Starting phenix.real_space_refine on Tue Feb 11 23:38:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8z7l_39819/02_2025/8z7l_39819.cif Found real_map, /net/cci-nas-00/data/ceres_data/8z7l_39819/02_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_39819/02_2025/8z7l_39819.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8z7l_39819/02_2025/8z7l_39819.map" model { file = "/net/cci-nas-00/data/ceres_data/8z7l_39819/02_2025/8z7l_39819.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8z7l_39819/02_2025/8z7l_39819.cif" } resolution = 3.42 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= -0.048 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: 5.43, per 1000 atoms: 0.80 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: 1.73 Conformation dependent library (CDL) restraints added in 950.9 milliseconds 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: 0.82 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: 1.80 Time building geometry restraints manager: 2.01 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: 0.05 Found NCS groups: ncs_group { reference = chain 'E' selection = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' } 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: 4.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 19.800 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.200 ------------------------------------------------------------------------------- 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 6909 Z= 0.163 Angle : 0.450 4.623 9381 Z= 0.231 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 (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: -2.92 (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 TRP 0.001 0.000 TRP A 64 HIS 0.001 0.000 HIS B 207 PHE 0.005 0.001 PHE C 562 TYR 0.004 0.000 TYR C 674 ARG 0.001 0.000 ARG B 34 *********************** 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 : 0.731 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: 0.7961 (mtp85) REVERT: A 643 PHE cc_start: 0.7212 (p90) cc_final: 0.6761 (p90) REVERT: B 221 SER cc_start: 0.8906 (m) cc_final: 0.8704 (p) REVERT: B 574 ASP cc_start: 0.8122 (t0) cc_final: 0.7905 (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: 0.2166 time to fit residues: 52.7083 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 : 0.755 ------------------------------------------------------------------------------- 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 70 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 21 optimal weight: 0.8980 chunk 42 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 chunk 25 optimal weight: 0.2980 chunk 40 optimal weight: 1.9990 chunk 49 optimal weight: 0.3980 chunk 76 optimal weight: 0.9990 overall best weight: 0.7184 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2724 r_free = 0.2724 target = 0.051547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2495 r_free = 0.2495 target = 0.043493 restraints weight = 21232.544| |-----------------------------------------------------------------------------| r_work (start): 0.2491 rms_B_bonded: 2.36 r_work: 0.2385 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2277 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8843 moved from start: 0.2411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 6909 Z= 0.299 Angle : 0.653 8.878 9381 Z= 0.339 Chirality : 0.048 0.241 1122 Planarity : 0.005 0.038 1185 Dihedral : 6.981 56.873 1164 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 5.98 % Allowed : 9.30 % Favored : 84.73 % 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: -2.13 (0.27), residues: 795 helix: -0.33 (1.09), residues: 27 sheet: -0.65 (0.29), residues: 252 loop : -1.98 (0.25), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 64 HIS 0.003 0.001 HIS A 49 PHE 0.017 0.002 PHE B 565 TYR 0.040 0.001 TYR C 660 ARG 0.006 0.001 ARG B 319 *********************** 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: 45 poor density : 105 time to evaluate : 0.772 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 319 ARG cc_start: 0.8935 (mtp85) cc_final: 0.8652 (mtp85) REVERT: A 592 PHE cc_start: 0.8643 (t80) cc_final: 0.8359 (t80) REVERT: A 654 GLU cc_start: 0.8730 (mm-30) cc_final: 0.8426 (mm-30) REVERT: C 571 ASP cc_start: 0.8802 (m-30) cc_final: 0.8593 (m-30) REVERT: C 592 PHE cc_start: 0.8638 (t80) cc_final: 0.8362 (t80) outliers start: 45 outliers final: 20 residues processed: 142 average time/residue: 0.1706 time to fit residues: 33.9981 Evaluate side-chains 105 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 85 time to evaluate : 0.773 ------------------------------------------------------------------------------- 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 658 ASN 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 82 optimal weight: 0.8980 chunk 83 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 14 optimal weight: 0.0670 chunk 35 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 75 optimal weight: 0.9980 chunk 24 optimal weight: 0.4980 chunk 68 optimal weight: 0.5980 chunk 55 optimal weight: 0.0870 overall best weight: 0.4296 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2722 r_free = 0.2722 target = 0.051460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2491 r_free = 0.2491 target = 0.043387 restraints weight = 21425.347| |-----------------------------------------------------------------------------| r_work (start): 0.2489 rms_B_bonded: 2.35 r_work: 0.2387 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2281 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8838 moved from start: 0.2704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 6909 Z= 0.228 Angle : 0.571 6.669 9381 Z= 0.304 Chirality : 0.047 0.281 1122 Planarity : 0.005 0.044 1185 Dihedral : 6.829 55.384 1157 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 4.38 % Allowed : 12.48 % Favored : 83.13 % 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: -1.86 (0.28), residues: 795 helix: -0.24 (1.15), residues: 30 sheet: -0.42 (0.29), residues: 252 loop : -1.82 (0.26), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 64 HIS 0.001 0.000 HIS A 49 PHE 0.026 0.001 PHE B 643 TYR 0.034 0.001 TYR C 660 ARG 0.005 0.000 ARG B 328 *********************** 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 126 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 93 time to evaluate : 0.780 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 319 ARG cc_start: 0.8942 (mtp85) cc_final: 0.8653 (mtp85) REVERT: A 592 PHE cc_start: 0.8659 (t80) cc_final: 0.8426 (t80) REVERT: A 654 GLU cc_start: 0.8705 (mm-30) cc_final: 0.8436 (mm-30) REVERT: B 675 GLN cc_start: 0.8239 (tp40) cc_final: 0.7957 (pp30) outliers start: 33 outliers final: 23 residues processed: 121 average time/residue: 0.1592 time to fit residues: 27.0677 Evaluate side-chains 111 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 88 time to evaluate : 0.802 ------------------------------------------------------------------------------- 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 650 LEU 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 215 ASP 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 544 ASN 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 54 optimal weight: 0.0000 chunk 57 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 chunk 48 optimal weight: 0.6980 chunk 73 optimal weight: 1.9990 chunk 52 optimal weight: 0.9990 chunk 18 optimal weight: 0.7980 chunk 12 optimal weight: 1.9990 chunk 70 optimal weight: 0.6980 chunk 20 optimal weight: 0.8980 chunk 68 optimal weight: 1.9990 overall best weight: 0.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 211 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2695 r_free = 0.2695 target = 0.050450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2462 r_free = 0.2462 target = 0.042390 restraints weight = 21796.660| |-----------------------------------------------------------------------------| r_work (start): 0.2458 rms_B_bonded: 2.35 r_work: 0.2355 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2247 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8863 moved from start: 0.3001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 6909 Z= 0.268 Angle : 0.573 6.282 9381 Z= 0.307 Chirality : 0.046 0.190 1122 Planarity : 0.005 0.033 1185 Dihedral : 6.826 57.938 1156 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 4.78 % Allowed : 12.08 % Favored : 83.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.69 (0.28), residues: 795 helix: 1.48 (1.27), residues: 24 sheet: -0.19 (0.30), residues: 252 loop : -1.85 (0.26), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 64 HIS 0.002 0.000 HIS A 49 PHE 0.024 0.002 PHE B 643 TYR 0.023 0.001 TYR C 660 ARG 0.002 0.000 ARG B 328 *********************** 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 128 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 92 time to evaluate : 0.756 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 281 GLU cc_start: 0.8283 (pm20) cc_final: 0.8068 (pm20) REVERT: A 319 ARG cc_start: 0.8958 (mtp85) cc_final: 0.8684 (mtp85) REVERT: A 592 PHE cc_start: 0.8668 (t80) cc_final: 0.8447 (t80) outliers start: 36 outliers final: 22 residues processed: 123 average time/residue: 0.1549 time to fit residues: 26.9115 Evaluate side-chains 106 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 84 time to evaluate : 0.798 ------------------------------------------------------------------------------- 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 211 ASN Chi-restraints excluded: chain B residue 215 ASP 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 551 VAL Chi-restraints excluded: chain C residue 580 GLN 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 21 optimal weight: 0.6980 chunk 31 optimal weight: 0.8980 chunk 44 optimal weight: 1.9990 chunk 52 optimal weight: 0.6980 chunk 0 optimal weight: 2.9990 chunk 19 optimal weight: 0.9980 chunk 55 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 79 optimal weight: 0.0980 chunk 67 optimal weight: 0.9980 chunk 80 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.2673 r_free = 0.2673 target = 0.049623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2438 r_free = 0.2438 target = 0.041617 restraints weight = 21428.891| |-----------------------------------------------------------------------------| r_work (start): 0.2434 rms_B_bonded: 2.33 r_work: 0.2331 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2223 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8880 moved from start: 0.3217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 6909 Z= 0.281 Angle : 0.587 6.628 9381 Z= 0.315 Chirality : 0.046 0.221 1122 Planarity : 0.005 0.032 1185 Dihedral : 6.908 58.869 1156 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 5.44 % Allowed : 12.35 % Favored : 82.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.52 (0.28), residues: 795 helix: 1.69 (1.27), residues: 24 sheet: -0.03 (0.30), residues: 252 loop : -1.76 (0.26), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 64 HIS 0.002 0.000 HIS A 49 PHE 0.024 0.002 PHE B 643 TYR 0.027 0.001 TYR A 660 ARG 0.003 0.000 ARG B 214 *********************** 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 129 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 88 time to evaluate : 0.771 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 281 GLU cc_start: 0.8349 (pm20) cc_final: 0.8131 (pm20) REVERT: A 319 ARG cc_start: 0.8980 (mtp85) cc_final: 0.8715 (mtp85) REVERT: A 592 PHE cc_start: 0.8663 (t80) cc_final: 0.8451 (t80) REVERT: A 643 PHE cc_start: 0.8046 (p90) cc_final: 0.7640 (p90) outliers start: 41 outliers final: 29 residues processed: 122 average time/residue: 0.1601 time to fit residues: 27.3813 Evaluate side-chains 115 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 86 time to evaluate : 0.866 ------------------------------------------------------------------------------- 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 693 ILE Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain B residue 211 ASN 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 580 GLN 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 23 optimal weight: 0.5980 chunk 78 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 39 optimal weight: 0.8980 chunk 56 optimal weight: 2.9990 chunk 17 optimal weight: 0.9980 chunk 58 optimal weight: 0.7980 chunk 40 optimal weight: 0.8980 chunk 44 optimal weight: 1.9990 chunk 6 optimal weight: 0.0170 overall best weight: 0.6418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 211 ASN B 658 ASN C 658 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2663 r_free = 0.2663 target = 0.049223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2428 r_free = 0.2428 target = 0.041262 restraints weight = 21431.903| |-----------------------------------------------------------------------------| r_work (start): 0.2424 rms_B_bonded: 2.33 r_work: 0.2319 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2210 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8894 moved from start: 0.3420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 6909 Z= 0.279 Angle : 0.586 7.518 9381 Z= 0.314 Chirality : 0.046 0.217 1122 Planarity : 0.005 0.033 1185 Dihedral : 6.954 59.672 1156 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 5.31 % Allowed : 13.01 % Favored : 81.67 % 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: -1.42 (0.29), residues: 795 helix: 1.44 (1.21), residues: 24 sheet: 0.06 (0.30), residues: 252 loop : -1.68 (0.26), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 64 HIS 0.001 0.000 HIS A 49 PHE 0.023 0.002 PHE B 643 TYR 0.031 0.001 TYR C 660 ARG 0.003 0.000 ARG C 319 *********************** 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 134 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 94 time to evaluate : 0.780 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: 0.8976 (mtp85) cc_final: 0.8716 (mtp85) REVERT: A 643 PHE cc_start: 0.8045 (p90) cc_final: 0.7745 (p90) REVERT: A 670 ILE cc_start: 0.8933 (mm) cc_final: 0.8680 (mm) outliers start: 40 outliers final: 32 residues processed: 126 average time/residue: 0.1554 time to fit residues: 27.2976 Evaluate side-chains 121 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 89 time to evaluate : 0.728 ------------------------------------------------------------------------------- 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 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 580 GLN 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 44 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 chunk 21 optimal weight: 0.4980 chunk 50 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 chunk 11 optimal weight: 0.5980 chunk 59 optimal weight: 0.9990 chunk 75 optimal weight: 1.9990 chunk 77 optimal weight: 0.5980 chunk 20 optimal weight: 0.6980 chunk 38 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.2660 r_free = 0.2660 target = 0.049190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2427 r_free = 0.2427 target = 0.041217 restraints weight = 21394.208| |-----------------------------------------------------------------------------| r_work (start): 0.2423 rms_B_bonded: 2.33 r_work: 0.2319 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2210 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8898 moved from start: 0.3520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 6909 Z= 0.280 Angle : 0.600 11.648 9381 Z= 0.319 Chirality : 0.046 0.187 1122 Planarity : 0.005 0.034 1185 Dihedral : 6.963 59.986 1156 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 4.52 % Allowed : 14.61 % Favored : 80.88 % 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: -1.33 (0.29), residues: 795 helix: 1.49 (1.22), residues: 24 sheet: 0.14 (0.30), residues: 252 loop : -1.63 (0.27), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 64 HIS 0.002 0.000 HIS A 207 PHE 0.026 0.002 PHE A 592 TYR 0.026 0.001 TYR C 660 ARG 0.005 0.000 ARG C 319 *********************** 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: 34 poor density : 91 time to evaluate : 1.012 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: 0.7767 (p90) REVERT: C 319 ARG cc_start: 0.8779 (mtp85) cc_final: 0.8333 (mtp85) outliers start: 34 outliers final: 30 residues processed: 119 average time/residue: 0.1706 time to fit residues: 27.9231 Evaluate side-chains 118 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 88 time to evaluate : 1.623 ------------------------------------------------------------------------------- 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 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 580 GLN 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 42 optimal weight: 1.9990 chunk 60 optimal weight: 0.0980 chunk 22 optimal weight: 1.9990 chunk 50 optimal weight: 0.7980 chunk 7 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 24 optimal weight: 0.9980 chunk 6 optimal weight: 2.9990 chunk 4 optimal weight: 0.0980 chunk 46 optimal weight: 1.9990 chunk 54 optimal weight: 0.8980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.2661 r_free = 0.2661 target = 0.049203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2424 r_free = 0.2424 target = 0.041140 restraints weight = 21597.661| |-----------------------------------------------------------------------------| r_work (start): 0.2419 rms_B_bonded: 2.35 r_work: 0.2314 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2204 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8899 moved from start: 0.3604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 6909 Z= 0.258 Angle : 0.595 12.928 9381 Z= 0.317 Chirality : 0.045 0.180 1122 Planarity : 0.005 0.036 1185 Dihedral : 6.899 59.622 1156 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 4.52 % Allowed : 14.87 % 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 (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: -1.24 (0.29), residues: 795 helix: 1.52 (1.22), residues: 24 sheet: 0.24 (0.30), residues: 252 loop : -1.59 (0.27), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 64 HIS 0.001 0.000 HIS A 49 PHE 0.030 0.002 PHE A 592 TYR 0.026 0.001 TYR C 660 ARG 0.008 0.000 ARG C 319 *********************** 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 127 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 93 time to evaluate : 0.630 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: 0.8020 (p90) cc_final: 0.7790 (p90) REVERT: B 654 GLU cc_start: 0.8894 (mm-30) cc_final: 0.8647 (mm-30) REVERT: C 319 ARG cc_start: 0.8774 (mtp85) cc_final: 0.8189 (mtp85) REVERT: C 592 PHE cc_start: 0.8472 (t80) cc_final: 0.8244 (t80) outliers start: 34 outliers final: 32 residues processed: 120 average time/residue: 0.1611 time to fit residues: 26.6203 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 : 0.743 ------------------------------------------------------------------------------- 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 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 580 GLN 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 3 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 47 optimal weight: 1.9990 chunk 42 optimal weight: 0.7980 chunk 14 optimal weight: 0.5980 chunk 64 optimal weight: 0.3980 chunk 73 optimal weight: 0.9980 chunk 50 optimal weight: 1.9990 chunk 80 optimal weight: 0.9980 chunk 48 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 658 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2647 r_free = 0.2647 target = 0.048648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2408 r_free = 0.2408 target = 0.040604 restraints weight = 21836.318| |-----------------------------------------------------------------------------| r_work (start): 0.2403 rms_B_bonded: 2.35 r_work: 0.2298 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2188 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8911 moved from start: 0.3708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 6909 Z= 0.314 Angle : 0.626 11.405 9381 Z= 0.335 Chirality : 0.046 0.179 1122 Planarity : 0.005 0.035 1185 Dihedral : 7.021 58.935 1156 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 4.91 % Allowed : 14.34 % Favored : 80.74 % 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: -1.24 (0.29), residues: 795 helix: 1.16 (1.16), residues: 24 sheet: 0.31 (0.30), residues: 267 loop : -1.67 (0.27), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 64 HIS 0.001 0.000 HIS C 207 PHE 0.026 0.002 PHE A 592 TYR 0.027 0.001 TYR C 660 ARG 0.009 0.001 ARG A 319 *********************** 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 130 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 93 time to evaluate : 0.774 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: 0.7992 (p90) cc_final: 0.7773 (p90) REVERT: B 654 GLU cc_start: 0.8919 (mm-30) cc_final: 0.8669 (mm-30) REVERT: C 319 ARG cc_start: 0.8774 (mtp85) cc_final: 0.8188 (mtp85) REVERT: C 592 PHE cc_start: 0.8530 (t80) cc_final: 0.8271 (t80) REVERT: C 661 GLU cc_start: 0.8936 (pm20) cc_final: 0.8625 (pm20) outliers start: 37 outliers final: 35 residues processed: 122 average time/residue: 0.1572 time to fit residues: 27.0014 Evaluate side-chains 126 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 91 time to evaluate : 0.798 ------------------------------------------------------------------------------- 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 583 GLU 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 63 THR 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 658 ASN 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 580 GLN 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 81 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 77 optimal weight: 0.5980 chunk 2 optimal weight: 1.9990 chunk 18 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 79 optimal weight: 0.0570 chunk 71 optimal weight: 0.9990 chunk 36 optimal weight: 0.6980 chunk 65 optimal weight: 0.9980 chunk 39 optimal weight: 0.9990 overall best weight: 0.6498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 658 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2653 r_free = 0.2653 target = 0.048869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2415 r_free = 0.2415 target = 0.040797 restraints weight = 21896.923| |-----------------------------------------------------------------------------| r_work (start): 0.2409 rms_B_bonded: 2.36 r_work: 0.2303 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2194 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8904 moved from start: 0.3728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 6909 Z= 0.281 Angle : 0.615 10.592 9381 Z= 0.330 Chirality : 0.046 0.177 1122 Planarity : 0.005 0.035 1185 Dihedral : 7.010 58.795 1156 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 4.65 % Allowed : 15.27 % 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 (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: -1.23 (0.29), residues: 795 helix: 1.21 (1.17), residues: 24 sheet: 0.30 (0.30), residues: 267 loop : -1.65 (0.27), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 64 HIS 0.001 0.000 HIS A 49 PHE 0.023 0.002 PHE A 592 TYR 0.028 0.001 TYR C 660 ARG 0.012 0.001 ARG A 319 ********************** 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 129 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 94 time to evaluate : 0.842 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 643 PHE cc_start: 0.8005 (p90) cc_final: 0.7763 (p90) REVERT: B 319 ARG cc_start: 0.8937 (mtp85) cc_final: 0.8408 (mtp85) REVERT: B 654 GLU cc_start: 0.8933 (mm-30) cc_final: 0.8707 (mm-30) REVERT: C 319 ARG cc_start: 0.8800 (mtp85) cc_final: 0.8190 (mtp85) REVERT: C 592 PHE cc_start: 0.8537 (t80) cc_final: 0.8274 (t80) REVERT: C 661 GLU cc_start: 0.8950 (pm20) cc_final: 0.8680 (pm20) outliers start: 35 outliers final: 32 residues processed: 120 average time/residue: 0.1754 time to fit residues: 29.5847 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 : 0.747 ------------------------------------------------------------------------------- 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 583 GLU 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 658 ASN 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 580 GLN 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 67 optimal weight: 0.5980 chunk 37 optimal weight: 0.6980 chunk 72 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 47 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 chunk 75 optimal weight: 0.5980 chunk 19 optimal weight: 0.9980 chunk 11 optimal weight: 0.9990 chunk 12 optimal weight: 0.6980 chunk 9 optimal weight: 0.3980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.2657 r_free = 0.2657 target = 0.048997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2418 r_free = 0.2418 target = 0.040911 restraints weight = 21796.199| |-----------------------------------------------------------------------------| r_work (start): 0.2414 rms_B_bonded: 2.36 r_work: 0.2309 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2200 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8904 moved from start: 0.3737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 6909 Z= 0.263 Angle : 0.613 10.411 9381 Z= 0.327 Chirality : 0.046 0.167 1122 Planarity : 0.005 0.035 1185 Dihedral : 6.952 58.690 1156 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 4.38 % Allowed : 15.41 % 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 (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: -1.21 (0.29), residues: 795 helix: 1.24 (1.18), residues: 24 sheet: 0.30 (0.30), residues: 267 loop : -1.63 (0.27), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C 64 HIS 0.001 0.000 HIS A 49 PHE 0.018 0.002 PHE C 592 TYR 0.025 0.001 TYR C 660 ARG 0.005 0.000 ARG C 319 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3525.03 seconds wall clock time: 63 minutes 29.97 seconds (3809.97 seconds total)