Fit side-chains REVERT: A 315 LEU cc_start: 0.5783 (mm) cc_final: 0.5500 (mm) REVERT: A 321 LYS cc_start: 0.7220 (ttpt) cc_final: 0.6735 (mtmm) REVERT: A 342 GLU cc_start: 0.8079 (mt-10) cc_final: 0.7769 (mt-10) REVERT: C 321 LYS cc_start: 0.6998 (ttpt) cc_final: 0.6495 (mttm) REVERT: C 345 ASP cc_start: 0.7522 (m-30) cc_final: 0.7098 (t70) REVERT: C 347 LYS cc_start: 0.7984 (OUTLIER) cc_final: 0.7656 (mptt) REVERT: E 311 LYS cc_start: 0.6631 (ttpt) cc_final: 0.6346 (ptmt) REVERT: E 314 ASP cc_start: 0.4644 (t0) cc_final: 0.4274 (t0) REVERT: E 321 LYS cc_start: 0.7921 (ttpt) cc_final: 0.7298 (mttm) REVERT: E 342 GLU cc_start: 0.8330 (tt0) cc_final: 0.7831 (mt-10) REVERT: E 345 ASP cc_start: 0.8002 (m-30) cc_final: 0.7605 (t70) REVERT: E 347 LYS cc_start: 0.8146 (tttt) cc_final: 0.7727 (mptt) REVERT: E 349 ARG cc_start: 0.4786 (pmt-80) cc_final: 0.4121 (mtt-85) outliers start: 1 outliers final: 0 residues processed: 47 average time/residue: 2.6176 time to fit residues: 124.8121 Evaluate side-chains 47 residues out of total 192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 46 time to evaluate : 0.281 ------------------------------------------------------------------------------- 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: 0.9990 chunk 18 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 17 optimal weight: 4.9990 chunk 11 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 chunk 5 optimal weight: 0.9980 chunk 12 optimal weight: 0.9980 overall best weight: 0.9986 ------------------------------------------------------------------------------- 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: 0.7450 moved from start: 0.4454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 1698 Z= 0.141 Angle : 0.475 3.982 2274 Z= 0.242 Chirality : 0.049 0.138 258 Planarity : 0.002 0.013 288 Dihedral : 4.554 11.232 222 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 0.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.47 % Favored : 99.53 % Rotamer: Outliers : 0.52 % Allowed : 16.15 % Favored : 83.33 % 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: -1.47 (0.48), residues: 213 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.11 (0.36), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 374 PHE 0.004 0.001 PHE A 346 TYR 0.007 0.001 TYR A 310 ARG 0.001 0.000 ARG C 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 50 residues out of total 192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 49 time to evaluate : 0.293 Fit side-chains REVERT: A 315 LEU cc_start: 0.5723 (mm) cc_final: 0.5421 (mm) REVERT: A 321 LYS cc_start: 0.7222 (ttpt) cc_final: 0.6737 (mtmm) REVERT: A 342 GLU cc_start: 0.8072 (mt-10) cc_final: 0.7759 (mt-10) REVERT: C 321 LYS cc_start: 0.6976 (ttpt) cc_final: 0.6483 (mttm) REVERT: C 345 ASP cc_start: 0.7525 (m-30) cc_final: 0.7077 (t70) REVERT: C 347 LYS cc_start: 0.7993 (OUTLIER) cc_final: 0.7375 (mptp) REVERT: E 311 LYS cc_start: 0.6667 (ttpt) cc_final: 0.6349 (ptmt) REVERT: E 314 ASP cc_start: 0.4616 (t0) cc_final: 0.4191 (t0) REVERT: E 321 LYS cc_start: 0.7960 (ttpt) cc_final: 0.7321 (mttm) REVERT: E 342 GLU cc_start: 0.8329 (tt0) cc_final: 0.7845 (mt-10) REVERT: E 345 ASP cc_start: 0.7989 (m-30) cc_final: 0.7600 (t70) REVERT: E 347 LYS cc_start: 0.8164 (tttt) cc_final: 0.7690 (mptt) REVERT: E 348 ASP cc_start: 0.5803 (t0) cc_final: 0.5378 (t0) REVERT: E 349 ARG cc_start: 0.4729 (pmt-80) cc_final: 0.4076 (mtt-85) outliers start: 1 outliers final: 0 residues processed: 49 average time/residue: 2.5066 time to fit residues: 124.7186 Evaluate side-chains 49 residues out of total 192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 48 time to evaluate : 0.257 ------------------------------------------------------------------------------- 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: 3.9990 chunk 12 optimal weight: 4.9990 chunk 9 optimal weight: 0.6980 chunk 13 optimal weight: 3.9990 chunk 20 optimal weight: 4.9990 chunk 16 optimal weight: 2.9990 chunk 1 optimal weight: 5.9990 chunk 10 optimal weight: 5.9990 chunk 17 optimal weight: 5.9990 chunk 5 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- 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: 0.7468 moved from start: 0.4465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 1698 Z= 0.227 Angle : 0.520 4.124 2274 Z= 0.272 Chirality : 0.049 0.143 258 Planarity : 0.002 0.013 288 Dihedral : 4.807 12.362 222 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 0.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % 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: -1.49 (0.47), residues: 213 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.12 (0.36), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 329 PHE 0.006 0.002 PHE A 346 TYR 0.011 0.003 TYR E 310 ARG 0.002 0.001 ARG E 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 47 residues out of total 192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 46 time to evaluate : 0.292 Fit side-chains REVERT: A 315 LEU cc_start: 0.5765 (mm) cc_final: 0.5504 (mm) REVERT: A 321 LYS cc_start: 0.7243 (ttpt) cc_final: 0.6742 (mtmm) REVERT: A 342 GLU cc_start: 0.8079 (mt-10) cc_final: 0.7790 (mt-10) REVERT: C 321 LYS cc_start: 0.7004 (ttpt) cc_final: 0.6498 (mttm) REVERT: C 345 ASP cc_start: 0.7537 (m-30) cc_final: 0.7095 (t70) REVERT: C 347 LYS cc_start: 0.7986 (OUTLIER) cc_final: 0.7736 (mptt) REVERT: E 311 LYS cc_start: 0.6724 (ttpt) cc_final: 0.6367 (pttt) REVERT: E 321 LYS cc_start: 0.7929 (ttpt) cc_final: 0.7289 (mttm) REVERT: E 342 GLU cc_start: 0.8344 (tt0) cc_final: 0.7847 (mt-10) REVERT: E 345 ASP cc_start: 0.7971 (m-30) cc_final: 0.7583 (t70) REVERT: E 347 LYS cc_start: 0.8209 (tttt) cc_final: 0.7751 (mptt) REVERT: E 349 ARG cc_start: 0.4706 (pmt-80) cc_final: 0.4011 (mtt180) outliers start: 1 outliers final: 0 residues processed: 46 average time/residue: 2.6959 time to fit residues: 125.7687 Evaluate side-chains 47 residues out of total 192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 46 time to evaluate : 0.284 ------------------------------------------------------------------------------- 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: 0.8980 chunk 6 optimal weight: 5.9990 chunk 17 optimal weight: 4.9990 chunk 3 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 chunk 0 optimal weight: 2.9990 chunk 12 optimal weight: 0.5980 chunk 19 optimal weight: 0.9990 chunk 11 optimal weight: 0.7980 overall best weight: 1.0584 ------------------------------------------------------------------------------- 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: 0.4535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 1698 Z= 0.145 Angle : 0.479 3.858 2274 Z= 0.244 Chirality : 0.049 0.136 258 Planarity : 0.002 0.011 288 Dihedral : 4.602 11.437 222 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 1.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.47 % Favored : 99.53 % Rotamer: Outliers : 0.52 % Allowed : 15.62 % 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 : -1.16 (0.36), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 374 PHE 0.004 0.001 PHE E 346 TYR 0.006 0.002 TYR E 310 ARG 0.001 0.000 ARG C 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 49 residues out of total 192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 48 time to evaluate : 0.306 Fit side-chains revert: symmetry clash REVERT: A 315 LEU cc_start: 0.5784 (mm) cc_final: 0.5482 (mm) REVERT: A 321 LYS cc_start: 0.7232 (ttpt) cc_final: 0.6735 (mtmm) REVERT: A 342 GLU cc_start: 0.8079 (mt-10) cc_final: 0.7711 (mt-10) REVERT: C 321 LYS cc_start: 0.6998 (ttpt) cc_final: 0.6502 (mttm) REVERT: C 345 ASP cc_start: 0.7552 (m-30) cc_final: 0.7119 (t70) REVERT: E 311 LYS cc_start: 0.6679 (ttpt) cc_final: 0.6353 (ptmt) REVERT: E 314 ASP cc_start: 0.4578 (t0) cc_final: 0.4207 (t0) REVERT: E 321 LYS cc_start: 0.7943 (ttpt) cc_final: 0.7307 (mttm) REVERT: E 342 GLU cc_start: 0.8359 (tt0) cc_final: 0.7863 (mt-10) REVERT: E 345 ASP cc_start: 0.7973 (m-30) cc_final: 0.7578 (t70) REVERT: E 347 LYS cc_start: 0.8171 (tttt) cc_final: 0.7670 (mptt) REVERT: E 349 ARG cc_start: 0.4702 (pmt-80) cc_final: 0.4066 (mtt180) outliers start: 1 outliers final: 1 residues processed: 48 average time/residue: 2.6475 time to fit residues: 129.0314 Evaluate side-chains 49 residues out of total 192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 48 time to evaluate : 0.290 ------------------------------------------------------------------------------- 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: 0.9980 chunk 0 optimal weight: 0.9990 chunk 13 optimal weight: 4.9990 chunk 12 optimal weight: 2.9990 chunk 8 optimal weight: 5.9990 chunk 7 optimal weight: 2.9990 chunk 20 optimal weight: 0.8980 chunk 3 optimal weight: 6.9990 chunk 2 optimal weight: 3.9990 chunk 4 optimal weight: 4.9990 chunk 16 optimal weight: 0.6980 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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: 0.7462 moved from start: 0.4558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 1698 Z= 0.164 Angle : 0.488 3.906 2274 Z= 0.250 Chirality : 0.049 0.140 258 Planarity : 0.002 0.013 288 Dihedral : 4.571 11.415 222 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 1.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.47 % Favored : 99.53 % Rotamer: Outliers : 0.52 % Allowed : 16.15 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.54 (0.47), residues: 213 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.16 (0.36), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS A 374 PHE 0.004 0.001 PHE E 346 TYR 0.008 0.002 TYR A 310 ARG 0.001 0.001 ARG E 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 49 residues out of total 192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 48 time to evaluate : 0.305 Fit side-chains REVERT: A 315 LEU cc_start: 0.5772 (mm) cc_final: 0.5468 (mm) REVERT: A 321 LYS cc_start: 0.7255 (ttpt) cc_final: 0.6745 (mtmm) REVERT: A 342 GLU cc_start: 0.8080 (mt-10) cc_final: 0.7707 (mt-10) REVERT: C 321 LYS cc_start: 0.7006 (ttpt) cc_final: 0.6521 (mttm) REVERT: C 345 ASP cc_start: 0.7544 (m-30) cc_final: 0.7089 (t70) REVERT: C 347 LYS cc_start: 0.7993 (OUTLIER) cc_final: 0.7682 (mptt) REVERT: E 311 LYS cc_start: 0.6687 (ttpt) cc_final: 0.6349 (pttt) REVERT: E 314 ASP cc_start: 0.4553 (t0) cc_final: 0.4159 (t0) REVERT: E 321 LYS cc_start: 0.7932 (ttpt) cc_final: 0.7303 (mttm) REVERT: E 342 GLU cc_start: 0.8348 (tt0) cc_final: 0.7864 (mt-10) REVERT: E 345 ASP cc_start: 0.7977 (m-30) cc_final: 0.7585 (t70) REVERT: E 347 LYS cc_start: 0.8119 (tttt) cc_final: 0.7699 (mptt) REVERT: E 349 ARG cc_start: 0.4807 (pmt-80) cc_final: 0.4032 (mtt180) outliers start: 1 outliers final: 0 residues processed: 48 average time/residue: 2.7051 time to fit residues: 131.7685 Evaluate side-chains 49 residues out of total 192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 48 time to evaluate : 0.310 ------------------------------------------------------------------------------- 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: 3.9990 chunk 0 optimal weight: 5.9990 chunk 8 optimal weight: 5.9990 chunk 2 optimal weight: 3.9990 chunk 5 optimal weight: 0.7980 chunk 4 optimal weight: 0.9990 chunk 13 optimal weight: 0.8980 chunk 7 optimal weight: 0.0670 chunk 3 optimal weight: 6.9990 chunk 10 optimal weight: 0.7980 chunk 20 optimal weight: 1.9990 overall best weight: 0.7120 ------------------------------------------------------------------------------- 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 = 0.4099 r_free = 0.4099 target = 0.134559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.123688 restraints weight = 6070.981| |-----------------------------------------------------------------------------| r_work (start): 0.3955 rms_B_bonded: 1.61 r_work: 0.3877 rms_B_bonded: 1.72 restraints_weight: 0.5000 r_work: 0.3799 rms_B_bonded: 3.00 restraints_weight: 0.2500 r_work (final): 0.3799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.4627 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= 0.126 Angle : 0.464 3.782 2274 Z= 0.235 Chirality : 0.050 0.135 258 Planarity : 0.002 0.011 288 Dihedral : 4.432 11.180 222 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 1.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Rotamer: Outliers : 0.52 % Allowed : 15.62 % 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: -1.52 (0.48), 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 C 330 PHE 0.003 0.001 PHE E 346 TYR 0.005 0.001 TYR E 310 ARG 0.001 0.000 ARG C 349 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3441.32 seconds wall clock time: 60 minutes 31.35 seconds (3631.35 seconds total)