Starting phenix.real_space_refine on Fri Aug 22 18:27:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8z7l_39819/08_2025/8z7l_39819.cif Found real_map, /net/cci-nas-00/data/ceres_data/8z7l_39819/08_2025/8z7l_39819.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.42 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8z7l_39819/08_2025/8z7l_39819.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8z7l_39819/08_2025/8z7l_39819.map" model { file = "/net/cci-nas-00/data/ceres_data/8z7l_39819/08_2025/8z7l_39819.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8z7l_39819/08_2025/8z7l_39819.cif" } resolution = 3.42 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= -0.048 sd= 0.260 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 27 5.16 5 C 4320 2.51 5 N 1098 2.21 5 O 1329 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 72 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6774 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 2202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 2202 Classifications: {'peptide': 281} Link IDs: {'PTRANS': 15, 'TRANS': 265} Chain breaks: 7 Chain: "B" Number of atoms: 2202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 2202 Classifications: {'peptide': 281} Link IDs: {'PTRANS': 15, 'TRANS': 265} Chain breaks: 7 Chain: "C" Number of atoms: 2202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 2202 Classifications: {'peptide': 281} Link IDs: {'PTRANS': 15, 'TRANS': 265} Chain breaks: 7 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 1.73, per 1000 atoms: 0.26 Number of scatterers: 6774 At special positions: 0 Unit cell: (129.548, 136.072, 65.24, 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 27 16.00 O 1329 8.00 N 1098 7.00 C 4320 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " NAG-ASN " NAG A1301 " - " ASN A 616 " " NAG A1302 " - " ASN A 282 " " NAG B1301 " - " ASN B 616 " " NAG B1302 " - " ASN B 282 " " NAG C1301 " - " ASN C 616 " " NAG C1302 " - " ASN C 282 " " NAG D 1 " - " ASN A 331 " " NAG E 1 " - " ASN B 331 " " NAG F 1 " - " ASN C 331 " Time building additional restraints: 0.41 Conformation dependent library (CDL) restraints added in 316.0 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 1590 Ramachandran restraints generated. 795 Oldfield, 0 Emsley, 795 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1578 Finding SS restraints... Secondary structure from input PDB file: 6 helices and 15 sheets defined 4.6% alpha, 36.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.28 Creating SS restraints... Processing helix chain 'A' and resid 297 through 304 Processing helix chain 'A' and resid 616 through 620 Processing helix chain 'B' and resid 297 through 304 Processing helix chain 'B' and resid 616 through 620 Processing helix chain 'C' and resid 297 through 304 Processing helix chain 'C' and resid 616 through 620 Processing sheet with id=AA1, first strand: chain 'A' and resid 35 through 37 removed outlier: 7.011A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 8.839A pdb=" N ALA A 222 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N HIS A 207 " --> pdb=" O ALA A 222 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 6.240A pdb=" N PHE A 43 " --> pdb=" O ARG B 567 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.599A pdb=" N VAL A 47 " --> pdb=" O TYR A 279 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 310 through 319 removed outlier: 5.323A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N PHE A 643 " --> pdb=" O LEU A 650 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 325 through 328 removed outlier: 5.470A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 664 through 665 Processing sheet with id=AA7, first strand: chain 'B' and resid 35 through 37 removed outlier: 6.993A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 8.878A pdb=" N ALA B 222 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N HIS B 207 " --> pdb=" O ALA B 222 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 42 through 43 removed outlier: 6.217A pdb=" N PHE B 43 " --> pdb=" O ARG C 567 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.573A pdb=" N VAL B 47 " --> pdb=" O TYR B 279 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 310 through 319 removed outlier: 5.315A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.320A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N PHE B 643 " --> pdb=" O LEU B 650 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 664 through 665 Processing sheet with id=AB3, first strand: chain 'C' and resid 35 through 37 removed outlier: 6.981A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 8.920A pdb=" N ALA C 222 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N HIS C 207 " --> pdb=" O ALA C 222 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N SER C 94 " --> pdb=" O ARG C 190 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.599A pdb=" N VAL C 47 " --> pdb=" O TYR C 279 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 310 through 319 removed outlier: 5.335A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.347A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.935A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N PHE C 643 " --> pdb=" O LEU C 650 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 664 through 665 210 hydrogen bonds defined for protein. 537 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.05 Time building geometry restraints manager: 0.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2130 1.34 - 1.46: 1658 1.46 - 1.58: 3091 1.58 - 1.69: 0 1.69 - 1.81: 30 Bond restraints: 6909 Sorted by residual: bond pdb=" C1 NAG F 2 " pdb=" O5 NAG F 2 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.14e+00 bond pdb=" C1 NAG D 2 " pdb=" O5 NAG D 2 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.09e+00 bond pdb=" C1 NAG D 1 " pdb=" O5 NAG D 1 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.04e+00 bond pdb=" C1 NAG C1302 " pdb=" O5 NAG C1302 " ideal model delta sigma weight residual 1.406 1.434 -0.028 2.00e-02 2.50e+03 2.02e+00 bond pdb=" C1 NAG E 2 " pdb=" O5 NAG E 2 " ideal model delta sigma weight residual 1.406 1.434 -0.028 2.00e-02 2.50e+03 2.01e+00 ... (remaining 6904 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.92: 9000 0.92 - 1.85: 264 1.85 - 2.77: 101 2.77 - 3.70: 10 3.70 - 4.62: 6 Bond angle restraints: 9381 Sorted by residual: angle pdb=" C PRO A 295 " pdb=" N LEU A 296 " pdb=" CA LEU A 296 " ideal model delta sigma weight residual 121.54 125.60 -4.06 1.91e+00 2.74e-01 4.51e+00 angle pdb=" C PRO C 295 " pdb=" N LEU C 296 " pdb=" CA LEU C 296 " ideal model delta sigma weight residual 121.54 125.57 -4.03 1.91e+00 2.74e-01 4.44e+00 angle pdb=" C PRO B 295 " pdb=" N LEU B 296 " pdb=" CA LEU B 296 " ideal model delta sigma weight residual 121.54 125.56 -4.02 1.91e+00 2.74e-01 4.44e+00 angle pdb=" N THR A 645 " pdb=" CA THR A 645 " pdb=" C THR A 645 " ideal model delta sigma weight residual 108.34 110.41 -2.07 1.31e+00 5.83e-01 2.51e+00 angle pdb=" NE ARG C 34 " pdb=" CZ ARG C 34 " pdb=" NH1 ARG C 34 " ideal model delta sigma weight residual 121.50 120.03 1.47 1.00e+00 1.00e+00 2.15e+00 ... (remaining 9376 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.96: 3944 11.96 - 23.92: 216 23.92 - 35.88: 77 35.88 - 47.84: 14 47.84 - 59.80: 9 Dihedral angle restraints: 4260 sinusoidal: 1827 harmonic: 2433 Sorted by residual: dihedral pdb=" N CYS B 617 " pdb=" CA CYS B 617 " pdb=" CB CYS B 617 " pdb=" SG CYS B 617 " ideal model delta sinusoidal sigma weight residual -60.00 -119.80 59.80 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" N CYS A 617 " pdb=" CA CYS A 617 " pdb=" CB CYS A 617 " pdb=" SG CYS A 617 " ideal model delta sinusoidal sigma weight residual -60.00 -119.34 59.34 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" N CYS C 617 " pdb=" CA CYS C 617 " pdb=" CB CYS C 617 " pdb=" SG CYS C 617 " ideal model delta sinusoidal sigma weight residual -180.00 -120.66 -59.34 3 1.50e+01 4.44e-03 9.48e+00 ... (remaining 4257 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.024: 622 0.024 - 0.049: 279 0.049 - 0.073: 91 0.073 - 0.098: 70 0.098 - 0.122: 60 Chirality restraints: 1122 Sorted by residual: chirality pdb=" CA ILE A 598 " pdb=" N ILE A 598 " pdb=" C ILE A 598 " pdb=" CB ILE A 598 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.72e-01 chirality pdb=" CA ILE B 598 " pdb=" N ILE B 598 " pdb=" C ILE B 598 " pdb=" CB ILE B 598 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.63e-01 chirality pdb=" CA VAL C 327 " pdb=" N VAL C 327 " pdb=" C VAL C 327 " pdb=" CB VAL C 327 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.61e-01 ... (remaining 1119 not shown) Planarity restraints: 1194 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP B 294 " 0.021 5.00e-02 4.00e+02 3.17e-02 1.61e+00 pdb=" N PRO B 295 " -0.055 5.00e-02 4.00e+02 pdb=" CA PRO B 295 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO B 295 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP C 294 " -0.021 5.00e-02 4.00e+02 3.17e-02 1.61e+00 pdb=" N PRO C 295 " 0.055 5.00e-02 4.00e+02 pdb=" CA PRO C 295 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO C 295 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 294 " -0.021 5.00e-02 4.00e+02 3.11e-02 1.55e+00 pdb=" N PRO A 295 " 0.054 5.00e-02 4.00e+02 pdb=" CA PRO A 295 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 295 " -0.017 5.00e-02 4.00e+02 ... (remaining 1191 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.84: 2138 2.84 - 3.35: 5502 3.35 - 3.87: 10618 3.87 - 4.38: 11780 4.38 - 4.90: 20988 Nonbonded interactions: 51026 Sorted by model distance: nonbonded pdb=" OH TYR B 37 " pdb=" O LEU B 54 " model vdw 2.324 3.040 nonbonded pdb=" OH TYR A 37 " pdb=" O LEU A 54 " model vdw 2.328 3.040 nonbonded pdb=" OH TYR C 37 " pdb=" O LEU C 54 " model vdw 2.331 3.040 nonbonded pdb=" NE2 GLN A 52 " pdb=" OG1 THR A 274 " model vdw 2.350 3.120 nonbonded pdb=" NH1 ARG C 328 " pdb=" O THR C 531 " model vdw 2.351 3.120 ... (remaining 51021 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.510 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: 0.020 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.230 Find NCS groups from input model: 0.050 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:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 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 0.029 6933 Z= 0.126 Angle : 0.456 4.623 9441 Z= 0.232 Chirality : 0.042 0.122 1122 Planarity : 0.004 0.032 1185 Dihedral : 8.760 59.800 2646 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 4.12 % Allowed : 5.44 % Favored : 90.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.92 (0.26), residues: 795 helix: -2.71 (0.73), residues: 27 sheet: -1.13 (0.28), residues: 249 loop : -2.46 (0.24), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 34 TYR 0.004 0.000 TYR C 674 PHE 0.005 0.001 PHE C 562 TRP 0.001 0.000 TRP A 64 HIS 0.001 0.000 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00249 ( 6909) covalent geometry : angle 0.45034 ( 9381) SS BOND : bond 0.00178 ( 12) SS BOND : angle 0.49658 ( 24) hydrogen bonds : bond 0.26064 ( 210) hydrogen bonds : angle 9.76528 ( 537) link_BETA1-4 : bond 0.00326 ( 3) link_BETA1-4 : angle 0.74077 ( 9) link_NAG-ASN : bond 0.00109 ( 9) link_NAG-ASN : angle 1.38312 ( 27) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1590 Ramachandran restraints generated. 795 Oldfield, 0 Emsley, 795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1590 Ramachandran restraints generated. 795 Oldfield, 0 Emsley, 795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 166 time to evaluate : 0.269 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 319 ARG cc_start: 0.8230 (mtp85) cc_final: 0.7962 (mtp85) REVERT: A 643 PHE cc_start: 0.7212 (p90) cc_final: 0.6762 (p90) REVERT: B 221 SER cc_start: 0.8906 (m) cc_final: 0.8705 (p) REVERT: B 574 ASP cc_start: 0.8122 (t0) cc_final: 0.7904 (t0) REVERT: C 571 ASP cc_start: 0.7812 (m-30) cc_final: 0.7591 (m-30) outliers start: 31 outliers final: 16 residues processed: 191 average time/residue: 0.0928 time to fit residues: 22.7885 Evaluate side-chains 111 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 95 time to evaluate : 0.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 693 ILE Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 616 ASN Chi-restraints excluded: chain C residue 693 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 49 optimal weight: 0.7980 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.9980 chunk 38 optimal weight: 0.0980 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 chunk 74 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN B 52 GLN C 52 GLN C 544 ASN ** C 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2731 r_free = 0.2731 target = 0.051799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2504 r_free = 0.2504 target = 0.043794 restraints weight = 21698.471| |-----------------------------------------------------------------------------| r_work (start): 0.2500 rms_B_bonded: 2.38 r_work: 0.2394 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2288 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8835 moved from start: 0.2312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 6933 Z= 0.196 Angle : 0.670 7.804 9441 Z= 0.344 Chirality : 0.047 0.230 1122 Planarity : 0.005 0.045 1185 Dihedral : 6.923 56.200 1164 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 5.84 % Allowed : 9.69 % Favored : 84.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.13 (0.27), residues: 795 helix: -0.49 (1.07), residues: 27 sheet: -0.66 (0.29), residues: 252 loop : -1.97 (0.25), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 273 TYR 0.036 0.001 TYR C 660 PHE 0.016 0.002 PHE B 565 TRP 0.008 0.002 TRP A 64 HIS 0.003 0.001 HIS A 49 Details of bonding type rmsd covalent geometry : bond 0.00454 ( 6909) covalent geometry : angle 0.64414 ( 9381) SS BOND : bond 0.00520 ( 12) SS BOND : angle 2.38637 ( 24) hydrogen bonds : bond 0.04249 ( 210) hydrogen bonds : angle 7.27441 ( 537) link_BETA1-4 : bond 0.00319 ( 3) link_BETA1-4 : angle 1.04111 ( 9) link_NAG-ASN : bond 0.00224 ( 9) link_NAG-ASN : angle 2.72687 ( 27) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1590 Ramachandran restraints generated. 795 Oldfield, 0 Emsley, 795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1590 Ramachandran restraints generated. 795 Oldfield, 0 Emsley, 795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 106 time to evaluate : 0.277 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 319 ARG cc_start: 0.8941 (mtp85) cc_final: 0.8661 (mtp85) REVERT: A 592 PHE cc_start: 0.8654 (t80) cc_final: 0.8366 (t80) REVERT: A 654 GLU cc_start: 0.8726 (mm-30) cc_final: 0.8428 (mm-30) REVERT: B 675 GLN cc_start: 0.8109 (tp40) cc_final: 0.7880 (pp30) REVERT: C 571 ASP cc_start: 0.8790 (m-30) cc_final: 0.8581 (m-30) REVERT: C 592 PHE cc_start: 0.8631 (t80) cc_final: 0.8368 (t80) outliers start: 44 outliers final: 19 residues processed: 143 average time/residue: 0.0655 time to fit residues: 13.0982 Evaluate side-chains 106 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 87 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 658 ASN Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 658 ASN Chi-restraints excluded: chain B residue 693 ILE Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 304 LYS Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 693 ILE Chi-restraints excluded: chain C residue 697 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 80 optimal weight: 0.0980 chunk 40 optimal weight: 1.9990 chunk 22 optimal weight: 0.1980 chunk 10 optimal weight: 0.5980 chunk 72 optimal weight: 2.9990 chunk 78 optimal weight: 0.8980 chunk 43 optimal weight: 0.9990 chunk 58 optimal weight: 0.8980 chunk 79 optimal weight: 0.5980 chunk 24 optimal weight: 0.8980 chunk 62 optimal weight: 2.9990 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 658 ASN B 658 ASN C 544 ASN C 658 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2720 r_free = 0.2720 target = 0.051377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2488 r_free = 0.2488 target = 0.043300 restraints weight = 21458.145| |-----------------------------------------------------------------------------| r_work (start): 0.2485 rms_B_bonded: 2.35 r_work: 0.2383 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2277 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8841 moved from start: 0.2723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 6933 Z= 0.148 Angle : 0.592 6.307 9441 Z= 0.307 Chirality : 0.046 0.267 1122 Planarity : 0.004 0.033 1185 Dihedral : 6.824 55.494 1157 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 3.85 % Allowed : 12.88 % Favored : 83.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.81 (0.28), residues: 795 helix: -0.35 (1.12), residues: 30 sheet: -0.37 (0.29), residues: 252 loop : -1.78 (0.26), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 328 TYR 0.030 0.001 TYR C 660 PHE 0.025 0.002 PHE B 643 TRP 0.008 0.001 TRP A 64 HIS 0.002 0.000 HIS A 49 Details of bonding type rmsd covalent geometry : bond 0.00344 ( 6909) covalent geometry : angle 0.56311 ( 9381) SS BOND : bond 0.00480 ( 12) SS BOND : angle 2.34496 ( 24) hydrogen bonds : bond 0.03276 ( 210) hydrogen bonds : angle 6.42620 ( 537) link_BETA1-4 : bond 0.00292 ( 3) link_BETA1-4 : angle 0.99649 ( 9) link_NAG-ASN : bond 0.00120 ( 9) link_NAG-ASN : angle 2.63673 ( 27) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1590 Ramachandran restraints generated. 795 Oldfield, 0 Emsley, 795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1590 Ramachandran restraints generated. 795 Oldfield, 0 Emsley, 795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 96 time to evaluate : 0.281 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 281 GLU cc_start: 0.8266 (pm20) cc_final: 0.8033 (pm20) REVERT: A 319 ARG cc_start: 0.8942 (mtp85) cc_final: 0.8652 (mtp85) REVERT: A 592 PHE cc_start: 0.8657 (t80) cc_final: 0.8411 (t80) REVERT: A 654 GLU cc_start: 0.8700 (mm-30) cc_final: 0.8439 (mm-30) REVERT: B 675 GLN cc_start: 0.8240 (tp40) cc_final: 0.7955 (pp30) outliers start: 29 outliers final: 20 residues processed: 120 average time/residue: 0.0742 time to fit residues: 12.5191 Evaluate side-chains 110 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 90 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 658 ASN Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 658 ASN Chi-restraints excluded: chain B residue 693 ILE Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 693 ILE Chi-restraints excluded: chain C residue 697 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 27 optimal weight: 1.9990 chunk 51 optimal weight: 0.7980 chunk 31 optimal weight: 0.8980 chunk 70 optimal weight: 0.4980 chunk 46 optimal weight: 1.9990 chunk 13 optimal weight: 0.0980 chunk 10 optimal weight: 0.0060 chunk 78 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 42 optimal weight: 0.3980 chunk 69 optimal weight: 0.9990 overall best weight: 0.3596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 211 ASN C 544 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2724 r_free = 0.2724 target = 0.051527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2490 r_free = 0.2490 target = 0.043368 restraints weight = 21496.204| |-----------------------------------------------------------------------------| r_work (start): 0.2486 rms_B_bonded: 2.43 r_work: 0.2382 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2275 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8844 moved from start: 0.2914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6933 Z= 0.125 Angle : 0.556 6.408 9441 Z= 0.288 Chirality : 0.045 0.163 1122 Planarity : 0.004 0.033 1185 Dihedral : 6.595 55.654 1156 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 5.44 % Allowed : 12.08 % Favored : 82.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.56 (0.28), residues: 795 helix: -0.13 (1.15), residues: 30 sheet: -0.16 (0.30), residues: 252 loop : -1.64 (0.27), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 319 TYR 0.022 0.001 TYR C 660 PHE 0.025 0.001 PHE B 643 TRP 0.005 0.001 TRP A 64 HIS 0.001 0.000 HIS A 655 Details of bonding type rmsd covalent geometry : bond 0.00284 ( 6909) covalent geometry : angle 0.53173 ( 9381) SS BOND : bond 0.00422 ( 12) SS BOND : angle 1.65213 ( 24) hydrogen bonds : bond 0.02899 ( 210) hydrogen bonds : angle 6.16048 ( 537) link_BETA1-4 : bond 0.00255 ( 3) link_BETA1-4 : angle 0.94060 ( 9) link_NAG-ASN : bond 0.00090 ( 9) link_NAG-ASN : angle 2.65793 ( 27) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1590 Ramachandran restraints generated. 795 Oldfield, 0 Emsley, 795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1590 Ramachandran restraints generated. 795 Oldfield, 0 Emsley, 795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 95 time to evaluate : 0.290 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 281 GLU cc_start: 0.8322 (pm20) cc_final: 0.8085 (pm20) REVERT: A 319 ARG cc_start: 0.8948 (mtp85) cc_final: 0.8686 (mtp85) REVERT: A 592 PHE cc_start: 0.8642 (t80) cc_final: 0.8438 (t80) REVERT: A 643 PHE cc_start: 0.8031 (p90) cc_final: 0.7546 (p90) REVERT: B 675 GLN cc_start: 0.8207 (tp40) cc_final: 0.7951 (pp30) outliers start: 41 outliers final: 22 residues processed: 130 average time/residue: 0.0707 time to fit residues: 13.1173 Evaluate side-chains 108 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 86 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 693 ILE Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 544 ASN Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 618 THR Chi-restraints excluded: chain C residue 658 ASN Chi-restraints excluded: chain C residue 693 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 26 optimal weight: 0.6980 chunk 0 optimal weight: 2.9990 chunk 4 optimal weight: 0.9990 chunk 39 optimal weight: 0.4980 chunk 20 optimal weight: 0.8980 chunk 38 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 67 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 70 optimal weight: 0.6980 chunk 61 optimal weight: 1.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 211 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2669 r_free = 0.2669 target = 0.049508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2433 r_free = 0.2433 target = 0.041428 restraints weight = 21673.364| |-----------------------------------------------------------------------------| r_work (start): 0.2429 rms_B_bonded: 2.35 r_work: 0.2325 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2216 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8889 moved from start: 0.3208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 6933 Z= 0.204 Angle : 0.620 6.527 9441 Z= 0.326 Chirality : 0.046 0.227 1122 Planarity : 0.005 0.052 1185 Dihedral : 6.919 59.383 1156 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 4.91 % Allowed : 13.28 % Favored : 81.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.49 (0.28), residues: 795 helix: 1.49 (1.23), residues: 24 sheet: 0.01 (0.30), residues: 252 loop : -1.73 (0.26), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 328 TYR 0.024 0.001 TYR A 660 PHE 0.023 0.002 PHE B 643 TRP 0.010 0.002 TRP A 64 HIS 0.002 0.000 HIS A 49 Details of bonding type rmsd covalent geometry : bond 0.00469 ( 6909) covalent geometry : angle 0.59241 ( 9381) SS BOND : bond 0.00586 ( 12) SS BOND : angle 2.10708 ( 24) hydrogen bonds : bond 0.03178 ( 210) hydrogen bonds : angle 6.21412 ( 537) link_BETA1-4 : bond 0.00050 ( 3) link_BETA1-4 : angle 1.20206 ( 9) link_NAG-ASN : bond 0.00261 ( 9) link_NAG-ASN : angle 2.82743 ( 27) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1590 Ramachandran restraints generated. 795 Oldfield, 0 Emsley, 795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1590 Ramachandran restraints generated. 795 Oldfield, 0 Emsley, 795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 88 time to evaluate : 0.489 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 319 ARG cc_start: 0.8971 (mtp85) cc_final: 0.8729 (mtp85) REVERT: A 592 PHE cc_start: 0.8682 (t80) cc_final: 0.8482 (t80) REVERT: A 643 PHE cc_start: 0.8035 (p90) cc_final: 0.7671 (p90) REVERT: B 675 GLN cc_start: 0.8300 (tp40) cc_final: 0.7934 (pp30) REVERT: C 319 ARG cc_start: 0.8871 (mtp85) cc_final: 0.8603 (mtp85) outliers start: 37 outliers final: 29 residues processed: 118 average time/residue: 0.0774 time to fit residues: 12.9715 Evaluate side-chains 117 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 88 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 580 GLN Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 580 GLN Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 693 ILE Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 693 ILE Chi-restraints excluded: chain C residue 697 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 19 optimal weight: 0.9980 chunk 6 optimal weight: 3.9990 chunk 66 optimal weight: 0.0980 chunk 62 optimal weight: 0.9990 chunk 38 optimal weight: 0.7980 chunk 32 optimal weight: 0.9990 chunk 20 optimal weight: 0.6980 chunk 17 optimal weight: 0.7980 chunk 39 optimal weight: 0.7980 chunk 7 optimal weight: 0.6980 chunk 72 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 211 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2669 r_free = 0.2669 target = 0.049486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2434 r_free = 0.2434 target = 0.041415 restraints weight = 22003.981| |-----------------------------------------------------------------------------| r_work (start): 0.2429 rms_B_bonded: 2.39 r_work: 0.2325 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2215 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8892 moved from start: 0.3402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 6933 Z= 0.169 Angle : 0.587 7.504 9441 Z= 0.308 Chirality : 0.045 0.175 1122 Planarity : 0.005 0.038 1185 Dihedral : 6.899 58.867 1156 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 4.65 % Allowed : 13.94 % Favored : 81.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.36 (0.29), residues: 795 helix: 1.54 (1.23), residues: 24 sheet: 0.09 (0.30), residues: 252 loop : -1.63 (0.27), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 319 TYR 0.019 0.001 TYR A 660 PHE 0.021 0.002 PHE B 643 TRP 0.012 0.002 TRP A 64 HIS 0.001 0.000 HIS A 49 Details of bonding type rmsd covalent geometry : bond 0.00389 ( 6909) covalent geometry : angle 0.56112 ( 9381) SS BOND : bond 0.00527 ( 12) SS BOND : angle 1.79458 ( 24) hydrogen bonds : bond 0.02986 ( 210) hydrogen bonds : angle 6.22220 ( 537) link_BETA1-4 : bond 0.00138 ( 3) link_BETA1-4 : angle 1.00264 ( 9) link_NAG-ASN : bond 0.00100 ( 9) link_NAG-ASN : angle 2.81270 ( 27) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1590 Ramachandran restraints generated. 795 Oldfield, 0 Emsley, 795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1590 Ramachandran restraints generated. 795 Oldfield, 0 Emsley, 795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 95 time to evaluate : 0.293 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 319 ARG cc_start: 0.8948 (mtp85) cc_final: 0.8692 (mtp85) REVERT: A 643 PHE cc_start: 0.8052 (p90) cc_final: 0.7759 (p90) REVERT: A 670 ILE cc_start: 0.8929 (mm) cc_final: 0.8581 (mm) REVERT: B 675 GLN cc_start: 0.8345 (tp40) cc_final: 0.7954 (pp30) REVERT: C 319 ARG cc_start: 0.8814 (mtp85) cc_final: 0.8169 (mtp85) REVERT: C 592 PHE cc_start: 0.8595 (t80) cc_final: 0.8103 (t80) outliers start: 35 outliers final: 28 residues processed: 125 average time/residue: 0.0758 time to fit residues: 13.2831 Evaluate side-chains 115 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 87 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 ASN Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 693 ILE Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 693 ILE Chi-restraints excluded: chain C residue 697 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 6 optimal weight: 2.9990 chunk 79 optimal weight: 0.5980 chunk 57 optimal weight: 0.3980 chunk 30 optimal weight: 1.9990 chunk 43 optimal weight: 0.0870 chunk 55 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 45 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 71 optimal weight: 0.5980 chunk 37 optimal weight: 0.9980 overall best weight: 0.4958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 211 ASN C 658 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2679 r_free = 0.2679 target = 0.049831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2445 r_free = 0.2445 target = 0.041802 restraints weight = 21481.042| |-----------------------------------------------------------------------------| r_work (start): 0.2440 rms_B_bonded: 2.35 r_work: 0.2338 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2229 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8879 moved from start: 0.3467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 6933 Z= 0.151 Angle : 0.600 11.635 9441 Z= 0.313 Chirality : 0.045 0.171 1122 Planarity : 0.004 0.035 1185 Dihedral : 6.816 58.499 1156 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 4.25 % Allowed : 15.14 % Favored : 80.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.27 (0.29), residues: 795 helix: 1.32 (1.20), residues: 24 sheet: 0.16 (0.30), residues: 252 loop : -1.56 (0.27), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 319 TYR 0.018 0.001 TYR C 660 PHE 0.027 0.002 PHE A 592 TRP 0.009 0.001 TRP A 64 HIS 0.001 0.000 HIS A 49 Details of bonding type rmsd covalent geometry : bond 0.00347 ( 6909) covalent geometry : angle 0.57564 ( 9381) SS BOND : bond 0.00630 ( 12) SS BOND : angle 1.79915 ( 24) hydrogen bonds : bond 0.02869 ( 210) hydrogen bonds : angle 6.18679 ( 537) link_BETA1-4 : bond 0.00210 ( 3) link_BETA1-4 : angle 1.02083 ( 9) link_NAG-ASN : bond 0.00092 ( 9) link_NAG-ASN : angle 2.76968 ( 27) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1590 Ramachandran restraints generated. 795 Oldfield, 0 Emsley, 795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1590 Ramachandran restraints generated. 795 Oldfield, 0 Emsley, 795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 93 time to evaluate : 0.278 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 643 PHE cc_start: 0.8046 (p90) cc_final: 0.7744 (p90) REVERT: A 670 ILE cc_start: 0.8937 (mm) cc_final: 0.8566 (mm) REVERT: B 675 GLN cc_start: 0.8339 (tp40) cc_final: 0.7957 (pp30) REVERT: C 319 ARG cc_start: 0.8830 (mtp85) cc_final: 0.8560 (mtp85) outliers start: 32 outliers final: 31 residues processed: 120 average time/residue: 0.0750 time to fit residues: 12.6339 Evaluate side-chains 121 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 90 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 ASN Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 693 ILE Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 658 ASN Chi-restraints excluded: chain C residue 693 ILE Chi-restraints excluded: chain C residue 697 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 82 optimal weight: 1.9990 chunk 41 optimal weight: 0.8980 chunk 38 optimal weight: 0.2980 chunk 55 optimal weight: 0.9980 chunk 37 optimal weight: 0.9980 chunk 53 optimal weight: 0.8980 chunk 48 optimal weight: 0.9990 chunk 63 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2651 r_free = 0.2651 target = 0.048857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2414 r_free = 0.2414 target = 0.040817 restraints weight = 21950.033| |-----------------------------------------------------------------------------| r_work (start): 0.2410 rms_B_bonded: 2.37 r_work: 0.2305 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2197 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8905 moved from start: 0.3575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 6933 Z= 0.209 Angle : 0.644 12.703 9441 Z= 0.337 Chirality : 0.046 0.178 1122 Planarity : 0.005 0.051 1185 Dihedral : 6.970 59.705 1156 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 4.78 % Allowed : 15.01 % Favored : 80.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.27 (0.29), residues: 795 helix: 1.38 (1.18), residues: 24 sheet: 0.26 (0.30), residues: 252 loop : -1.62 (0.27), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 319 TYR 0.021 0.001 TYR C 660 PHE 0.035 0.002 PHE A 592 TRP 0.013 0.002 TRP A 64 HIS 0.002 0.001 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00483 ( 6909) covalent geometry : angle 0.61816 ( 9381) SS BOND : bond 0.00645 ( 12) SS BOND : angle 1.97638 ( 24) hydrogen bonds : bond 0.03074 ( 210) hydrogen bonds : angle 6.23207 ( 537) link_BETA1-4 : bond 0.00049 ( 3) link_BETA1-4 : angle 1.12909 ( 9) link_NAG-ASN : bond 0.00228 ( 9) link_NAG-ASN : angle 2.86016 ( 27) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1590 Ramachandran restraints generated. 795 Oldfield, 0 Emsley, 795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1590 Ramachandran restraints generated. 795 Oldfield, 0 Emsley, 795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 93 time to evaluate : 0.276 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 643 PHE cc_start: 0.8055 (p90) cc_final: 0.7800 (p90) REVERT: C 319 ARG cc_start: 0.8769 (mtp85) cc_final: 0.8219 (mtp85) REVERT: C 592 PHE cc_start: 0.8622 (t80) cc_final: 0.8274 (t80) outliers start: 36 outliers final: 33 residues processed: 122 average time/residue: 0.0689 time to fit residues: 11.8626 Evaluate side-chains 120 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 87 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 580 GLN Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 580 GLN Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 693 ILE Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 618 THR Chi-restraints excluded: chain C residue 658 ASN Chi-restraints excluded: chain C residue 693 ILE Chi-restraints excluded: chain C residue 697 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 70 optimal weight: 0.6980 chunk 3 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 chunk 60 optimal weight: 0.8980 chunk 14 optimal weight: 0.9980 chunk 67 optimal weight: 0.8980 chunk 51 optimal weight: 0.6980 chunk 32 optimal weight: 0.9990 chunk 48 optimal weight: 0.6980 chunk 52 optimal weight: 0.6980 chunk 68 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2646 r_free = 0.2646 target = 0.048650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2409 r_free = 0.2409 target = 0.040634 restraints weight = 21860.548| |-----------------------------------------------------------------------------| r_work (start): 0.2404 rms_B_bonded: 2.36 r_work: 0.2299 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2190 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8909 moved from start: 0.3657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 6933 Z= 0.199 Angle : 0.648 12.694 9441 Z= 0.340 Chirality : 0.046 0.175 1122 Planarity : 0.005 0.041 1185 Dihedral : 7.024 59.427 1156 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 4.78 % Allowed : 15.14 % Favored : 80.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.21 (0.29), residues: 795 helix: 1.39 (1.18), residues: 24 sheet: 0.31 (0.30), residues: 267 loop : -1.65 (0.27), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 319 TYR 0.020 0.001 TYR C 660 PHE 0.020 0.002 PHE A 592 TRP 0.016 0.002 TRP A 64 HIS 0.001 0.000 HIS A 49 Details of bonding type rmsd covalent geometry : bond 0.00458 ( 6909) covalent geometry : angle 0.62347 ( 9381) SS BOND : bond 0.00612 ( 12) SS BOND : angle 1.92975 ( 24) hydrogen bonds : bond 0.03093 ( 210) hydrogen bonds : angle 6.27166 ( 537) link_BETA1-4 : bond 0.00070 ( 3) link_BETA1-4 : angle 1.09160 ( 9) link_NAG-ASN : bond 0.00210 ( 9) link_NAG-ASN : angle 2.85879 ( 27) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1590 Ramachandran restraints generated. 795 Oldfield, 0 Emsley, 795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1590 Ramachandran restraints generated. 795 Oldfield, 0 Emsley, 795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 90 time to evaluate : 0.279 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: A 643 PHE cc_start: 0.8052 (p90) cc_final: 0.7837 (p90) REVERT: B 319 ARG cc_start: 0.8929 (mtp85) cc_final: 0.8417 (mtp85) REVERT: C 319 ARG cc_start: 0.8778 (mtp85) cc_final: 0.8331 (mtp85) REVERT: C 592 PHE cc_start: 0.8594 (t80) cc_final: 0.8276 (t80) outliers start: 36 outliers final: 32 residues processed: 119 average time/residue: 0.0731 time to fit residues: 12.2872 Evaluate side-chains 123 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 91 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 580 GLN Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 693 ILE Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 618 THR Chi-restraints excluded: chain C residue 693 ILE Chi-restraints excluded: chain C residue 697 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 53 optimal weight: 0.4980 chunk 18 optimal weight: 0.9980 chunk 72 optimal weight: 1.9990 chunk 77 optimal weight: 0.6980 chunk 59 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 46 optimal weight: 0.7980 chunk 7 optimal weight: 1.9990 chunk 1 optimal weight: 0.7980 chunk 67 optimal weight: 0.6980 chunk 23 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2646 r_free = 0.2646 target = 0.048670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2409 r_free = 0.2409 target = 0.040655 restraints weight = 21729.346| |-----------------------------------------------------------------------------| r_work (start): 0.2405 rms_B_bonded: 2.35 r_work: 0.2299 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2190 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8910 moved from start: 0.3724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 6933 Z= 0.192 Angle : 0.655 12.733 9441 Z= 0.343 Chirality : 0.046 0.173 1122 Planarity : 0.005 0.040 1185 Dihedral : 7.045 59.430 1156 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 4.25 % Allowed : 15.54 % Favored : 80.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.18 (0.29), residues: 795 helix: 1.45 (1.19), residues: 24 sheet: 0.33 (0.30), residues: 267 loop : -1.63 (0.27), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 319 TYR 0.018 0.001 TYR C 660 PHE 0.016 0.002 PHE C 592 TRP 0.013 0.002 TRP A 64 HIS 0.001 0.000 HIS A 49 Details of bonding type rmsd covalent geometry : bond 0.00446 ( 6909) covalent geometry : angle 0.63089 ( 9381) SS BOND : bond 0.00596 ( 12) SS BOND : angle 1.91992 ( 24) hydrogen bonds : bond 0.03055 ( 210) hydrogen bonds : angle 6.27388 ( 537) link_BETA1-4 : bond 0.00105 ( 3) link_BETA1-4 : angle 1.09603 ( 9) link_NAG-ASN : bond 0.00206 ( 9) link_NAG-ASN : angle 2.84058 ( 27) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1590 Ramachandran restraints generated. 795 Oldfield, 0 Emsley, 795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1590 Ramachandran restraints generated. 795 Oldfield, 0 Emsley, 795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 92 time to evaluate : 0.306 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: A 574 ASP cc_start: 0.8613 (t0) cc_final: 0.8402 (t0) REVERT: A 643 PHE cc_start: 0.7981 (p90) cc_final: 0.7775 (p90) REVERT: B 319 ARG cc_start: 0.8934 (mtp85) cc_final: 0.8463 (mtp85) REVERT: C 319 ARG cc_start: 0.8814 (mtp85) cc_final: 0.8151 (mtp85) REVERT: C 592 PHE cc_start: 0.8624 (t80) cc_final: 0.8150 (t80) outliers start: 32 outliers final: 30 residues processed: 119 average time/residue: 0.0741 time to fit residues: 12.4533 Evaluate side-chains 122 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 92 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 580 GLN Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 693 ILE Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 693 ILE Chi-restraints excluded: chain C residue 697 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 22 optimal weight: 1.9990 chunk 33 optimal weight: 0.6980 chunk 16 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 chunk 25 optimal weight: 0.8980 chunk 7 optimal weight: 2.9990 chunk 29 optimal weight: 0.5980 chunk 50 optimal weight: 1.9990 chunk 75 optimal weight: 0.7980 chunk 35 optimal weight: 2.9990 chunk 73 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2635 r_free = 0.2635 target = 0.048268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2397 r_free = 0.2397 target = 0.040264 restraints weight = 21883.020| |-----------------------------------------------------------------------------| r_work (start): 0.2393 rms_B_bonded: 2.35 r_work: 0.2286 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2177 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8919 moved from start: 0.3784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 6933 Z= 0.213 Angle : 0.685 12.793 9441 Z= 0.358 Chirality : 0.046 0.176 1122 Planarity : 0.005 0.045 1185 Dihedral : 7.144 59.428 1156 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 4.52 % Allowed : 15.27 % Favored : 80.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.19 (0.29), residues: 795 helix: 1.44 (1.18), residues: 24 sheet: 0.22 (0.29), residues: 297 loop : -1.67 (0.28), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 319 TYR 0.015 0.001 TYR A 660 PHE 0.017 0.002 PHE B 643 TRP 0.014 0.003 TRP C 64 HIS 0.001 0.000 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00494 ( 6909) covalent geometry : angle 0.66035 ( 9381) SS BOND : bond 0.00629 ( 12) SS BOND : angle 1.99129 ( 24) hydrogen bonds : bond 0.03191 ( 210) hydrogen bonds : angle 6.31069 ( 537) link_BETA1-4 : bond 0.00036 ( 3) link_BETA1-4 : angle 1.11320 ( 9) link_NAG-ASN : bond 0.00251 ( 9) link_NAG-ASN : angle 2.90529 ( 27) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1776.45 seconds wall clock time: 31 minutes 29.53 seconds (1889.53 seconds total)