Starting phenix.real_space_refine on Fri Aug 2 15:52:53 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q7f_18215/08_2024/8q7f_18215.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q7f_18215/08_2024/8q7f_18215.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.72 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q7f_18215/08_2024/8q7f_18215.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q7f_18215/08_2024/8q7f_18215.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q7f_18215/08_2024/8q7f_18215.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q7f_18215/08_2024/8q7f_18215.cif" } resolution = 3.72 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= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 6 5.16 5 C 2136 2.51 5 N 618 2.21 5 O 642 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 342": "OE1" <-> "OE2" Residue "F PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 342": "OE1" <-> "OE2" Residue "E GLU 342": "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: 3402 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 567 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "D" Number of atoms: 567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 567 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "F" Number of atoms: 567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 567 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "A" Number of atoms: 567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 567 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "C" Number of atoms: 567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 567 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "E" Number of atoms: 567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 567 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Time building chain proxies: 3.67, per 1000 atoms: 1.08 Number of scatterers: 3402 At special positions: 0 Unit cell: (106.142, 107.596, 37.804, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 6 16.00 O 642 8.00 N 618 7.00 C 2136 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 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: 1.26 Conformation dependent library (CDL) restraints added in 667.8 milliseconds 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 780 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 18 sheets defined 0.0% alpha, 53.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.54 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'D' and resid 305 through 310 removed outlier: 6.581A pdb=" N SER B 305 " --> pdb=" O VAL D 306 " (cutoff:3.500A) removed outlier: 8.239A pdb=" N ILE D 308 " --> pdb=" O SER B 305 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N GLN B 307 " --> pdb=" O ILE D 308 " (cutoff:3.500A) removed outlier: 7.914A pdb=" N TYR D 310 " --> pdb=" O GLN B 307 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N VAL B 309 " --> pdb=" O TYR D 310 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 313 through 314 removed outlier: 6.992A pdb=" N VAL B 313 " --> pdb=" O ASP D 314 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 317 through 325 removed outlier: 6.326A pdb=" N LYS B 317 " --> pdb=" O VAL D 318 " (cutoff:3.500A) removed outlier: 7.968A pdb=" N SER D 320 " --> pdb=" O LYS B 317 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N THR B 319 " --> pdb=" O SER D 320 " (cutoff:3.500A) removed outlier: 7.952A pdb=" N CYS D 322 " --> pdb=" O THR B 319 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N LYS B 321 " --> pdb=" O CYS D 322 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N SER D 324 " --> pdb=" O LYS B 321 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N GLY B 323 " --> pdb=" O SER D 324 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 328 through 330 removed outlier: 6.448A pdb=" N ILE B 328 " --> pdb=" O HIS D 329 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 337 through 342 removed outlier: 6.652A pdb=" N VAL B 337 " --> pdb=" O GLU F 338 " (cutoff:3.500A) removed outlier: 8.115A pdb=" N LYS F 340 " --> pdb=" O VAL B 337 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N VAL B 339 " --> pdb=" O LYS F 340 " (cutoff:3.500A) removed outlier: 8.211A pdb=" N GLU F 342 " --> pdb=" O VAL B 339 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N SER B 341 " --> pdb=" O GLU F 342 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 345 through 346 removed outlier: 6.687A pdb=" N ASP B 345 " --> pdb=" O PHE D 346 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N PHE B 346 " --> pdb=" O ASP F 345 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'D' and resid 350 through 354 removed outlier: 6.612A pdb=" N GLN B 351 " --> pdb=" O SER D 352 " (cutoff:3.500A) removed outlier: 8.181A pdb=" N ILE D 354 " --> pdb=" O GLN B 351 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N LYS B 353 " --> pdb=" O ILE D 354 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 357 through 362 removed outlier: 6.715A pdb=" N LEU B 357 " --> pdb=" O ASP F 358 " (cutoff:3.500A) removed outlier: 8.334A pdb=" N ILE F 360 " --> pdb=" O LEU B 357 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N ASN B 359 " --> pdb=" O ILE F 360 " (cutoff:3.500A) removed outlier: 8.232A pdb=" N HIS F 362 " --> pdb=" O ASN B 359 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N THR B 361 " --> pdb=" O HIS F 362 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 368 through 377 removed outlier: 6.555A pdb=" N LYS B 369 " --> pdb=" O LYS D 370 " (cutoff:3.500A) removed outlier: 8.209A pdb=" N GLU D 372 " --> pdb=" O LYS B 369 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N ILE B 371 " --> pdb=" O GLU D 372 " (cutoff:3.500A) removed outlier: 8.180A pdb=" N HIS D 374 " --> pdb=" O ILE B 371 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N THR B 373 " --> pdb=" O HIS D 374 " (cutoff:3.500A) removed outlier: 7.787A pdb=" N LEU D 376 " --> pdb=" O THR B 373 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N LYS B 375 " --> pdb=" O LEU D 376 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 305 through 310 removed outlier: 6.581A pdb=" N SER A 305 " --> pdb=" O VAL C 306 " (cutoff:3.500A) removed outlier: 8.239A pdb=" N ILE C 308 " --> pdb=" O SER A 305 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N GLN A 307 " --> pdb=" O ILE C 308 " (cutoff:3.500A) removed outlier: 7.914A pdb=" N TYR C 310 " --> pdb=" O GLN A 307 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N VAL A 309 " --> pdb=" O TYR C 310 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 313 through 314 removed outlier: 6.991A pdb=" N VAL A 313 " --> pdb=" O ASP C 314 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 317 through 325 removed outlier: 6.326A pdb=" N LYS A 317 " --> pdb=" O VAL C 318 " (cutoff:3.500A) removed outlier: 7.969A pdb=" N SER C 320 " --> pdb=" O LYS A 317 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N THR A 319 " --> pdb=" O SER C 320 " (cutoff:3.500A) removed outlier: 7.951A pdb=" N CYS C 322 " --> pdb=" O THR A 319 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N LYS A 321 " --> pdb=" O CYS C 322 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N SER C 324 " --> pdb=" O LYS A 321 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N GLY A 323 " --> pdb=" O SER C 324 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 328 through 330 removed outlier: 6.448A pdb=" N ILE A 328 " --> pdb=" O HIS C 329 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 337 through 342 removed outlier: 6.653A pdb=" N VAL A 337 " --> pdb=" O GLU E 338 " (cutoff:3.500A) removed outlier: 8.068A pdb=" N LYS E 340 " --> pdb=" O VAL A 337 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N VAL A 339 " --> pdb=" O LYS E 340 " (cutoff:3.500A) removed outlier: 7.927A pdb=" N GLU E 342 " --> pdb=" O VAL A 339 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N SER A 341 " --> pdb=" O GLU E 342 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 345 through 346 removed outlier: 6.823A pdb=" N ASP A 345 " --> pdb=" O PHE C 346 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 350 through 354 removed outlier: 6.381A pdb=" N VAL A 350 " --> pdb=" O GLN E 351 " (cutoff:3.500A) removed outlier: 8.094A pdb=" N LYS E 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N SER A 352 " --> pdb=" O LYS E 353 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 357 through 362 removed outlier: 6.732A pdb=" N LEU A 357 " --> pdb=" O ASP E 358 " (cutoff:3.500A) removed outlier: 8.303A pdb=" N ILE E 360 " --> pdb=" O LEU A 357 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N ASN A 359 " --> pdb=" O ILE E 360 " (cutoff:3.500A) removed outlier: 8.232A pdb=" N HIS E 362 " --> pdb=" O ASN A 359 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N THR A 361 " --> pdb=" O HIS E 362 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 368 through 377 88 hydrogen bonds defined for protein. 264 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.82 Time building geometry restraints manager: 1.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 708 1.33 - 1.45: 664 1.45 - 1.57: 2078 1.57 - 1.69: 0 1.69 - 1.81: 6 Bond restraints: 3456 Sorted by residual: bond pdb=" CZ ARG C 349 " pdb=" NH2 ARG C 349 " ideal model delta sigma weight residual 1.330 1.286 0.044 1.30e-02 5.92e+03 1.17e+01 bond pdb=" CZ ARG A 349 " pdb=" NH2 ARG A 349 " ideal model delta sigma weight residual 1.330 1.294 0.036 1.30e-02 5.92e+03 7.72e+00 bond pdb=" CZ ARG E 349 " pdb=" NH2 ARG E 349 " ideal model delta sigma weight residual 1.330 1.294 0.036 1.30e-02 5.92e+03 7.51e+00 bond pdb=" CA ASP F 345 " pdb=" C ASP F 345 " ideal model delta sigma weight residual 1.521 1.552 -0.031 1.20e-02 6.94e+03 6.76e+00 bond pdb=" CZ ARG B 349 " pdb=" NH2 ARG B 349 " ideal model delta sigma weight residual 1.330 1.296 0.034 1.30e-02 5.92e+03 6.73e+00 ... (remaining 3451 not shown) Histogram of bond angle deviations from ideal: 101.97 - 107.52: 235 107.52 - 113.07: 1706 113.07 - 118.61: 847 118.61 - 124.16: 1584 124.16 - 129.70: 254 Bond angle restraints: 4626 Sorted by residual: angle pdb=" CA PHE F 346 " pdb=" CB PHE F 346 " pdb=" CG PHE F 346 " ideal model delta sigma weight residual 113.80 121.73 -7.93 1.00e+00 1.00e+00 6.29e+01 angle pdb=" CA ASP F 358 " pdb=" CB ASP F 358 " pdb=" CG ASP F 358 " ideal model delta sigma weight residual 112.60 118.20 -5.60 1.00e+00 1.00e+00 3.14e+01 angle pdb=" CA PHE E 346 " pdb=" CB PHE E 346 " pdb=" CG PHE E 346 " ideal model delta sigma weight residual 113.80 119.13 -5.33 1.00e+00 1.00e+00 2.84e+01 angle pdb=" CA ASP B 358 " pdb=" CB ASP B 358 " pdb=" CG ASP B 358 " ideal model delta sigma weight residual 112.60 117.89 -5.29 1.00e+00 1.00e+00 2.79e+01 angle pdb=" CA ASP C 358 " pdb=" CB ASP C 358 " pdb=" CG ASP C 358 " ideal model delta sigma weight residual 112.60 117.82 -5.22 1.00e+00 1.00e+00 2.72e+01 ... (remaining 4621 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.23: 1972 17.23 - 34.47: 82 34.47 - 51.70: 28 51.70 - 68.93: 4 68.93 - 86.17: 8 Dihedral angle restraints: 2094 sinusoidal: 864 harmonic: 1230 Sorted by residual: dihedral pdb=" CA SER E 356 " pdb=" C SER E 356 " pdb=" N LEU E 357 " pdb=" CA LEU E 357 " ideal model delta harmonic sigma weight residual 180.00 151.39 28.61 0 5.00e+00 4.00e-02 3.27e+01 dihedral pdb=" CA LYS C 347 " pdb=" C LYS C 347 " pdb=" N ASP C 348 " pdb=" CA ASP C 348 " ideal model delta harmonic sigma weight residual -180.00 -151.73 -28.27 0 5.00e+00 4.00e-02 3.20e+01 dihedral pdb=" CA LYS D 347 " pdb=" C LYS D 347 " pdb=" N ASP D 348 " pdb=" CA ASP D 348 " ideal model delta harmonic sigma weight residual -180.00 -151.77 -28.23 0 5.00e+00 4.00e-02 3.19e+01 ... (remaining 2091 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.088: 362 0.088 - 0.175: 129 0.175 - 0.263: 17 0.263 - 0.350: 11 0.350 - 0.437: 3 Chirality restraints: 522 Sorted by residual: chirality pdb=" CA LYS E 343 " pdb=" N LYS E 343 " pdb=" C LYS E 343 " pdb=" CB LYS E 343 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.78e+00 chirality pdb=" CA LYS F 343 " pdb=" N LYS F 343 " pdb=" C LYS F 343 " pdb=" CB LYS F 343 " both_signs ideal model delta sigma weight residual False 2.51 2.09 0.42 2.00e-01 2.50e+01 4.37e+00 chirality pdb=" CA PHE F 346 " pdb=" N PHE F 346 " pdb=" C PHE F 346 " pdb=" CB PHE F 346 " both_signs ideal model delta sigma weight residual False 2.51 2.87 -0.36 2.00e-01 2.50e+01 3.31e+00 ... (remaining 519 not shown) Planarity restraints: 588 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 310 " 0.129 2.00e-02 2.50e+03 7.14e-02 1.02e+02 pdb=" CG TYR A 310 " -0.038 2.00e-02 2.50e+03 pdb=" CD1 TYR A 310 " -0.054 2.00e-02 2.50e+03 pdb=" CD2 TYR A 310 " -0.061 2.00e-02 2.50e+03 pdb=" CE1 TYR A 310 " -0.046 2.00e-02 2.50e+03 pdb=" CE2 TYR A 310 " -0.037 2.00e-02 2.50e+03 pdb=" CZ TYR A 310 " -0.005 2.00e-02 2.50e+03 pdb=" OH TYR A 310 " 0.111 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 310 " -0.117 2.00e-02 2.50e+03 6.38e-02 8.15e+01 pdb=" CG TYR B 310 " 0.035 2.00e-02 2.50e+03 pdb=" CD1 TYR B 310 " 0.052 2.00e-02 2.50e+03 pdb=" CD2 TYR B 310 " 0.055 2.00e-02 2.50e+03 pdb=" CE1 TYR B 310 " 0.039 2.00e-02 2.50e+03 pdb=" CE2 TYR B 310 " 0.032 2.00e-02 2.50e+03 pdb=" CZ TYR B 310 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR B 310 " -0.097 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR F 310 " -0.110 2.00e-02 2.50e+03 6.25e-02 7.81e+01 pdb=" CG TYR F 310 " 0.029 2.00e-02 2.50e+03 pdb=" CD1 TYR F 310 " 0.044 2.00e-02 2.50e+03 pdb=" CD2 TYR F 310 " 0.054 2.00e-02 2.50e+03 pdb=" CE1 TYR F 310 " 0.042 2.00e-02 2.50e+03 pdb=" CE2 TYR F 310 " 0.032 2.00e-02 2.50e+03 pdb=" CZ TYR F 310 " 0.012 2.00e-02 2.50e+03 pdb=" OH TYR F 310 " -0.102 2.00e-02 2.50e+03 ... (remaining 585 not shown) Histogram of nonbonded interaction distances: 2.49 - 2.97: 1477 2.97 - 3.46: 2642 3.46 - 3.94: 5446 3.94 - 4.42: 5403 4.42 - 4.90: 10518 Nonbonded interactions: 25486 Sorted by model distance: nonbonded pdb=" OD1 ASP E 314 " pdb=" OG SER E 316 " model vdw 2.492 3.040 nonbonded pdb=" OD1 ASP F 314 " pdb=" OG SER F 316 " model vdw 2.504 3.040 nonbonded pdb=" OD1 ASP A 314 " pdb=" OG SER A 316 " model vdw 2.508 3.040 nonbonded pdb=" OD1 ASP B 314 " pdb=" OG SER B 316 " model vdw 2.508 3.040 nonbonded pdb=" OD1 ASP C 314 " pdb=" OG SER C 316 " model vdw 2.567 3.040 ... (remaining 25481 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.280 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 15.550 Find NCS groups from input model: 0.110 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:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7059 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 0.044 3456 Z= 0.765 Angle : 1.876 7.933 4626 Z= 1.252 Chirality : 0.099 0.437 522 Planarity : 0.011 0.071 588 Dihedral : 12.868 86.167 1314 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Cbeta Deviations : 0.51 % 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: -1.74 (0.32), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.32 (0.25), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS D 362 PHE 0.063 0.013 PHE E 346 TYR 0.129 0.046 TYR A 310 ARG 0.009 0.002 ARG C 349 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 147 time to evaluate : 0.437 Fit side-chains REVERT: B 325 LEU cc_start: 0.7851 (mp) cc_final: 0.7613 (mt) REVERT: B 337 VAL cc_start: 0.8207 (t) cc_final: 0.7963 (p) REVERT: B 338 GLU cc_start: 0.7651 (mt-10) cc_final: 0.7149 (tm-30) REVERT: B 340 LYS cc_start: 0.7414 (tttt) cc_final: 0.7091 (mttm) REVERT: B 345 ASP cc_start: 0.7560 (t0) cc_final: 0.6947 (t70) REVERT: B 347 LYS cc_start: 0.7861 (mmtt) cc_final: 0.7402 (mmtt) REVERT: B 375 LYS cc_start: 0.7749 (tttt) cc_final: 0.7047 (tttm) REVERT: D 311 LYS cc_start: 0.8160 (mttt) cc_final: 0.7846 (mttp) REVERT: D 331 LYS cc_start: 0.8258 (mttt) cc_final: 0.7683 (mtpt) REVERT: D 340 LYS cc_start: 0.7824 (tttt) cc_final: 0.7336 (mtpt) REVERT: D 375 LYS cc_start: 0.8314 (tttt) cc_final: 0.7801 (tttp) REVERT: F 311 LYS cc_start: 0.7389 (mttt) cc_final: 0.6788 (tppt) REVERT: F 331 LYS cc_start: 0.8102 (mttt) cc_final: 0.7335 (mtpp) REVERT: F 338 GLU cc_start: 0.7508 (mt-10) cc_final: 0.6972 (tt0) REVERT: F 340 LYS cc_start: 0.7464 (tttt) cc_final: 0.6987 (mttm) REVERT: F 349 ARG cc_start: 0.6727 (mmt90) cc_final: 0.5364 (mmp-170) REVERT: F 362 HIS cc_start: 0.7671 (t-170) cc_final: 0.7450 (m-70) REVERT: F 375 LYS cc_start: 0.7625 (tttt) cc_final: 0.7056 (tttm) REVERT: A 331 LYS cc_start: 0.8133 (mttt) cc_final: 0.7763 (mttp) REVERT: A 349 ARG cc_start: 0.7415 (mmt90) cc_final: 0.6527 (mmm160) REVERT: A 351 GLN cc_start: 0.6186 (mp10) cc_final: 0.5762 (mt0) REVERT: A 369 LYS cc_start: 0.7461 (tttt) cc_final: 0.6668 (ttmm) REVERT: C 311 LYS cc_start: 0.8106 (mttt) cc_final: 0.7794 (mtpp) REVERT: C 349 ARG cc_start: 0.7078 (mmt90) cc_final: 0.6402 (mtm180) REVERT: C 361 THR cc_start: 0.8773 (m) cc_final: 0.8568 (m) REVERT: C 369 LYS cc_start: 0.7628 (tttt) cc_final: 0.6976 (ttmm) REVERT: C 375 LYS cc_start: 0.7418 (tttt) cc_final: 0.6951 (tttm) REVERT: E 311 LYS cc_start: 0.7634 (mttt) cc_final: 0.6977 (mmtt) REVERT: E 342 GLU cc_start: 0.7776 (pt0) cc_final: 0.6898 (mm-30) REVERT: E 369 LYS cc_start: 0.7369 (tttt) cc_final: 0.6375 (mtpt) REVERT: E 375 LYS cc_start: 0.6512 (tttt) cc_final: 0.6205 (tttm) outliers start: 0 outliers final: 0 residues processed: 147 average time/residue: 0.2313 time to fit residues: 38.4844 Evaluate side-chains 108 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 108 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 0.8980 chunk 31 optimal weight: 5.9990 chunk 17 optimal weight: 10.0000 chunk 10 optimal weight: 8.9990 chunk 21 optimal weight: 5.9990 chunk 32 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 20 optimal weight: 7.9990 chunk 24 optimal weight: 1.9990 chunk 38 optimal weight: 9.9990 chunk 11 optimal weight: 1.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 329 HIS F 329 HIS C 327 ASN E 329 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7147 moved from start: 0.2796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 3456 Z= 0.201 Angle : 0.651 5.255 4626 Z= 0.339 Chirality : 0.052 0.135 522 Planarity : 0.003 0.028 588 Dihedral : 5.930 20.572 456 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.77 % Allowed : 7.69 % Favored : 91.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.19 (0.35), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.90 (0.26), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.001 HIS B 362 PHE 0.015 0.001 PHE F 346 TYR 0.013 0.003 TYR A 310 ARG 0.002 0.000 ARG B 349 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 118 time to evaluate : 0.399 Fit side-chains REVERT: B 338 GLU cc_start: 0.7315 (mt-10) cc_final: 0.6934 (tt0) REVERT: B 345 ASP cc_start: 0.7610 (t0) cc_final: 0.6823 (t70) REVERT: B 375 LYS cc_start: 0.8046 (tttt) cc_final: 0.7213 (tttm) REVERT: D 311 LYS cc_start: 0.8104 (mttt) cc_final: 0.7852 (mttp) REVERT: D 314 ASP cc_start: 0.8106 (t0) cc_final: 0.7719 (t0) REVERT: D 315 LEU cc_start: 0.8305 (mp) cc_final: 0.8077 (mt) REVERT: D 331 LYS cc_start: 0.8140 (mttt) cc_final: 0.7683 (mttm) REVERT: D 340 LYS cc_start: 0.8005 (tttt) cc_final: 0.7415 (mtpt) REVERT: D 345 ASP cc_start: 0.7939 (t0) cc_final: 0.7707 (t70) REVERT: D 347 LYS cc_start: 0.7773 (mmtt) cc_final: 0.6594 (mtmm) REVERT: D 375 LYS cc_start: 0.8383 (tttt) cc_final: 0.7972 (tttp) REVERT: F 311 LYS cc_start: 0.7446 (mttt) cc_final: 0.6904 (tppt) REVERT: F 331 LYS cc_start: 0.8015 (mttt) cc_final: 0.7268 (mtpp) REVERT: F 338 GLU cc_start: 0.7385 (mt-10) cc_final: 0.6957 (pt0) REVERT: F 340 LYS cc_start: 0.7580 (tttt) cc_final: 0.7012 (mttm) REVERT: F 349 ARG cc_start: 0.6668 (mmt90) cc_final: 0.5454 (mmp-170) REVERT: F 356 SER cc_start: 0.8595 (m) cc_final: 0.8276 (p) REVERT: F 362 HIS cc_start: 0.7742 (t-170) cc_final: 0.7453 (m-70) REVERT: F 375 LYS cc_start: 0.7922 (tttt) cc_final: 0.7319 (tttm) REVERT: A 316 SER cc_start: 0.8750 (p) cc_final: 0.8384 (p) REVERT: A 336 GLN cc_start: 0.7113 (mp10) cc_final: 0.6775 (mm-40) REVERT: A 348 ASP cc_start: 0.6915 (t0) cc_final: 0.6564 (t0) REVERT: A 349 ARG cc_start: 0.7470 (mmt90) cc_final: 0.7069 (mmt180) REVERT: A 369 LYS cc_start: 0.7583 (tttt) cc_final: 0.6751 (ttmm) REVERT: C 311 LYS cc_start: 0.8138 (mttt) cc_final: 0.7762 (mtpp) REVERT: C 342 GLU cc_start: 0.8171 (pm20) cc_final: 0.7571 (pm20) REVERT: C 369 LYS cc_start: 0.7532 (tttt) cc_final: 0.6865 (ttmm) REVERT: C 375 LYS cc_start: 0.7840 (tttt) cc_final: 0.7043 (tmtt) REVERT: E 311 LYS cc_start: 0.7671 (mttt) cc_final: 0.6876 (mmtt) REVERT: E 342 GLU cc_start: 0.7828 (pt0) cc_final: 0.6820 (mm-30) REVERT: E 349 ARG cc_start: 0.5816 (mmt90) cc_final: 0.4389 (mmp-170) REVERT: E 369 LYS cc_start: 0.7583 (tttt) cc_final: 0.6529 (mtpt) outliers start: 3 outliers final: 2 residues processed: 120 average time/residue: 0.2059 time to fit residues: 28.6097 Evaluate side-chains 110 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 108 time to evaluate : 0.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 353 LYS Chi-restraints excluded: chain A residue 378 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 31 optimal weight: 7.9990 chunk 25 optimal weight: 3.9990 chunk 10 optimal weight: 10.0000 chunk 38 optimal weight: 8.9990 chunk 41 optimal weight: 9.9990 chunk 34 optimal weight: 9.9990 chunk 37 optimal weight: 9.9990 chunk 13 optimal weight: 7.9990 chunk 30 optimal weight: 9.9990 chunk 28 optimal weight: 5.9990 chunk 19 optimal weight: 10.0000 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 368 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7279 moved from start: 0.3854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.039 3456 Z= 0.510 Angle : 0.792 5.202 4626 Z= 0.420 Chirality : 0.056 0.169 522 Planarity : 0.004 0.033 588 Dihedral : 6.207 22.872 456 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.46 % Favored : 99.54 % Rotamer: Outliers : 2.05 % Allowed : 10.26 % Favored : 87.69 % 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: -1.30 (0.35), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.98 (0.27), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS B 362 PHE 0.024 0.003 PHE F 346 TYR 0.022 0.005 TYR A 310 ARG 0.003 0.001 ARG E 349 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 106 time to evaluate : 0.462 Fit side-chains revert: symmetry clash REVERT: B 338 GLU cc_start: 0.7471 (mt-10) cc_final: 0.7177 (tm-30) REVERT: B 345 ASP cc_start: 0.7640 (t0) cc_final: 0.6925 (t70) REVERT: B 375 LYS cc_start: 0.8166 (tttt) cc_final: 0.7411 (tttm) REVERT: D 311 LYS cc_start: 0.8109 (mttt) cc_final: 0.7617 (mtmt) REVERT: D 331 LYS cc_start: 0.8203 (mttt) cc_final: 0.7885 (mttm) REVERT: D 337 VAL cc_start: 0.8561 (p) cc_final: 0.8276 (m) REVERT: D 340 LYS cc_start: 0.8027 (tttt) cc_final: 0.7478 (mtpt) REVERT: D 375 LYS cc_start: 0.8346 (tttt) cc_final: 0.7822 (tttp) REVERT: F 311 LYS cc_start: 0.7638 (mttt) cc_final: 0.7045 (tppt) REVERT: F 338 GLU cc_start: 0.7367 (mt-10) cc_final: 0.7055 (tm-30) REVERT: F 349 ARG cc_start: 0.7135 (mmt90) cc_final: 0.5497 (mmm160) REVERT: F 362 HIS cc_start: 0.7655 (t-170) cc_final: 0.7350 (m170) REVERT: A 316 SER cc_start: 0.8881 (p) cc_final: 0.8516 (p) REVERT: A 336 GLN cc_start: 0.7057 (mp10) cc_final: 0.6620 (mm-40) REVERT: A 348 ASP cc_start: 0.6601 (t0) cc_final: 0.6362 (t0) REVERT: A 349 ARG cc_start: 0.7428 (mmt90) cc_final: 0.6837 (mmt180) REVERT: A 369 LYS cc_start: 0.7879 (tttt) cc_final: 0.6933 (ttmm) REVERT: C 369 LYS cc_start: 0.7983 (tttt) cc_final: 0.7197 (ttmm) REVERT: E 311 LYS cc_start: 0.7806 (mttt) cc_final: 0.7151 (mmtt) REVERT: E 316 SER cc_start: 0.8843 (p) cc_final: 0.8572 (p) REVERT: E 336 GLN cc_start: 0.7365 (mp10) cc_final: 0.7122 (mp10) REVERT: E 342 GLU cc_start: 0.7799 (pt0) cc_final: 0.6859 (mm-30) REVERT: E 349 ARG cc_start: 0.6010 (mmt90) cc_final: 0.4336 (mmp-170) REVERT: E 369 LYS cc_start: 0.7837 (tttt) cc_final: 0.6785 (mtpt) outliers start: 8 outliers final: 7 residues processed: 109 average time/residue: 0.2141 time to fit residues: 27.1302 Evaluate side-chains 105 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 98 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 373 THR Chi-restraints excluded: chain F residue 353 LYS Chi-restraints excluded: chain A residue 341 SER Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 378 PHE Chi-restraints excluded: chain C residue 378 PHE Chi-restraints excluded: chain E residue 378 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 4 optimal weight: 2.9990 chunk 18 optimal weight: 5.9990 chunk 25 optimal weight: 0.7980 chunk 38 optimal weight: 10.0000 chunk 40 optimal weight: 5.9990 chunk 20 optimal weight: 5.9990 chunk 36 optimal weight: 2.9990 chunk 10 optimal weight: 7.9990 chunk 33 optimal weight: 5.9990 chunk 23 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 362 HIS E 359 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7252 moved from start: 0.4033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3456 Z= 0.239 Angle : 0.634 6.411 4626 Z= 0.319 Chirality : 0.051 0.152 522 Planarity : 0.003 0.037 588 Dihedral : 5.467 16.913 456 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.46 % Favored : 99.54 % Rotamer: Outliers : 1.79 % Allowed : 13.85 % Favored : 84.36 % 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 (0.36), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.03 (0.27), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 362 PHE 0.012 0.001 PHE F 346 TYR 0.016 0.002 TYR A 310 ARG 0.001 0.000 ARG D 349 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 106 time to evaluate : 0.447 Fit side-chains REVERT: B 315 LEU cc_start: 0.7996 (mp) cc_final: 0.7734 (mt) REVERT: B 331 LYS cc_start: 0.7974 (mttt) cc_final: 0.7439 (mtpt) REVERT: B 336 GLN cc_start: 0.8078 (mt0) cc_final: 0.7874 (mm-40) REVERT: B 338 GLU cc_start: 0.7348 (mt-10) cc_final: 0.6999 (tt0) REVERT: B 345 ASP cc_start: 0.7661 (t0) cc_final: 0.6905 (t70) REVERT: B 349 ARG cc_start: 0.7563 (mtm-85) cc_final: 0.7163 (mtm-85) REVERT: B 375 LYS cc_start: 0.8136 (tttt) cc_final: 0.7372 (tttm) REVERT: D 311 LYS cc_start: 0.8054 (mttt) cc_final: 0.7659 (mttm) REVERT: D 331 LYS cc_start: 0.8211 (mttt) cc_final: 0.7892 (mttm) REVERT: D 337 VAL cc_start: 0.8515 (p) cc_final: 0.8245 (m) REVERT: D 340 LYS cc_start: 0.8017 (tttt) cc_final: 0.7462 (mtpt) REVERT: D 347 LYS cc_start: 0.7926 (mmtt) cc_final: 0.6495 (mtmm) REVERT: D 349 ARG cc_start: 0.7682 (mtt90) cc_final: 0.6995 (mtt90) REVERT: D 375 LYS cc_start: 0.8379 (tttt) cc_final: 0.7873 (tttp) REVERT: F 311 LYS cc_start: 0.7618 (mttt) cc_final: 0.7028 (tppt) REVERT: F 338 GLU cc_start: 0.7391 (mt-10) cc_final: 0.7155 (tm-30) REVERT: F 340 LYS cc_start: 0.7525 (tttt) cc_final: 0.7007 (mttm) REVERT: F 349 ARG cc_start: 0.7136 (mmt90) cc_final: 0.5468 (mmm160) REVERT: F 356 SER cc_start: 0.8868 (m) cc_final: 0.8480 (p) REVERT: F 362 HIS cc_start: 0.7661 (t-170) cc_final: 0.7396 (m170) REVERT: F 375 LYS cc_start: 0.8046 (tttt) cc_final: 0.7496 (tttm) REVERT: A 316 SER cc_start: 0.8976 (p) cc_final: 0.8671 (p) REVERT: A 336 GLN cc_start: 0.7105 (mp10) cc_final: 0.6717 (mm-40) REVERT: A 349 ARG cc_start: 0.7363 (mmt90) cc_final: 0.6797 (mmt180) REVERT: A 369 LYS cc_start: 0.7835 (tttt) cc_final: 0.6855 (ttmm) REVERT: C 311 LYS cc_start: 0.8384 (mtpp) cc_final: 0.8084 (mtpp) REVERT: C 369 LYS cc_start: 0.7903 (tttt) cc_final: 0.7098 (ttmm) REVERT: E 311 LYS cc_start: 0.7733 (mttt) cc_final: 0.7009 (mmtt) REVERT: E 316 SER cc_start: 0.8920 (p) cc_final: 0.8688 (p) REVERT: E 336 GLN cc_start: 0.7257 (mp10) cc_final: 0.6975 (mp10) REVERT: E 342 GLU cc_start: 0.7828 (pt0) cc_final: 0.6938 (mm-30) REVERT: E 348 ASP cc_start: 0.6893 (t0) cc_final: 0.6479 (t0) REVERT: E 349 ARG cc_start: 0.5828 (mmt90) cc_final: 0.4378 (mmp-170) REVERT: E 369 LYS cc_start: 0.7760 (tttt) cc_final: 0.6685 (mtpt) outliers start: 7 outliers final: 6 residues processed: 109 average time/residue: 0.2042 time to fit residues: 25.7110 Evaluate side-chains 110 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 104 time to evaluate : 0.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 373 THR Chi-restraints excluded: chain A residue 341 SER Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 378 PHE Chi-restraints excluded: chain C residue 378 PHE Chi-restraints excluded: chain E residue 378 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 30 optimal weight: 0.0070 chunk 16 optimal weight: 20.0000 chunk 34 optimal weight: 9.9990 chunk 28 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 20 optimal weight: 6.9990 chunk 36 optimal weight: 5.9990 chunk 10 optimal weight: 5.9990 chunk 13 optimal weight: 5.9990 chunk 8 optimal weight: 9.9990 chunk 23 optimal weight: 0.6980 overall best weight: 3.5404 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 327 ASN E 359 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7264 moved from start: 0.4308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 3456 Z= 0.284 Angle : 0.651 7.975 4626 Z= 0.328 Chirality : 0.051 0.157 522 Planarity : 0.003 0.044 588 Dihedral : 5.371 15.608 456 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % Rotamer: Outliers : 2.31 % Allowed : 15.13 % Favored : 82.56 % 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 (0.37), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.09 (0.28), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS D 362 PHE 0.013 0.002 PHE F 346 TYR 0.024 0.004 TYR B 310 ARG 0.002 0.000 ARG A 349 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 105 time to evaluate : 0.383 Fit side-chains REVERT: B 310 TYR cc_start: 0.8840 (t80) cc_final: 0.8598 (t80) REVERT: B 331 LYS cc_start: 0.7970 (mttt) cc_final: 0.7546 (mttm) REVERT: B 336 GLN cc_start: 0.8079 (mt0) cc_final: 0.7838 (mm-40) REVERT: B 338 GLU cc_start: 0.7288 (mt-10) cc_final: 0.7002 (tt0) REVERT: B 345 ASP cc_start: 0.7648 (t0) cc_final: 0.6939 (t70) REVERT: B 375 LYS cc_start: 0.8137 (tttt) cc_final: 0.7419 (tttm) REVERT: D 311 LYS cc_start: 0.8063 (mttt) cc_final: 0.7686 (mttm) REVERT: D 331 LYS cc_start: 0.8232 (mttt) cc_final: 0.7915 (mttm) REVERT: D 337 VAL cc_start: 0.8545 (OUTLIER) cc_final: 0.8276 (m) REVERT: D 340 LYS cc_start: 0.7983 (tttt) cc_final: 0.7513 (mtpt) REVERT: D 347 LYS cc_start: 0.7909 (mmtt) cc_final: 0.6520 (mtmm) REVERT: D 375 LYS cc_start: 0.8323 (tttt) cc_final: 0.7822 (tttp) REVERT: F 311 LYS cc_start: 0.7669 (mttt) cc_final: 0.7036 (tppt) REVERT: F 338 GLU cc_start: 0.7419 (mt-10) cc_final: 0.7122 (tm-30) REVERT: F 340 LYS cc_start: 0.7357 (tttt) cc_final: 0.6943 (mttm) REVERT: F 349 ARG cc_start: 0.7183 (mmt90) cc_final: 0.5488 (mmm160) REVERT: F 362 HIS cc_start: 0.7620 (t-170) cc_final: 0.7389 (m170) REVERT: F 375 LYS cc_start: 0.8031 (tttt) cc_final: 0.7491 (tttm) REVERT: A 316 SER cc_start: 0.8956 (p) cc_final: 0.8649 (p) REVERT: A 336 GLN cc_start: 0.7094 (mp10) cc_final: 0.6657 (mm-40) REVERT: A 348 ASP cc_start: 0.6509 (t0) cc_final: 0.6158 (t0) REVERT: A 349 ARG cc_start: 0.7232 (mmt90) cc_final: 0.6467 (mmt180) REVERT: A 369 LYS cc_start: 0.7785 (tttt) cc_final: 0.6892 (ttmm) REVERT: C 311 LYS cc_start: 0.8323 (mtpp) cc_final: 0.8078 (mtpp) REVERT: C 369 LYS cc_start: 0.7905 (tttt) cc_final: 0.7100 (ttmm) REVERT: E 311 LYS cc_start: 0.7769 (mttt) cc_final: 0.7060 (mmtt) REVERT: E 316 SER cc_start: 0.8889 (p) cc_final: 0.8634 (p) REVERT: E 340 LYS cc_start: 0.7315 (ttmm) cc_final: 0.6937 (mttm) REVERT: E 342 GLU cc_start: 0.7755 (pt0) cc_final: 0.6885 (mm-30) REVERT: E 348 ASP cc_start: 0.6934 (t0) cc_final: 0.6732 (t0) REVERT: E 369 LYS cc_start: 0.7773 (tttt) cc_final: 0.6715 (mtpt) outliers start: 9 outliers final: 7 residues processed: 107 average time/residue: 0.2062 time to fit residues: 25.5404 Evaluate side-chains 113 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 105 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 342 GLU Chi-restraints excluded: chain D residue 337 VAL Chi-restraints excluded: chain D residue 373 THR Chi-restraints excluded: chain A residue 341 SER Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 378 PHE Chi-restraints excluded: chain C residue 378 PHE Chi-restraints excluded: chain E residue 378 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 10 optimal weight: 10.0000 chunk 40 optimal weight: 10.0000 chunk 33 optimal weight: 10.0000 chunk 18 optimal weight: 4.9990 chunk 3 optimal weight: 10.0000 chunk 13 optimal weight: 4.9990 chunk 21 optimal weight: 10.0000 chunk 39 optimal weight: 8.9990 chunk 4 optimal weight: 5.9990 chunk 23 optimal weight: 2.9990 chunk 29 optimal weight: 5.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 329 HIS C 359 ASN E 359 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7282 moved from start: 0.4487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 3456 Z= 0.376 Angle : 0.689 8.364 4626 Z= 0.352 Chirality : 0.053 0.159 522 Planarity : 0.004 0.052 588 Dihedral : 5.578 16.237 456 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Rotamer: Outliers : 2.82 % Allowed : 14.62 % Favored : 82.56 % 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: -1.58 (0.37), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.19 (0.28), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS D 362 PHE 0.013 0.002 PHE F 346 TYR 0.022 0.004 TYR B 310 ARG 0.002 0.000 ARG A 349 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 104 time to evaluate : 0.472 Fit side-chains revert: symmetry clash REVERT: B 338 GLU cc_start: 0.7376 (mt-10) cc_final: 0.7098 (tm-30) REVERT: B 345 ASP cc_start: 0.7611 (t0) cc_final: 0.6945 (t70) REVERT: B 375 LYS cc_start: 0.8170 (tttt) cc_final: 0.7443 (tttm) REVERT: D 311 LYS cc_start: 0.8050 (mttt) cc_final: 0.7696 (mttm) REVERT: D 331 LYS cc_start: 0.8268 (mttt) cc_final: 0.8028 (mttm) REVERT: D 337 VAL cc_start: 0.8582 (OUTLIER) cc_final: 0.8304 (m) REVERT: D 340 LYS cc_start: 0.7979 (tttt) cc_final: 0.7490 (mtpt) REVERT: D 347 LYS cc_start: 0.8036 (mmtt) cc_final: 0.6764 (mtmt) REVERT: D 375 LYS cc_start: 0.8320 (tttt) cc_final: 0.7777 (tttp) REVERT: D 376 LEU cc_start: 0.7939 (tp) cc_final: 0.7574 (tt) REVERT: F 311 LYS cc_start: 0.7663 (mttt) cc_final: 0.6993 (tppt) REVERT: F 338 GLU cc_start: 0.7329 (mt-10) cc_final: 0.7000 (tm-30) REVERT: F 340 LYS cc_start: 0.7256 (tttt) cc_final: 0.6838 (mttm) REVERT: F 347 LYS cc_start: 0.7533 (mmtt) cc_final: 0.7326 (mmtm) REVERT: F 349 ARG cc_start: 0.7203 (mmt90) cc_final: 0.5480 (mmm160) REVERT: F 362 HIS cc_start: 0.7633 (t-170) cc_final: 0.7314 (m170) REVERT: A 316 SER cc_start: 0.8931 (p) cc_final: 0.8624 (p) REVERT: A 336 GLN cc_start: 0.7018 (mp10) cc_final: 0.6537 (mm-40) REVERT: A 348 ASP cc_start: 0.6399 (t0) cc_final: 0.6058 (t0) REVERT: A 349 ARG cc_start: 0.7342 (mmt90) cc_final: 0.6425 (mmt180) REVERT: A 369 LYS cc_start: 0.7779 (tttt) cc_final: 0.6873 (ttmm) REVERT: C 311 LYS cc_start: 0.8328 (mtpp) cc_final: 0.8093 (mtpp) REVERT: C 369 LYS cc_start: 0.7941 (tttt) cc_final: 0.7107 (ttmm) REVERT: E 311 LYS cc_start: 0.7766 (mttt) cc_final: 0.7108 (mmtt) REVERT: E 316 SER cc_start: 0.8876 (p) cc_final: 0.8620 (p) REVERT: E 342 GLU cc_start: 0.7769 (pt0) cc_final: 0.6884 (mm-30) REVERT: E 348 ASP cc_start: 0.6847 (t0) cc_final: 0.6599 (t0) REVERT: E 369 LYS cc_start: 0.7785 (tttt) cc_final: 0.7021 (ttmm) outliers start: 11 outliers final: 7 residues processed: 109 average time/residue: 0.2120 time to fit residues: 26.5911 Evaluate side-chains 109 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 101 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 342 GLU Chi-restraints excluded: chain D residue 337 VAL Chi-restraints excluded: chain D residue 373 THR Chi-restraints excluded: chain A residue 341 SER Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 378 PHE Chi-restraints excluded: chain C residue 378 PHE Chi-restraints excluded: chain E residue 378 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 22 optimal weight: 9.9990 chunk 34 optimal weight: 2.9990 chunk 40 optimal weight: 7.9990 chunk 25 optimal weight: 10.0000 chunk 24 optimal weight: 8.9990 chunk 18 optimal weight: 8.9990 chunk 16 optimal weight: 20.0000 chunk 12 optimal weight: 8.9990 chunk 7 optimal weight: 10.0000 chunk 27 optimal weight: 5.9990 chunk 20 optimal weight: 5.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 359 ASN E 359 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7299 moved from start: 0.4674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.044 3456 Z= 0.473 Angle : 0.744 7.794 4626 Z= 0.383 Chirality : 0.054 0.162 522 Planarity : 0.004 0.057 588 Dihedral : 5.769 17.436 456 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 2.56 % Allowed : 15.13 % Favored : 82.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.77 (0.37), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.34 (0.28), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS D 329 PHE 0.013 0.002 PHE C 346 TYR 0.020 0.004 TYR A 310 ARG 0.002 0.001 ARG D 349 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 103 time to evaluate : 0.448 Fit side-chains REVERT: B 338 GLU cc_start: 0.7426 (mt-10) cc_final: 0.7100 (tm-30) REVERT: B 340 LYS cc_start: 0.7457 (tttt) cc_final: 0.6937 (mttm) REVERT: B 345 ASP cc_start: 0.7597 (t0) cc_final: 0.6928 (t70) REVERT: B 347 LYS cc_start: 0.8114 (mmtt) cc_final: 0.7332 (mmtt) REVERT: B 375 LYS cc_start: 0.8153 (tttt) cc_final: 0.7647 (tttp) REVERT: D 331 LYS cc_start: 0.8332 (mttt) cc_final: 0.8100 (mttm) REVERT: D 337 VAL cc_start: 0.8613 (OUTLIER) cc_final: 0.8338 (m) REVERT: D 340 LYS cc_start: 0.7970 (tttt) cc_final: 0.7498 (mtpt) REVERT: D 375 LYS cc_start: 0.8296 (tttt) cc_final: 0.7796 (tttp) REVERT: D 376 LEU cc_start: 0.7993 (tp) cc_final: 0.7621 (tt) REVERT: F 311 LYS cc_start: 0.7722 (mttt) cc_final: 0.7018 (tppt) REVERT: F 338 GLU cc_start: 0.7320 (mt-10) cc_final: 0.6977 (tm-30) REVERT: F 340 LYS cc_start: 0.7251 (tttt) cc_final: 0.6820 (mttm) REVERT: F 347 LYS cc_start: 0.7634 (mmtt) cc_final: 0.7366 (mmtm) REVERT: F 349 ARG cc_start: 0.7199 (mmt90) cc_final: 0.5473 (mmm160) REVERT: F 375 LYS cc_start: 0.7990 (tttt) cc_final: 0.7445 (tttm) REVERT: A 316 SER cc_start: 0.8919 (p) cc_final: 0.8602 (p) REVERT: A 336 GLN cc_start: 0.6969 (mp10) cc_final: 0.6468 (mm-40) REVERT: A 348 ASP cc_start: 0.6329 (t0) cc_final: 0.6114 (t0) REVERT: A 349 ARG cc_start: 0.7408 (mmt90) cc_final: 0.6436 (mmt180) REVERT: A 369 LYS cc_start: 0.7783 (tttt) cc_final: 0.6852 (ttmm) REVERT: C 369 LYS cc_start: 0.7954 (tttt) cc_final: 0.7127 (ttmm) REVERT: E 311 LYS cc_start: 0.7748 (mttt) cc_final: 0.7086 (mmtt) REVERT: E 316 SER cc_start: 0.8852 (p) cc_final: 0.8586 (p) REVERT: E 348 ASP cc_start: 0.6740 (t0) cc_final: 0.6488 (t0) REVERT: E 369 LYS cc_start: 0.7777 (tttt) cc_final: 0.7021 (ttmm) outliers start: 10 outliers final: 9 residues processed: 106 average time/residue: 0.2012 time to fit residues: 24.7227 Evaluate side-chains 110 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 100 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 342 GLU Chi-restraints excluded: chain D residue 337 VAL Chi-restraints excluded: chain D residue 342 GLU Chi-restraints excluded: chain D residue 349 ARG Chi-restraints excluded: chain D residue 373 THR Chi-restraints excluded: chain A residue 341 SER Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 378 PHE Chi-restraints excluded: chain C residue 378 PHE Chi-restraints excluded: chain E residue 378 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 3 optimal weight: 20.0000 chunk 31 optimal weight: 6.9990 chunk 36 optimal weight: 1.9990 chunk 38 optimal weight: 6.9990 chunk 35 optimal weight: 2.9990 chunk 37 optimal weight: 8.9990 chunk 22 optimal weight: 8.9990 chunk 16 optimal weight: 9.9990 chunk 29 optimal weight: 7.9990 chunk 11 optimal weight: 0.7980 chunk 34 optimal weight: 6.9990 overall best weight: 3.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 359 ASN E 359 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7285 moved from start: 0.4723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 3456 Z= 0.311 Angle : 0.670 7.258 4626 Z= 0.338 Chirality : 0.052 0.159 522 Planarity : 0.004 0.061 588 Dihedral : 5.496 16.216 456 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 2.82 % Allowed : 16.92 % Favored : 80.26 % 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: -1.71 (0.37), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.29 (0.28), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS D 362 PHE 0.011 0.002 PHE F 346 TYR 0.016 0.003 TYR A 310 ARG 0.002 0.000 ARG D 349 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 100 time to evaluate : 0.394 Fit side-chains revert: symmetry clash REVERT: B 338 GLU cc_start: 0.7334 (mt-10) cc_final: 0.7092 (tm-30) REVERT: B 340 LYS cc_start: 0.7405 (tttt) cc_final: 0.6880 (mttm) REVERT: B 345 ASP cc_start: 0.7597 (t0) cc_final: 0.6945 (t70) REVERT: B 347 LYS cc_start: 0.8108 (mmtt) cc_final: 0.7333 (mmtt) REVERT: B 375 LYS cc_start: 0.8188 (tttt) cc_final: 0.7430 (tttm) REVERT: D 331 LYS cc_start: 0.8304 (mttt) cc_final: 0.8052 (mttm) REVERT: D 337 VAL cc_start: 0.8598 (OUTLIER) cc_final: 0.8327 (m) REVERT: D 340 LYS cc_start: 0.7990 (tttt) cc_final: 0.7514 (mtpt) REVERT: D 347 LYS cc_start: 0.8089 (mmtt) cc_final: 0.6680 (mtmt) REVERT: D 349 ARG cc_start: 0.7753 (OUTLIER) cc_final: 0.7084 (mtt90) REVERT: D 375 LYS cc_start: 0.8266 (tttt) cc_final: 0.7798 (tttp) REVERT: F 311 LYS cc_start: 0.7698 (mttt) cc_final: 0.7036 (tppt) REVERT: F 338 GLU cc_start: 0.7286 (mt-10) cc_final: 0.7011 (tm-30) REVERT: F 340 LYS cc_start: 0.7279 (tttt) cc_final: 0.6854 (mttm) REVERT: F 347 LYS cc_start: 0.7444 (mmtt) cc_final: 0.7205 (mmtm) REVERT: F 349 ARG cc_start: 0.7197 (mmt90) cc_final: 0.5508 (mmm160) REVERT: A 316 SER cc_start: 0.8940 (p) cc_final: 0.8646 (p) REVERT: A 336 GLN cc_start: 0.6961 (mp10) cc_final: 0.6465 (mm-40) REVERT: A 349 ARG cc_start: 0.7453 (mmt90) cc_final: 0.6531 (mmt180) REVERT: A 369 LYS cc_start: 0.7814 (tttt) cc_final: 0.6922 (ttmm) REVERT: C 369 LYS cc_start: 0.7933 (tttt) cc_final: 0.7096 (ttmm) REVERT: E 311 LYS cc_start: 0.7757 (mttt) cc_final: 0.7110 (mmtt) REVERT: E 316 SER cc_start: 0.8901 (p) cc_final: 0.8647 (p) REVERT: E 349 ARG cc_start: 0.6001 (mmt90) cc_final: 0.4395 (mmp-170) REVERT: E 369 LYS cc_start: 0.7762 (tttt) cc_final: 0.6980 (ttmm) outliers start: 11 outliers final: 9 residues processed: 103 average time/residue: 0.2073 time to fit residues: 24.8105 Evaluate side-chains 111 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 100 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 342 GLU Chi-restraints excluded: chain D residue 337 VAL Chi-restraints excluded: chain D residue 338 GLU Chi-restraints excluded: chain D residue 342 GLU Chi-restraints excluded: chain D residue 349 ARG Chi-restraints excluded: chain D residue 373 THR Chi-restraints excluded: chain A residue 341 SER Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 378 PHE Chi-restraints excluded: chain C residue 378 PHE Chi-restraints excluded: chain E residue 378 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 7.9990 chunk 37 optimal weight: 10.0000 chunk 24 optimal weight: 7.9990 chunk 39 optimal weight: 4.9990 chunk 18 optimal weight: 9.9990 chunk 27 optimal weight: 2.9990 chunk 41 optimal weight: 0.9990 chunk 38 optimal weight: 8.9990 chunk 33 optimal weight: 9.9990 chunk 3 optimal weight: 20.0000 chunk 25 optimal weight: 5.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 359 ASN E 359 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7290 moved from start: 0.4776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 3456 Z= 0.356 Angle : 0.713 7.039 4626 Z= 0.365 Chirality : 0.052 0.159 522 Planarity : 0.004 0.060 588 Dihedral : 5.544 15.993 456 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 2.56 % Allowed : 16.92 % Favored : 80.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.78 (0.37), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.35 (0.28), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS F 362 PHE 0.011 0.002 PHE F 346 TYR 0.017 0.003 TYR A 310 ARG 0.002 0.000 ARG D 349 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 100 time to evaluate : 0.443 Fit side-chains revert: symmetry clash REVERT: B 338 GLU cc_start: 0.7356 (mt-10) cc_final: 0.7092 (tm-30) REVERT: B 340 LYS cc_start: 0.7389 (tttt) cc_final: 0.6870 (mttm) REVERT: B 345 ASP cc_start: 0.7587 (t0) cc_final: 0.6937 (t70) REVERT: B 347 LYS cc_start: 0.8113 (mmtt) cc_final: 0.7278 (mmtt) REVERT: B 375 LYS cc_start: 0.8185 (tttt) cc_final: 0.7440 (tttm) REVERT: D 331 LYS cc_start: 0.8309 (mttt) cc_final: 0.8047 (mttm) REVERT: D 337 VAL cc_start: 0.8614 (OUTLIER) cc_final: 0.8351 (m) REVERT: D 340 LYS cc_start: 0.7975 (tttt) cc_final: 0.7487 (mtpt) REVERT: D 349 ARG cc_start: 0.7771 (OUTLIER) cc_final: 0.7083 (mtt90) REVERT: D 375 LYS cc_start: 0.8260 (tttt) cc_final: 0.7792 (tttp) REVERT: F 311 LYS cc_start: 0.7711 (mttt) cc_final: 0.7029 (tppt) REVERT: F 331 LYS cc_start: 0.8067 (mttt) cc_final: 0.7570 (mttm) REVERT: F 338 GLU cc_start: 0.7278 (mt-10) cc_final: 0.7008 (tm-30) REVERT: F 340 LYS cc_start: 0.7272 (tttt) cc_final: 0.6845 (mttm) REVERT: F 347 LYS cc_start: 0.7453 (mmtt) cc_final: 0.7206 (mmtm) REVERT: F 349 ARG cc_start: 0.7213 (mmt90) cc_final: 0.5517 (mmm160) REVERT: F 375 LYS cc_start: 0.7989 (tttt) cc_final: 0.7548 (tttp) REVERT: A 316 SER cc_start: 0.8930 (p) cc_final: 0.8628 (p) REVERT: A 336 GLN cc_start: 0.6939 (mp10) cc_final: 0.6449 (mm-40) REVERT: A 369 LYS cc_start: 0.7792 (tttt) cc_final: 0.6851 (ttmm) REVERT: C 369 LYS cc_start: 0.7967 (tttt) cc_final: 0.7121 (ttmm) REVERT: E 311 LYS cc_start: 0.7694 (mttt) cc_final: 0.7045 (mmtt) REVERT: E 316 SER cc_start: 0.8886 (p) cc_final: 0.8622 (p) REVERT: E 342 GLU cc_start: 0.7908 (pt0) cc_final: 0.7682 (pt0) REVERT: E 348 ASP cc_start: 0.6704 (t0) cc_final: 0.6446 (t0) REVERT: E 369 LYS cc_start: 0.7775 (tttt) cc_final: 0.7020 (ttmm) outliers start: 10 outliers final: 8 residues processed: 103 average time/residue: 0.1971 time to fit residues: 23.6753 Evaluate side-chains 108 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 98 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 342 GLU Chi-restraints excluded: chain D residue 337 VAL Chi-restraints excluded: chain D residue 342 GLU Chi-restraints excluded: chain D residue 349 ARG Chi-restraints excluded: chain D residue 373 THR Chi-restraints excluded: chain A residue 341 SER Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 378 PHE Chi-restraints excluded: chain C residue 378 PHE Chi-restraints excluded: chain E residue 378 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 20 optimal weight: 1.9990 chunk 26 optimal weight: 9.9990 chunk 35 optimal weight: 0.8980 chunk 10 optimal weight: 20.0000 chunk 30 optimal weight: 7.9990 chunk 4 optimal weight: 10.0000 chunk 9 optimal weight: 0.9990 chunk 33 optimal weight: 0.5980 chunk 13 optimal weight: 2.9990 chunk 34 optimal weight: 9.9990 chunk 6 optimal weight: 0.5980 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 359 ASN E 359 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7244 moved from start: 0.4826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 3456 Z= 0.148 Angle : 0.620 6.825 4626 Z= 0.306 Chirality : 0.050 0.146 522 Planarity : 0.003 0.058 588 Dihedral : 4.904 14.306 456 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 1.79 % Allowed : 18.21 % Favored : 80.00 % 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: -1.71 (0.37), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.30 (0.28), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS E 330 PHE 0.007 0.001 PHE F 346 TYR 0.008 0.001 TYR A 310 ARG 0.001 0.000 ARG F 349 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 103 time to evaluate : 0.455 Fit side-chains revert: symmetry clash REVERT: B 331 LYS cc_start: 0.8009 (mttt) cc_final: 0.7616 (mttm) REVERT: B 345 ASP cc_start: 0.7648 (t0) cc_final: 0.7057 (t70) REVERT: B 356 SER cc_start: 0.8402 (p) cc_final: 0.8200 (p) REVERT: B 375 LYS cc_start: 0.8148 (tttt) cc_final: 0.7604 (tttp) REVERT: D 331 LYS cc_start: 0.8249 (mttt) cc_final: 0.7978 (mttm) REVERT: D 337 VAL cc_start: 0.8543 (p) cc_final: 0.8303 (m) REVERT: D 340 LYS cc_start: 0.8029 (tttt) cc_final: 0.7501 (mtpt) REVERT: D 347 LYS cc_start: 0.7851 (mmtm) cc_final: 0.6395 (mtmm) REVERT: D 375 LYS cc_start: 0.8234 (tttt) cc_final: 0.7785 (tttp) REVERT: F 311 LYS cc_start: 0.7718 (mttt) cc_final: 0.6946 (tppt) REVERT: F 340 LYS cc_start: 0.7316 (tttt) cc_final: 0.6830 (mtmt) REVERT: F 349 ARG cc_start: 0.7089 (mmt90) cc_final: 0.5446 (mmm160) REVERT: F 375 LYS cc_start: 0.8093 (tttt) cc_final: 0.7513 (tttm) REVERT: A 316 SER cc_start: 0.8960 (p) cc_final: 0.8691 (p) REVERT: A 336 GLN cc_start: 0.6947 (mp10) cc_final: 0.6469 (mm-40) REVERT: A 369 LYS cc_start: 0.7683 (tttt) cc_final: 0.6792 (ttmm) REVERT: C 369 LYS cc_start: 0.7899 (tttt) cc_final: 0.7081 (ttmm) REVERT: E 311 LYS cc_start: 0.7634 (mttt) cc_final: 0.6906 (mmtt) REVERT: E 316 SER cc_start: 0.8980 (p) cc_final: 0.8753 (p) REVERT: E 340 LYS cc_start: 0.7557 (ttmm) cc_final: 0.7201 (mttm) REVERT: E 348 ASP cc_start: 0.6714 (t0) cc_final: 0.6495 (t0) REVERT: E 349 ARG cc_start: 0.5740 (mmt90) cc_final: 0.4120 (mmp-170) REVERT: E 369 LYS cc_start: 0.7704 (tttt) cc_final: 0.6607 (mtpt) outliers start: 7 outliers final: 6 residues processed: 105 average time/residue: 0.2171 time to fit residues: 26.2425 Evaluate side-chains 107 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 101 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 338 GLU Chi-restraints excluded: chain D residue 342 GLU Chi-restraints excluded: chain D residue 349 ARG Chi-restraints excluded: chain D residue 373 THR Chi-restraints excluded: chain A residue 341 SER Chi-restraints excluded: chain C residue 378 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 29 optimal weight: 6.9990 chunk 1 optimal weight: 20.0000 chunk 24 optimal weight: 10.0000 chunk 38 optimal weight: 9.9990 chunk 22 optimal weight: 5.9990 chunk 28 optimal weight: 7.9990 chunk 26 optimal weight: 9.9990 chunk 25 optimal weight: 1.9990 chunk 16 optimal weight: 0.0670 chunk 15 optimal weight: 2.9990 chunk 41 optimal weight: 9.9990 overall best weight: 3.6126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 359 ASN E 359 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.143676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.133180 restraints weight = 4769.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.135423 restraints weight = 2430.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.136832 restraints weight = 1505.095| |-----------------------------------------------------------------------------| r_work (final): 0.3998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.4933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 3456 Z= 0.282 Angle : 0.667 6.745 4626 Z= 0.339 Chirality : 0.051 0.150 522 Planarity : 0.004 0.056 588 Dihedral : 5.121 14.812 456 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Rotamer: Outliers : 1.79 % Allowed : 18.72 % Favored : 79.49 % 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 (0.38), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.26 (0.29), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS D 362 PHE 0.009 0.002 PHE F 346 TYR 0.014 0.003 TYR A 310 ARG 0.002 0.000 ARG D 349 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1317.11 seconds wall clock time: 24 minutes 19.54 seconds (1459.54 seconds total)