Starting phenix.real_space_refine on Fri Mar 15 13:57:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pim_13442/03_2024/7pim_13442_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pim_13442/03_2024/7pim_13442.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pim_13442/03_2024/7pim_13442.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pim_13442/03_2024/7pim_13442.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pim_13442/03_2024/7pim_13442_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pim_13442/03_2024/7pim_13442_updated.pdb" } resolution = 4.6 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: 6 Type Number sf(0) Gaussians Fe 4 7.16 5 S 36 5.16 5 C 7192 2.51 5 N 1932 2.21 5 O 2156 1.98 5 H 524 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B PHE 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 370": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 388": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 422": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 370": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 388": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 422": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 370": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 388": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 422": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 370": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 388": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 422": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 11844 Number of models: 1 Model: "" Number of chains: 12 Chain: "B" Number of atoms: 2688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2688 Classifications: {'peptide': 335} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 18, 'TRANS': 316} Chain: "G" Number of atoms: 261 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 261 Classifications: {'peptide': 18} Link IDs: {'TRANS': 17} Chain: "A" Number of atoms: 2688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2688 Classifications: {'peptide': 335} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 18, 'TRANS': 316} Chain: "C" Number of atoms: 261 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 261 Classifications: {'peptide': 18} Link IDs: {'TRANS': 17} Chain: "D" Number of atoms: 2688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2688 Classifications: {'peptide': 335} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 18, 'TRANS': 316} Chain: "E" Number of atoms: 261 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 261 Classifications: {'peptide': 18} Link IDs: {'TRANS': 17} Chain: "F" Number of atoms: 2688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2688 Classifications: {'peptide': 335} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 18, 'TRANS': 316} Chain: "H" Number of atoms: 261 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 261 Classifications: {'peptide': 18} Link IDs: {'TRANS': 17} Chain: "B" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 12 Unusual residues: {' FE': 1, 'LDP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 12 Unusual residues: {' FE': 1, 'LDP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 12 Unusual residues: {' FE': 1, 'LDP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 12 Unusual residues: {' FE': 1, 'LDP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 6.61, per 1000 atoms: 0.56 Number of scatterers: 11844 At special positions: 0 Unit cell: (103.984, 91.12, 121.136, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Fe 4 26.01 S 36 16.00 O 2156 8.00 N 1932 7.00 C 7192 6.00 H 524 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: 5.79 Conformation dependent library (CDL) restraints added in 2.0 seconds 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2688 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 68 helices and 16 sheets defined 53.8% alpha, 7.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.35 Creating SS restraints... Processing helix chain 'B' and resid 170 through 180 Processing helix chain 'B' and resid 197 through 212 Processing helix chain 'B' and resid 226 through 242 Processing helix chain 'B' and resid 249 through 261 removed outlier: 3.593A pdb=" N GLU B 253 " --> pdb=" O GLY B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 283 Processing helix chain 'B' and resid 296 through 304 Processing helix chain 'B' and resid 317 through 319 No H-bonds generated for 'chain 'B' and resid 317 through 319' Processing helix chain 'B' and resid 328 through 334 Processing helix chain 'B' and resid 336 through 339 No H-bonds generated for 'chain 'B' and resid 336 through 339' Processing helix chain 'B' and resid 342 through 355 Processing helix chain 'B' and resid 360 through 373 removed outlier: 3.523A pdb=" N TYR B 370 " --> pdb=" O LEU B 366 " (cutoff:3.500A) Processing helix chain 'B' and resid 390 through 394 Processing helix chain 'B' and resid 396 through 403 removed outlier: 3.911A pdb=" N LEU B 403 " --> pdb=" O LEU B 399 " (cutoff:3.500A) Processing helix chain 'B' and resid 414 through 419 Processing helix chain 'B' and resid 437 through 450 Processing helix chain 'B' and resid 472 through 495 removed outlier: 3.540A pdb=" N GLY B 481 " --> pdb=" O ARG B 477 " (cutoff:3.500A) Processing helix chain 'G' and resid 41 through 54 Processing helix chain 'A' and resid 170 through 180 Processing helix chain 'A' and resid 197 through 212 Processing helix chain 'A' and resid 226 through 242 Processing helix chain 'A' and resid 249 through 261 removed outlier: 3.592A pdb=" N GLU A 253 " --> pdb=" O GLY A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 283 Processing helix chain 'A' and resid 296 through 304 Processing helix chain 'A' and resid 317 through 319 No H-bonds generated for 'chain 'A' and resid 317 through 319' Processing helix chain 'A' and resid 328 through 334 Processing helix chain 'A' and resid 336 through 339 No H-bonds generated for 'chain 'A' and resid 336 through 339' Processing helix chain 'A' and resid 342 through 355 Processing helix chain 'A' and resid 360 through 373 removed outlier: 3.523A pdb=" N TYR A 370 " --> pdb=" O LEU A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 390 through 394 Processing helix chain 'A' and resid 396 through 403 removed outlier: 3.912A pdb=" N LEU A 403 " --> pdb=" O LEU A 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 419 Processing helix chain 'A' and resid 437 through 450 Processing helix chain 'A' and resid 472 through 495 removed outlier: 3.541A pdb=" N GLY A 481 " --> pdb=" O ARG A 477 " (cutoff:3.500A) Processing helix chain 'C' and resid 41 through 54 Processing helix chain 'D' and resid 170 through 180 Processing helix chain 'D' and resid 197 through 212 Processing helix chain 'D' and resid 226 through 242 Processing helix chain 'D' and resid 249 through 261 removed outlier: 3.592A pdb=" N GLU D 253 " --> pdb=" O GLY D 249 " (cutoff:3.500A) Processing helix chain 'D' and resid 273 through 283 Processing helix chain 'D' and resid 296 through 304 Processing helix chain 'D' and resid 317 through 319 No H-bonds generated for 'chain 'D' and resid 317 through 319' Processing helix chain 'D' and resid 328 through 334 Processing helix chain 'D' and resid 336 through 339 No H-bonds generated for 'chain 'D' and resid 336 through 339' Processing helix chain 'D' and resid 342 through 355 Processing helix chain 'D' and resid 360 through 373 removed outlier: 3.523A pdb=" N TYR D 370 " --> pdb=" O LEU D 366 " (cutoff:3.500A) Processing helix chain 'D' and resid 390 through 394 Processing helix chain 'D' and resid 396 through 403 removed outlier: 3.912A pdb=" N LEU D 403 " --> pdb=" O LEU D 399 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 419 Processing helix chain 'D' and resid 437 through 450 Processing helix chain 'D' and resid 472 through 495 removed outlier: 3.541A pdb=" N GLY D 481 " --> pdb=" O ARG D 477 " (cutoff:3.500A) Processing helix chain 'E' and resid 41 through 54 Processing helix chain 'F' and resid 170 through 180 Processing helix chain 'F' and resid 197 through 212 Processing helix chain 'F' and resid 226 through 242 Processing helix chain 'F' and resid 249 through 261 removed outlier: 3.593A pdb=" N GLU F 253 " --> pdb=" O GLY F 249 " (cutoff:3.500A) Processing helix chain 'F' and resid 273 through 283 Processing helix chain 'F' and resid 296 through 304 Processing helix chain 'F' and resid 317 through 319 No H-bonds generated for 'chain 'F' and resid 317 through 319' Processing helix chain 'F' and resid 328 through 334 Processing helix chain 'F' and resid 336 through 339 No H-bonds generated for 'chain 'F' and resid 336 through 339' Processing helix chain 'F' and resid 342 through 355 Processing helix chain 'F' and resid 360 through 373 removed outlier: 3.524A pdb=" N TYR F 370 " --> pdb=" O LEU F 366 " (cutoff:3.500A) Processing helix chain 'F' and resid 390 through 394 Processing helix chain 'F' and resid 396 through 403 removed outlier: 3.912A pdb=" N LEU F 403 " --> pdb=" O LEU F 399 " (cutoff:3.500A) Processing helix chain 'F' and resid 414 through 419 Processing helix chain 'F' and resid 437 through 450 Processing helix chain 'F' and resid 472 through 495 removed outlier: 3.541A pdb=" N GLY F 481 " --> pdb=" O ARG F 477 " (cutoff:3.500A) Processing helix chain 'H' and resid 41 through 54 Processing sheet with id= A, first strand: chain 'B' and resid 286 through 289 Processing sheet with id= B, first strand: chain 'B' and resid 378 through 381 Processing sheet with id= C, first strand: chain 'B' and resid 408 through 411 Processing sheet with id= D, first strand: chain 'B' and resid 456 through 460 Processing sheet with id= E, first strand: chain 'A' and resid 286 through 289 Processing sheet with id= F, first strand: chain 'A' and resid 378 through 381 Processing sheet with id= G, first strand: chain 'A' and resid 408 through 411 Processing sheet with id= H, first strand: chain 'A' and resid 456 through 460 Processing sheet with id= I, first strand: chain 'D' and resid 286 through 289 Processing sheet with id= J, first strand: chain 'D' and resid 378 through 381 Processing sheet with id= K, first strand: chain 'D' and resid 408 through 411 Processing sheet with id= L, first strand: chain 'D' and resid 456 through 460 Processing sheet with id= M, first strand: chain 'F' and resid 286 through 289 Processing sheet with id= N, first strand: chain 'F' and resid 378 through 381 Processing sheet with id= O, first strand: chain 'F' and resid 408 through 411 Processing sheet with id= P, first strand: chain 'F' and resid 456 through 460 540 hydrogen bonds defined for protein. 1584 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: 3.34 Time building geometry restraints manager: 6.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 524 1.03 - 1.23: 0 1.23 - 1.42: 5068 1.42 - 1.62: 6480 1.62 - 1.81: 44 Bond restraints: 12116 Sorted by residual: bond pdb=" C3 LDP D 501 " pdb=" O1 LDP D 501 " ideal model delta sigma weight residual 1.353 1.401 -0.048 2.00e-02 2.50e+03 5.84e+00 bond pdb=" C3 LDP B 501 " pdb=" O1 LDP B 501 " ideal model delta sigma weight residual 1.353 1.401 -0.048 2.00e-02 2.50e+03 5.75e+00 bond pdb=" C3 LDP A 501 " pdb=" O1 LDP A 501 " ideal model delta sigma weight residual 1.353 1.400 -0.047 2.00e-02 2.50e+03 5.63e+00 bond pdb=" C3 LDP F 501 " pdb=" O1 LDP F 501 " ideal model delta sigma weight residual 1.353 1.400 -0.047 2.00e-02 2.50e+03 5.58e+00 bond pdb=" C4 LDP A 501 " pdb=" O2 LDP A 501 " ideal model delta sigma weight residual 1.355 1.402 -0.047 2.00e-02 2.50e+03 5.43e+00 ... (remaining 12111 not shown) Histogram of bond angle deviations from ideal: 79.27 - 90.21: 32 90.21 - 101.15: 5 101.15 - 112.09: 6751 112.09 - 123.03: 9450 123.03 - 133.97: 666 Bond angle restraints: 16904 Sorted by residual: angle pdb=" CA ALA C 52 " pdb=" CB ALA C 52 " pdb=" HB3 ALA C 52 " ideal model delta sigma weight residual 109.00 79.27 29.73 3.00e+00 1.11e-01 9.82e+01 angle pdb=" CA ALA H 52 " pdb=" CB ALA H 52 " pdb=" HB3 ALA H 52 " ideal model delta sigma weight residual 109.00 79.31 29.69 3.00e+00 1.11e-01 9.79e+01 angle pdb=" CA ALA G 52 " pdb=" CB ALA G 52 " pdb=" HB3 ALA G 52 " ideal model delta sigma weight residual 109.00 79.33 29.67 3.00e+00 1.11e-01 9.78e+01 angle pdb=" CA ALA E 52 " pdb=" CB ALA E 52 " pdb=" HB3 ALA E 52 " ideal model delta sigma weight residual 109.00 79.37 29.63 3.00e+00 1.11e-01 9.75e+01 angle pdb=" CA ALA G 52 " pdb=" CB ALA G 52 " pdb=" HB1 ALA G 52 " ideal model delta sigma weight residual 109.00 79.60 29.40 3.00e+00 1.11e-01 9.60e+01 ... (remaining 16899 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.80: 6728 13.80 - 27.61: 272 27.61 - 41.41: 52 41.41 - 55.22: 16 55.22 - 69.02: 8 Dihedral angle restraints: 7076 sinusoidal: 2924 harmonic: 4152 Sorted by residual: dihedral pdb=" CA ILE G 42 " pdb=" CB ILE G 42 " pdb=" CG1 ILE G 42 " pdb=" CD1 ILE G 42 " ideal model delta sinusoidal sigma weight residual 60.00 113.79 -53.79 3 1.50e+01 4.44e-03 9.23e+00 dihedral pdb=" CA ILE C 42 " pdb=" CB ILE C 42 " pdb=" CG1 ILE C 42 " pdb=" CD1 ILE C 42 " ideal model delta sinusoidal sigma weight residual 60.00 113.75 -53.75 3 1.50e+01 4.44e-03 9.23e+00 dihedral pdb=" CA ILE H 42 " pdb=" CB ILE H 42 " pdb=" CG1 ILE H 42 " pdb=" CD1 ILE H 42 " ideal model delta sinusoidal sigma weight residual 60.00 113.75 -53.75 3 1.50e+01 4.44e-03 9.23e+00 ... (remaining 7073 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.022: 1096 0.022 - 0.045: 341 0.045 - 0.067: 143 0.067 - 0.089: 52 0.089 - 0.112: 52 Chirality restraints: 1684 Sorted by residual: chirality pdb=" CA ILE B 409 " pdb=" N ILE B 409 " pdb=" C ILE B 409 " pdb=" CB ILE B 409 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.11 2.00e-01 2.50e+01 3.12e-01 chirality pdb=" CA ILE D 409 " pdb=" N ILE D 409 " pdb=" C ILE D 409 " pdb=" CB ILE D 409 " both_signs ideal model delta sigma weight residual False 2.43 2.54 -0.11 2.00e-01 2.50e+01 3.11e-01 chirality pdb=" CA ILE A 466 " pdb=" N ILE A 466 " pdb=" C ILE A 466 " pdb=" CB ILE A 466 " both_signs ideal model delta sigma weight residual False 2.43 2.54 -0.11 2.00e-01 2.50e+01 3.05e-01 ... (remaining 1681 not shown) Planarity restraints: 2136 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE F 166 " -0.015 5.00e-02 4.00e+02 2.31e-02 8.56e-01 pdb=" N PRO F 167 " 0.040 5.00e-02 4.00e+02 pdb=" CA PRO F 167 " -0.012 5.00e-02 4.00e+02 pdb=" CD PRO F 167 " -0.013 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE B 166 " 0.015 5.00e-02 4.00e+02 2.30e-02 8.46e-01 pdb=" N PRO B 167 " -0.040 5.00e-02 4.00e+02 pdb=" CA PRO B 167 " 0.012 5.00e-02 4.00e+02 pdb=" CD PRO B 167 " 0.013 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A 166 " 0.015 5.00e-02 4.00e+02 2.29e-02 8.42e-01 pdb=" N PRO A 167 " -0.040 5.00e-02 4.00e+02 pdb=" CA PRO A 167 " 0.012 5.00e-02 4.00e+02 pdb=" CD PRO A 167 " 0.013 5.00e-02 4.00e+02 ... (remaining 2133 not shown) Histogram of nonbonded interaction distances: 1.67 - 2.25: 196 2.25 - 2.84: 6184 2.84 - 3.43: 17860 3.43 - 4.01: 24751 4.01 - 4.60: 35799 Nonbonded interactions: 84790 Sorted by model distance: nonbonded pdb="HG13 ILE E 42 " pdb="HD12 ILE E 42 " model vdw 1.666 1.952 nonbonded pdb="HG13 ILE H 42 " pdb="HD12 ILE H 42 " model vdw 1.667 1.952 nonbonded pdb="HG13 ILE C 42 " pdb="HD12 ILE C 42 " model vdw 1.667 1.952 nonbonded pdb="HG13 ILE G 42 " pdb="HD12 ILE G 42 " model vdw 1.668 1.952 nonbonded pdb="HG12 ILE E 42 " pdb="HD11 ILE E 42 " model vdw 1.676 1.952 ... (remaining 84785 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 'B' selection = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'C' selection = chain 'E' selection = chain 'G' selection = chain 'H' } Set up NCS constraints Number of NCS constrained groups: 2 pdb_interpretation.ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'D' selection = chain 'F' } pdb_interpretation.ncs_group { reference = chain 'C' selection = chain 'E' selection = chain 'G' selection = chain 'H' } Set refine NCS operators NCS operators will be refined. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=0.95 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: 0.180 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: 0.300 Extract box with map and model: 1.540 Check model and map are aligned: 0.180 Set scattering table: 0.110 Process input model: 36.250 Find NCS groups from input model: 0.830 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 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 : 0.002 0.048 11592 Z= 0.128 Angle : 0.406 3.557 15712 Z= 0.230 Chirality : 0.032 0.112 1684 Planarity : 0.002 0.023 2068 Dihedral : 8.305 69.020 4252 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 45.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 0.67 % Allowed : 6.02 % Favored : 93.31 % 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: 2.23 (0.24), residues: 1396 helix: 2.56 (0.20), residues: 760 sheet: -0.61 (0.47), residues: 136 loop : 0.49 (0.28), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP F 371 HIS 0.001 0.000 HIS F 316 PHE 0.003 0.000 PHE A 285 TYR 0.004 0.001 TYR A 313 ARG 0.001 0.000 ARG A 453 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 109 time to evaluate : 0.344 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 197 GLN cc_start: 0.9491 (tp40) cc_final: 0.9273 (tp-100) REVERT: A 198 VAL cc_start: 0.9435 (m) cc_final: 0.9202 (p) REVERT: A 201 GLN cc_start: 0.9499 (mm110) cc_final: 0.9295 (pt0) REVERT: A 233 LYS cc_start: 0.9503 (ttpp) cc_final: 0.9215 (ttpp) REVERT: A 251 HIS cc_start: 0.9097 (t-90) cc_final: 0.8889 (t70) REVERT: A 264 TYR cc_start: 0.7727 (m-10) cc_final: 0.7280 (m-10) REVERT: A 266 GLU cc_start: 0.9248 (pm20) cc_final: 0.8977 (pm20) REVERT: A 268 ASN cc_start: 0.8882 (t0) cc_final: 0.8575 (p0) REVERT: A 308 PHE cc_start: 0.8445 (t80) cc_final: 0.7858 (t80) REVERT: A 339 LEU cc_start: 0.9166 (mm) cc_final: 0.8897 (mm) REVERT: A 344 PHE cc_start: 0.9385 (t80) cc_final: 0.8766 (t80) REVERT: A 356 LEU cc_start: 0.9635 (tt) cc_final: 0.9379 (tt) REVERT: A 362 GLU cc_start: 0.9405 (mp0) cc_final: 0.9168 (mp0) REVERT: A 441 LYS cc_start: 0.9228 (ttmm) cc_final: 0.8781 (mtpt) REVERT: A 491 HIS cc_start: 0.9169 (m170) cc_final: 0.8508 (t-170) outliers start: 1 outliers final: 0 residues processed: 110 average time/residue: 0.1755 time to fit residues: 22.2638 Evaluate side-chains 80 residues out of total 288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 80 time to evaluate : 0.346 Evaluate side-chains 7 residues out of total 11 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 6 time to evaluate : 0.023 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 6 average time/residue: 0.7352 time to fit residues: 4.4650 Evaluate side-chains 3 residues out of total 11 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 3 time to evaluate : 0.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 114 optimal weight: 0.8980 chunk 103 optimal weight: 0.7980 chunk 57 optimal weight: 2.9990 chunk 35 optimal weight: 4.9990 chunk 69 optimal weight: 5.9990 chunk 55 optimal weight: 0.6980 chunk 106 optimal weight: 10.0000 chunk 41 optimal weight: 7.9990 chunk 64 optimal weight: 0.0170 chunk 79 optimal weight: 10.0000 chunk 123 optimal weight: 0.0170 overall best weight: 0.4856 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 286 GLN ** F 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 moved from start: 0.3070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 11592 Z= 0.176 Angle : 0.463 6.164 15712 Z= 0.239 Chirality : 0.036 0.187 1684 Planarity : 0.004 0.062 2068 Dihedral : 4.158 52.315 1568 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 57.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 0.33 % Allowed : 1.34 % Favored : 98.33 % 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: 1.04 (0.22), residues: 1396 helix: 1.14 (0.18), residues: 788 sheet: -0.70 (0.46), residues: 136 loop : 0.62 (0.29), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 371 HIS 0.004 0.001 HIS A 178 PHE 0.025 0.001 PHE D 255 TYR 0.022 0.001 TYR F 422 ARG 0.005 0.000 ARG D 445 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2126 Ramachandran restraints generated. 1063 Oldfield, 0 Emsley, 1063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2126 Ramachandran restraints generated. 1063 Oldfield, 0 Emsley, 1063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 90 time to evaluate : 0.300 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 197 GLN cc_start: 0.9477 (tp40) cc_final: 0.9256 (tp-100) REVERT: F 198 VAL cc_start: 0.9465 (m) cc_final: 0.9186 (p) REVERT: F 201 GLN cc_start: 0.9452 (mm110) cc_final: 0.9196 (pt0) REVERT: F 233 LYS cc_start: 0.9559 (ttpp) cc_final: 0.9222 (ttpp) REVERT: F 251 HIS cc_start: 0.8831 (t-90) cc_final: 0.8621 (t70) REVERT: F 266 GLU cc_start: 0.9139 (pm20) cc_final: 0.8863 (pm20) REVERT: F 268 ASN cc_start: 0.8739 (t0) cc_final: 0.8455 (p0) REVERT: F 308 PHE cc_start: 0.8594 (t80) cc_final: 0.7830 (t80) REVERT: F 321 MET cc_start: 0.8045 (tpt) cc_final: 0.7736 (tpt) REVERT: F 339 LEU cc_start: 0.9109 (mm) cc_final: 0.8833 (mm) REVERT: F 341 ASP cc_start: 0.9142 (t0) cc_final: 0.8892 (t0) REVERT: F 344 PHE cc_start: 0.9455 (t80) cc_final: 0.8772 (t80) REVERT: F 350 ASP cc_start: 0.7930 (m-30) cc_final: 0.7464 (m-30) REVERT: F 362 GLU cc_start: 0.9309 (mp0) cc_final: 0.8978 (mp0) REVERT: F 369 LEU cc_start: 0.9748 (tp) cc_final: 0.9538 (mt) REVERT: F 396 TYR cc_start: 0.9282 (t80) cc_final: 0.9064 (t80) REVERT: F 410 ARG cc_start: 0.8890 (ptp-170) cc_final: 0.8440 (ptp-170) REVERT: F 441 LYS cc_start: 0.9011 (ttmm) cc_final: 0.8782 (mtpt) REVERT: F 466 ILE cc_start: 0.8811 (mm) cc_final: 0.8554 (mm) REVERT: F 473 GLN cc_start: 0.9322 (mp10) cc_final: 0.9056 (mp10) REVERT: F 491 HIS cc_start: 0.9225 (m170) cc_final: 0.8528 (t-170) outliers start: 1 outliers final: 1 residues processed: 90 average time/residue: 0.1787 time to fit residues: 18.5148 Evaluate side-chains 79 residues out of total 288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 78 time to evaluate : 0.287 Evaluate side-chains 3 residues out of total 11 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 3 time to evaluate : 0.022 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 3 average time/residue: 0.9216 time to fit residues: 2.8088 Evaluate side-chains 2 residues out of total 11 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 2 time to evaluate : 0.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 68 optimal weight: 10.0000 chunk 38 optimal weight: 8.9990 chunk 102 optimal weight: 10.0000 chunk 84 optimal weight: 20.0000 chunk 34 optimal weight: 10.0000 chunk 123 optimal weight: 4.9990 chunk 133 optimal weight: 7.9990 chunk 110 optimal weight: 0.0970 chunk 122 optimal weight: 0.9980 chunk 42 optimal weight: 0.0270 chunk 99 optimal weight: 6.9990 overall best weight: 2.6240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.3796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 11592 Z= 0.218 Angle : 0.622 11.993 15712 Z= 0.308 Chirality : 0.037 0.137 1684 Planarity : 0.005 0.074 2068 Dihedral : 4.360 45.395 1568 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 65.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 0.33 % Allowed : 1.67 % Favored : 97.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.22), residues: 1396 helix: 0.52 (0.18), residues: 776 sheet: -0.86 (0.46), residues: 136 loop : 0.49 (0.28), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 165 HIS 0.004 0.001 HIS A 178 PHE 0.015 0.001 PHE D 255 TYR 0.016 0.001 TYR A 422 ARG 0.028 0.001 ARG D 476 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 80 time to evaluate : 0.338 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 197 GLN cc_start: 0.9471 (tp40) cc_final: 0.9199 (tp-100) REVERT: F 198 VAL cc_start: 0.9477 (m) cc_final: 0.9232 (p) REVERT: F 201 GLN cc_start: 0.9444 (mm110) cc_final: 0.9168 (pt0) REVERT: F 233 LYS cc_start: 0.9561 (ttpp) cc_final: 0.9205 (ttpp) REVERT: F 264 TYR cc_start: 0.7626 (m-10) cc_final: 0.7276 (m-80) REVERT: F 266 GLU cc_start: 0.9280 (pm20) cc_final: 0.8944 (pm20) REVERT: F 268 ASN cc_start: 0.8935 (t0) cc_final: 0.8495 (p0) REVERT: F 280 LYS cc_start: 0.9166 (mmmm) cc_final: 0.8806 (mmmm) REVERT: F 308 PHE cc_start: 0.8635 (t80) cc_final: 0.8012 (t80) REVERT: F 321 MET cc_start: 0.8190 (tpt) cc_final: 0.7874 (tpt) REVERT: F 338 MET cc_start: 0.8943 (mmp) cc_final: 0.8601 (mmp) REVERT: F 341 ASP cc_start: 0.9147 (t0) cc_final: 0.8882 (t0) REVERT: F 344 PHE cc_start: 0.9386 (t80) cc_final: 0.8689 (t80) REVERT: F 346 GLN cc_start: 0.8518 (tp-100) cc_final: 0.8150 (tp-100) REVERT: F 350 ASP cc_start: 0.7842 (m-30) cc_final: 0.7340 (m-30) REVERT: F 362 GLU cc_start: 0.9336 (mp0) cc_final: 0.9068 (mp0) REVERT: F 441 LYS cc_start: 0.9239 (ttmm) cc_final: 0.8851 (mtpp) REVERT: F 455 PHE cc_start: 0.8391 (p90) cc_final: 0.8114 (p90) REVERT: F 473 GLN cc_start: 0.9420 (mp10) cc_final: 0.9166 (mp10) REVERT: F 491 HIS cc_start: 0.9064 (m170) cc_final: 0.8109 (t70) outliers start: 1 outliers final: 1 residues processed: 80 average time/residue: 0.1913 time to fit residues: 17.6286 Evaluate side-chains 75 residues out of total 288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 74 time to evaluate : 0.320 Evaluate side-chains 2 residues out of total 11 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 2 time to evaluate : 0.024 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 2 average time/residue: 1.2995 time to fit residues: 2.6419 Evaluate side-chains 2 residues out of total 11 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 2 time to evaluate : 0.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 122 optimal weight: 3.9990 chunk 93 optimal weight: 6.9990 chunk 64 optimal weight: 0.0370 chunk 13 optimal weight: 3.9990 chunk 59 optimal weight: 0.2980 chunk 83 optimal weight: 20.0000 chunk 124 optimal weight: 5.9990 chunk 131 optimal weight: 0.0570 chunk 117 optimal weight: 20.0000 chunk 35 optimal weight: 8.9990 chunk 109 optimal weight: 0.8980 overall best weight: 1.0578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.4137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 11592 Z= 0.154 Angle : 0.495 10.334 15712 Z= 0.243 Chirality : 0.036 0.192 1684 Planarity : 0.003 0.038 2068 Dihedral : 4.080 37.177 1568 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 61.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.22), residues: 1396 helix: 0.59 (0.18), residues: 784 sheet: -1.00 (0.44), residues: 136 loop : 0.59 (0.28), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 371 HIS 0.002 0.001 HIS A 178 PHE 0.016 0.001 PHE A 255 TYR 0.012 0.001 TYR A 422 ARG 0.013 0.001 ARG B 476 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 79 time to evaluate : 0.346 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 166 PHE cc_start: 0.9533 (p90) cc_final: 0.9294 (p90) REVERT: F 197 GLN cc_start: 0.9462 (tp40) cc_final: 0.9248 (tp-100) REVERT: F 198 VAL cc_start: 0.9488 (m) cc_final: 0.9241 (p) REVERT: F 233 LYS cc_start: 0.9559 (ttpp) cc_final: 0.9184 (ttpp) REVERT: F 251 HIS cc_start: 0.8937 (t70) cc_final: 0.8631 (t70) REVERT: F 264 TYR cc_start: 0.7531 (m-10) cc_final: 0.7191 (m-80) REVERT: F 266 GLU cc_start: 0.9271 (pm20) cc_final: 0.8812 (pm20) REVERT: F 299 PHE cc_start: 0.8920 (t80) cc_final: 0.8682 (t80) REVERT: F 308 PHE cc_start: 0.8523 (t80) cc_final: 0.7943 (t80) REVERT: F 338 MET cc_start: 0.8875 (mmp) cc_final: 0.8485 (mmp) REVERT: F 339 LEU cc_start: 0.9192 (mm) cc_final: 0.8917 (mm) REVERT: F 341 ASP cc_start: 0.9049 (t0) cc_final: 0.8800 (t0) REVERT: F 344 PHE cc_start: 0.9396 (t80) cc_final: 0.8690 (t80) REVERT: F 346 GLN cc_start: 0.8554 (tp-100) cc_final: 0.8287 (tp-100) REVERT: F 445 ARG cc_start: 0.8205 (ttt180) cc_final: 0.7944 (ttt180) REVERT: F 466 ILE cc_start: 0.8864 (mm) cc_final: 0.8574 (mm) REVERT: F 473 GLN cc_start: 0.9417 (mp10) cc_final: 0.9199 (mp10) REVERT: F 483 GLN cc_start: 0.9077 (mt0) cc_final: 0.8850 (mt0) REVERT: F 491 HIS cc_start: 0.8999 (m170) cc_final: 0.8002 (t-170) outliers start: 0 outliers final: 0 residues processed: 79 average time/residue: 0.1746 time to fit residues: 15.9792 Evaluate side-chains 71 residues out of total 288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 71 time to evaluate : 0.279 Evaluate side-chains 2 residues out of total 11 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 2 time to evaluate : 0.018 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 2 average time/residue: 1.2151 time to fit residues: 2.4692 Evaluate side-chains 2 residues out of total 11 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 2 time to evaluate : 0.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 74 optimal weight: 5.9990 chunk 1 optimal weight: 0.3980 chunk 97 optimal weight: 10.0000 chunk 54 optimal weight: 2.9990 chunk 112 optimal weight: 10.0000 chunk 90 optimal weight: 0.5980 chunk 0 optimal weight: 10.0000 chunk 67 optimal weight: 3.9990 chunk 117 optimal weight: 0.1980 chunk 33 optimal weight: 10.0000 chunk 44 optimal weight: 20.0000 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.4522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 11592 Z= 0.155 Angle : 0.509 11.560 15712 Z= 0.254 Chirality : 0.038 0.220 1684 Planarity : 0.003 0.031 2068 Dihedral : 3.935 32.234 1568 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 67.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.22), residues: 1396 helix: 0.63 (0.18), residues: 780 sheet: -1.23 (0.42), residues: 136 loop : 0.37 (0.28), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP F 165 HIS 0.002 0.001 HIS A 177 PHE 0.014 0.001 PHE B 255 TYR 0.009 0.001 TYR D 264 ARG 0.010 0.001 ARG B 476 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 80 time to evaluate : 0.313 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 166 PHE cc_start: 0.9572 (p90) cc_final: 0.9287 (p90) REVERT: F 233 LYS cc_start: 0.9583 (ttpp) cc_final: 0.9203 (ttpp) REVERT: F 251 HIS cc_start: 0.9010 (t70) cc_final: 0.8058 (t70) REVERT: F 252 LEU cc_start: 0.8979 (mm) cc_final: 0.8709 (mm) REVERT: F 255 PHE cc_start: 0.8810 (p90) cc_final: 0.8310 (p90) REVERT: F 264 TYR cc_start: 0.7695 (m-10) cc_final: 0.6698 (m-80) REVERT: F 299 PHE cc_start: 0.8931 (t80) cc_final: 0.8670 (t80) REVERT: F 308 PHE cc_start: 0.8498 (t80) cc_final: 0.7981 (t80) REVERT: F 338 MET cc_start: 0.8940 (mmp) cc_final: 0.8538 (mmp) REVERT: F 339 LEU cc_start: 0.9207 (mm) cc_final: 0.8985 (mm) REVERT: F 341 ASP cc_start: 0.9048 (t0) cc_final: 0.8792 (t0) REVERT: F 344 PHE cc_start: 0.9359 (t80) cc_final: 0.8713 (t80) REVERT: F 350 ASP cc_start: 0.7986 (m-30) cc_final: 0.7566 (m-30) REVERT: F 441 LYS cc_start: 0.9351 (tmtt) cc_final: 0.8923 (ttmt) REVERT: F 466 ILE cc_start: 0.8876 (mm) cc_final: 0.8630 (mm) REVERT: F 473 GLN cc_start: 0.9381 (mp10) cc_final: 0.9072 (mp10) REVERT: F 491 HIS cc_start: 0.9015 (m170) cc_final: 0.8107 (t-170) outliers start: 0 outliers final: 0 residues processed: 80 average time/residue: 0.1819 time to fit residues: 17.0982 Evaluate side-chains 69 residues out of total 288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 69 time to evaluate : 0.309 Evaluate side-chains 2 residues out of total 11 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 2 time to evaluate : 0.024 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 2 average time/residue: 1.3377 time to fit residues: 2.7248 Evaluate side-chains 2 residues out of total 11 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 2 time to evaluate : 0.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 118 optimal weight: 0.0040 chunk 25 optimal weight: 0.0070 chunk 77 optimal weight: 0.9990 chunk 32 optimal weight: 7.9990 chunk 131 optimal weight: 0.0570 chunk 109 optimal weight: 0.8980 chunk 60 optimal weight: 7.9990 chunk 10 optimal weight: 0.9980 chunk 43 optimal weight: 1.9990 chunk 69 optimal weight: 6.9990 chunk 126 optimal weight: 7.9990 overall best weight: 0.3928 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.4697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 11592 Z= 0.149 Angle : 0.507 11.591 15712 Z= 0.249 Chirality : 0.037 0.220 1684 Planarity : 0.003 0.041 2068 Dihedral : 3.813 28.148 1568 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 65.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % 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: 0.55 (0.22), residues: 1396 helix: 0.73 (0.18), residues: 788 sheet: -1.14 (0.42), residues: 136 loop : 0.51 (0.29), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP D 232 HIS 0.001 0.000 HIS D 491 PHE 0.014 0.001 PHE F 255 TYR 0.007 0.001 TYR F 264 ARG 0.007 0.000 ARG F 476 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 77 time to evaluate : 0.341 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 166 PHE cc_start: 0.9517 (p90) cc_final: 0.9281 (p90) REVERT: F 251 HIS cc_start: 0.8842 (t70) cc_final: 0.7722 (t70) REVERT: F 252 LEU cc_start: 0.8967 (mm) cc_final: 0.8715 (mm) REVERT: F 255 PHE cc_start: 0.8820 (p90) cc_final: 0.8390 (p90) REVERT: F 264 TYR cc_start: 0.7541 (m-10) cc_final: 0.7205 (m-80) REVERT: F 265 ARG cc_start: 0.8253 (mpp-170) cc_final: 0.7771 (mmt180) REVERT: F 266 GLU cc_start: 0.9383 (pm20) cc_final: 0.9154 (pm20) REVERT: F 286 GLN cc_start: 0.8885 (mt0) cc_final: 0.8418 (mm110) REVERT: F 299 PHE cc_start: 0.8903 (t80) cc_final: 0.8667 (t80) REVERT: F 308 PHE cc_start: 0.8387 (t80) cc_final: 0.7943 (t80) REVERT: F 338 MET cc_start: 0.8760 (mmp) cc_final: 0.8421 (mmp) REVERT: F 339 LEU cc_start: 0.9209 (mm) cc_final: 0.8942 (mm) REVERT: F 341 ASP cc_start: 0.9006 (t0) cc_final: 0.8761 (t0) REVERT: F 344 PHE cc_start: 0.9356 (t80) cc_final: 0.8698 (t80) REVERT: F 350 ASP cc_start: 0.7968 (m-30) cc_final: 0.7704 (m-30) REVERT: F 441 LYS cc_start: 0.9296 (tmtt) cc_final: 0.8794 (ttmt) REVERT: F 445 ARG cc_start: 0.7705 (ttt180) cc_final: 0.6893 (ttm110) REVERT: F 455 PHE cc_start: 0.8236 (p90) cc_final: 0.7986 (p90) REVERT: F 466 ILE cc_start: 0.8838 (mm) cc_final: 0.8566 (mm) REVERT: F 473 GLN cc_start: 0.9356 (mp10) cc_final: 0.9024 (mp10) REVERT: F 491 HIS cc_start: 0.9011 (m170) cc_final: 0.8082 (t-170) outliers start: 0 outliers final: 0 residues processed: 77 average time/residue: 0.1709 time to fit residues: 15.4101 Evaluate side-chains 72 residues out of total 288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 72 time to evaluate : 0.288 Evaluate side-chains 2 residues out of total 11 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 2 time to evaluate : 0.020 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 2 average time/residue: 1.2693 time to fit residues: 2.5766 Evaluate side-chains 2 residues out of total 11 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 2 time to evaluate : 0.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 14 optimal weight: 6.9990 chunk 74 optimal weight: 5.9990 chunk 96 optimal weight: 3.9990 chunk 110 optimal weight: 1.9990 chunk 73 optimal weight: 0.9980 chunk 131 optimal weight: 0.0170 chunk 82 optimal weight: 7.9990 chunk 79 optimal weight: 0.6980 chunk 60 optimal weight: 5.9990 chunk 81 optimal weight: 4.9990 chunk 52 optimal weight: 9.9990 overall best weight: 1.5422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.4772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 11592 Z= 0.160 Angle : 0.477 11.803 15712 Z= 0.234 Chirality : 0.035 0.205 1684 Planarity : 0.003 0.025 2068 Dihedral : 3.801 26.924 1568 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 65.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.22), residues: 1396 helix: 0.82 (0.18), residues: 784 sheet: -1.14 (0.42), residues: 136 loop : 0.40 (0.28), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP D 165 HIS 0.002 0.001 HIS D 330 PHE 0.012 0.001 PHE F 255 TYR 0.011 0.001 TYR F 264 ARG 0.004 0.000 ARG A 476 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 79 time to evaluate : 0.296 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 166 PHE cc_start: 0.9541 (p90) cc_final: 0.9296 (p90) REVERT: F 223 GLU cc_start: 0.9322 (pm20) cc_final: 0.9104 (pp20) REVERT: F 251 HIS cc_start: 0.8898 (t70) cc_final: 0.7887 (t70) REVERT: F 252 LEU cc_start: 0.8957 (mm) cc_final: 0.8714 (mm) REVERT: F 255 PHE cc_start: 0.8823 (p90) cc_final: 0.8418 (p90) REVERT: F 264 TYR cc_start: 0.7613 (m-10) cc_final: 0.7258 (m-80) REVERT: F 265 ARG cc_start: 0.8427 (mpp-170) cc_final: 0.8034 (mmt180) REVERT: F 266 GLU cc_start: 0.9408 (pm20) cc_final: 0.9159 (pm20) REVERT: F 299 PHE cc_start: 0.8950 (t80) cc_final: 0.8720 (t80) REVERT: F 308 PHE cc_start: 0.8409 (t80) cc_final: 0.7964 (t80) REVERT: F 338 MET cc_start: 0.8800 (mmp) cc_final: 0.8453 (mmp) REVERT: F 339 LEU cc_start: 0.9201 (mm) cc_final: 0.8957 (mm) REVERT: F 341 ASP cc_start: 0.9035 (t0) cc_final: 0.8781 (t0) REVERT: F 344 PHE cc_start: 0.9359 (t80) cc_final: 0.8712 (t80) REVERT: F 350 ASP cc_start: 0.7995 (m-30) cc_final: 0.7714 (m-30) REVERT: F 441 LYS cc_start: 0.9288 (tmtt) cc_final: 0.8785 (ttmt) REVERT: F 445 ARG cc_start: 0.7698 (ttt180) cc_final: 0.6897 (ttm110) REVERT: F 455 PHE cc_start: 0.8296 (p90) cc_final: 0.8022 (p90) REVERT: F 466 ILE cc_start: 0.8865 (mm) cc_final: 0.8583 (mm) REVERT: F 473 GLN cc_start: 0.9366 (mp10) cc_final: 0.9055 (mp10) REVERT: F 491 HIS cc_start: 0.9034 (m170) cc_final: 0.8108 (t-170) outliers start: 0 outliers final: 0 residues processed: 79 average time/residue: 0.1686 time to fit residues: 15.5302 Evaluate side-chains 66 residues out of total 288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 66 time to evaluate : 0.317 Evaluate side-chains 2 residues out of total 11 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 2 time to evaluate : 0.022 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 2 average time/residue: 1.2725 time to fit residues: 2.5829 Evaluate side-chains 2 residues out of total 11 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 2 time to evaluate : 0.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 78 optimal weight: 9.9990 chunk 39 optimal weight: 4.9990 chunk 25 optimal weight: 0.0050 chunk 83 optimal weight: 0.4980 chunk 89 optimal weight: 0.0770 chunk 64 optimal weight: 0.0010 chunk 12 optimal weight: 6.9990 chunk 103 optimal weight: 7.9990 chunk 119 optimal weight: 5.9990 chunk 125 optimal weight: 9.9990 chunk 114 optimal weight: 6.9990 overall best weight: 1.1160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.4787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 11592 Z= 0.160 Angle : 0.477 11.803 15712 Z= 0.234 Chirality : 0.035 0.205 1684 Planarity : 0.003 0.025 2068 Dihedral : 3.800 26.924 1568 Min Nonbonded Distance : 1.561 Molprobity Statistics. All-atom Clashscore : 71.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: 0.58 (0.22), residues: 1396 helix: 0.82 (0.18), residues: 784 sheet: -1.14 (0.42), residues: 136 loop : 0.40 (0.28), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP D 165 HIS 0.002 0.001 HIS F 178 PHE 0.012 0.001 PHE A 255 TYR 0.011 0.001 TYR F 264 ARG 0.004 0.000 ARG F 476 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 78 time to evaluate : 0.369 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 166 PHE cc_start: 0.9540 (p90) cc_final: 0.9297 (p90) REVERT: F 223 GLU cc_start: 0.9320 (pm20) cc_final: 0.9104 (pp20) REVERT: F 251 HIS cc_start: 0.8898 (t70) cc_final: 0.7887 (t70) REVERT: F 252 LEU cc_start: 0.8958 (mm) cc_final: 0.8714 (mm) REVERT: F 255 PHE cc_start: 0.8822 (p90) cc_final: 0.8418 (p90) REVERT: F 264 TYR cc_start: 0.7612 (m-10) cc_final: 0.7259 (m-80) REVERT: F 265 ARG cc_start: 0.8426 (mpp-170) cc_final: 0.8034 (mmt180) REVERT: F 266 GLU cc_start: 0.9374 (pm20) cc_final: 0.9158 (pm20) REVERT: F 286 GLN cc_start: 0.8929 (mt0) cc_final: 0.8707 (mp10) REVERT: F 299 PHE cc_start: 0.8950 (t80) cc_final: 0.8719 (t80) REVERT: F 308 PHE cc_start: 0.8408 (t80) cc_final: 0.7968 (t80) REVERT: F 321 MET cc_start: 0.8171 (tpt) cc_final: 0.7764 (tpt) REVERT: F 338 MET cc_start: 0.8801 (mmp) cc_final: 0.8453 (mmp) REVERT: F 339 LEU cc_start: 0.9202 (mm) cc_final: 0.8955 (mm) REVERT: F 341 ASP cc_start: 0.9035 (t0) cc_final: 0.8779 (t0) REVERT: F 344 PHE cc_start: 0.9359 (t80) cc_final: 0.8712 (t80) REVERT: F 350 ASP cc_start: 0.7998 (m-30) cc_final: 0.7715 (m-30) REVERT: F 441 LYS cc_start: 0.9290 (tmtt) cc_final: 0.8786 (ttmt) REVERT: F 445 ARG cc_start: 0.7697 (ttt180) cc_final: 0.6895 (ttm110) REVERT: F 455 PHE cc_start: 0.8296 (p90) cc_final: 0.8022 (p90) REVERT: F 466 ILE cc_start: 0.8866 (mm) cc_final: 0.8582 (mm) REVERT: F 473 GLN cc_start: 0.9366 (mp10) cc_final: 0.9055 (mp10) REVERT: F 491 HIS cc_start: 0.9034 (m170) cc_final: 0.8109 (t-170) outliers start: 0 outliers final: 0 residues processed: 78 average time/residue: 0.1711 time to fit residues: 15.5541 Evaluate side-chains 66 residues out of total 288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 66 time to evaluate : 0.310 Evaluate side-chains 2 residues out of total 11 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 2 time to evaluate : 0.021 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 2 average time/residue: 1.2640 time to fit residues: 2.5683 Evaluate side-chains 2 residues out of total 11 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 2 time to evaluate : 0.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 122 optimal weight: 4.9990 chunk 125 optimal weight: 6.9990 chunk 73 optimal weight: 2.9990 chunk 53 optimal weight: 0.2980 chunk 95 optimal weight: 3.9990 chunk 37 optimal weight: 10.0000 chunk 110 optimal weight: 0.0020 chunk 115 optimal weight: 2.9990 chunk 121 optimal weight: 0.0000 chunk 80 optimal weight: 4.9990 chunk 129 optimal weight: 3.9990 overall best weight: 1.2596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.4787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 11592 Z= 0.160 Angle : 0.477 11.803 15712 Z= 0.234 Chirality : 0.035 0.205 1684 Planarity : 0.003 0.025 2068 Dihedral : 3.800 26.924 1568 Min Nonbonded Distance : 1.561 Molprobity Statistics. All-atom Clashscore : 70.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: 0.58 (0.22), residues: 1396 helix: 0.82 (0.18), residues: 784 sheet: -1.14 (0.42), residues: 136 loop : 0.40 (0.28), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP D 165 HIS 0.002 0.001 HIS F 178 PHE 0.012 0.001 PHE D 255 TYR 0.011 0.001 TYR F 264 ARG 0.004 0.000 ARG F 476 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1396 Ramachandran restraints generated. 698 Oldfield, 0 Emsley, 698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1396 Ramachandran restraints generated. 698 Oldfield, 0 Emsley, 698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 76 time to evaluate : 0.369 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 166 PHE cc_start: 0.9537 (p90) cc_final: 0.9300 (p90) REVERT: A 223 GLU cc_start: 0.9265 (pm20) cc_final: 0.9057 (pp20) REVERT: A 251 HIS cc_start: 0.8892 (t70) cc_final: 0.7862 (t70) REVERT: A 252 LEU cc_start: 0.8947 (mm) cc_final: 0.8694 (mm) REVERT: A 255 PHE cc_start: 0.8809 (p90) cc_final: 0.8394 (p90) REVERT: A 264 TYR cc_start: 0.7597 (m-10) cc_final: 0.7253 (m-80) REVERT: A 265 ARG cc_start: 0.8415 (mpp-170) cc_final: 0.8028 (mmt180) REVERT: A 266 GLU cc_start: 0.9393 (pm20) cc_final: 0.9137 (pm20) REVERT: A 299 PHE cc_start: 0.8958 (t80) cc_final: 0.8724 (t80) REVERT: A 305 PHE cc_start: 0.9138 (m-80) cc_final: 0.8778 (m-80) REVERT: A 308 PHE cc_start: 0.8321 (t80) cc_final: 0.7910 (t80) REVERT: A 321 MET cc_start: 0.8096 (tpt) cc_final: 0.7728 (tpt) REVERT: A 338 MET cc_start: 0.8791 (mmp) cc_final: 0.8455 (mmp) REVERT: A 339 LEU cc_start: 0.9222 (mm) cc_final: 0.8964 (mm) REVERT: A 341 ASP cc_start: 0.9048 (t0) cc_final: 0.8797 (t0) REVERT: A 344 PHE cc_start: 0.9359 (t80) cc_final: 0.8709 (t80) REVERT: A 350 ASP cc_start: 0.7994 (m-30) cc_final: 0.7712 (m-30) REVERT: A 441 LYS cc_start: 0.9283 (tmtt) cc_final: 0.8776 (ttmt) REVERT: A 445 ARG cc_start: 0.7698 (ttt180) cc_final: 0.6895 (ttm110) REVERT: A 455 PHE cc_start: 0.8304 (p90) cc_final: 0.8023 (p90) REVERT: A 466 ILE cc_start: 0.8863 (mm) cc_final: 0.8601 (mm) REVERT: A 473 GLN cc_start: 0.9367 (mp10) cc_final: 0.9057 (mp10) REVERT: A 491 HIS cc_start: 0.9041 (m170) cc_final: 0.8117 (t-170) outliers start: 0 outliers final: 0 residues processed: 76 average time/residue: 0.2182 time to fit residues: 18.9629 Evaluate side-chains 65 residues out of total 288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 65 time to evaluate : 0.336 Evaluate side-chains 2 residues out of total 11 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 2 time to evaluate : 0.023 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 2 average time/residue: 1.2984 time to fit residues: 2.6425 Evaluate side-chains 2 residues out of total 11 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 2 time to evaluate : 0.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 78 optimal weight: 9.9990 chunk 61 optimal weight: 4.9990 chunk 89 optimal weight: 8.9990 chunk 135 optimal weight: 7.9990 chunk 124 optimal weight: 0.0050 chunk 107 optimal weight: 4.9990 chunk 11 optimal weight: 10.0000 chunk 83 optimal weight: 8.9990 chunk 66 optimal weight: 4.9990 chunk 85 optimal weight: 3.9990 chunk 114 optimal weight: 2.9990 overall best weight: 3.4002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.4787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 11592 Z= 0.160 Angle : 0.477 11.803 15712 Z= 0.234 Chirality : 0.035 0.205 1684 Planarity : 0.003 0.025 2068 Dihedral : 3.800 26.924 1568 Min Nonbonded Distance : 1.561 Molprobity Statistics. All-atom Clashscore : 70.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: 0.58 (0.22), residues: 1396 helix: 0.82 (0.18), residues: 784 sheet: -1.14 (0.42), residues: 136 loop : 0.40 (0.28), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP D 165 HIS 0.002 0.001 HIS F 178 PHE 0.012 0.001 PHE D 255 TYR 0.011 0.001 TYR F 264 ARG 0.004 0.000 ARG F 476 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1396 Ramachandran restraints generated. 698 Oldfield, 0 Emsley, 698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1396 Ramachandran restraints generated. 698 Oldfield, 0 Emsley, 698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 78 time to evaluate : 0.296 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 166 PHE cc_start: 0.9540 (p90) cc_final: 0.9297 (p90) REVERT: F 223 GLU cc_start: 0.9321 (pm20) cc_final: 0.9104 (pp20) REVERT: F 251 HIS cc_start: 0.8898 (t70) cc_final: 0.7887 (t70) REVERT: F 252 LEU cc_start: 0.8958 (mm) cc_final: 0.8714 (mm) REVERT: F 255 PHE cc_start: 0.8822 (p90) cc_final: 0.8418 (p90) REVERT: F 264 TYR cc_start: 0.7612 (m-10) cc_final: 0.7259 (m-80) REVERT: F 265 ARG cc_start: 0.8426 (mpp-170) cc_final: 0.8034 (mmt180) REVERT: F 266 GLU cc_start: 0.9406 (pm20) cc_final: 0.9158 (pm20) REVERT: F 299 PHE cc_start: 0.8950 (t80) cc_final: 0.8719 (t80) REVERT: F 308 PHE cc_start: 0.8408 (t80) cc_final: 0.7964 (t80) REVERT: F 321 MET cc_start: 0.8170 (tpt) cc_final: 0.7761 (tpt) REVERT: F 338 MET cc_start: 0.8801 (mmp) cc_final: 0.8453 (mmp) REVERT: F 339 LEU cc_start: 0.9202 (mm) cc_final: 0.8957 (mm) REVERT: F 341 ASP cc_start: 0.9035 (t0) cc_final: 0.8781 (t0) REVERT: F 344 PHE cc_start: 0.9359 (t80) cc_final: 0.8712 (t80) REVERT: F 350 ASP cc_start: 0.7998 (m-30) cc_final: 0.7714 (m-30) REVERT: F 441 LYS cc_start: 0.9290 (tmtt) cc_final: 0.8785 (ttmt) REVERT: F 445 ARG cc_start: 0.7697 (ttt180) cc_final: 0.6897 (ttm110) REVERT: F 455 PHE cc_start: 0.8296 (p90) cc_final: 0.8022 (p90) REVERT: F 466 ILE cc_start: 0.8866 (mm) cc_final: 0.8583 (mm) REVERT: F 473 GLN cc_start: 0.9366 (mp10) cc_final: 0.9055 (mp10) REVERT: F 491 HIS cc_start: 0.9034 (m170) cc_final: 0.8108 (t-170) outliers start: 0 outliers final: 0 residues processed: 78 average time/residue: 0.1735 time to fit residues: 15.7612 Evaluate side-chains 66 residues out of total 288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 66 time to evaluate : 0.329 Evaluate side-chains 2 residues out of total 11 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 2 time to evaluate : 0.023 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 2 average time/residue: 1.3051 time to fit residues: 2.6539 Evaluate side-chains 2 residues out of total 11 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 2 time to evaluate : 0.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 33 optimal weight: 80.0000 chunk 99 optimal weight: 0.0470 chunk 15 optimal weight: 9.9990 chunk 29 optimal weight: 7.9990 chunk 108 optimal weight: 6.9990 chunk 45 optimal weight: 10.0000 chunk 110 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 19 optimal weight: 0.4980 chunk 94 optimal weight: 8.9990 chunk 6 optimal weight: 6.9990 overall best weight: 2.0882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.089232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.067676 restraints weight = 10263.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.069802 restraints weight = 7116.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.071382 restraints weight = 5474.474| |-----------------------------------------------------------------------------| r_work (final): 0.3318 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4722 r_free = 0.4722 target = 0.225854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4575 r_free = 0.4575 target = 0.194081 restraints weight = 602.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4619 r_free = 0.4619 target = 0.199521 restraints weight = 304.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4638 r_free = 0.4638 target = 0.202695 restraints weight = 199.217| |-----------------------------------------------------------------------------| r_work (final): 0.4808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.4787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 11592 Z= 0.160 Angle : 0.477 11.803 15712 Z= 0.234 Chirality : 0.035 0.205 1684 Planarity : 0.003 0.025 2068 Dihedral : 3.800 26.924 1568 Min Nonbonded Distance : 1.561 Molprobity Statistics. All-atom Clashscore : 70.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: 0.58 (0.22), residues: 1396 helix: 0.82 (0.18), residues: 784 sheet: -1.14 (0.42), residues: 136 loop : 0.40 (0.28), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP D 165 HIS 0.002 0.001 HIS F 178 PHE 0.012 0.001 PHE F 255 TYR 0.011 0.001 TYR D 264 ARG 0.004 0.000 ARG D 476 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1976.10 seconds wall clock time: 37 minutes 16.26 seconds (2236.26 seconds total)