Starting phenix.real_space_refine on Tue Mar 11 23:11:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8z7l_39819/03_2025/8z7l_39819.cif Found real_map, /net/cci-nas-00/data/ceres_data/8z7l_39819/03_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_39819/03_2025/8z7l_39819.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8z7l_39819/03_2025/8z7l_39819.map" model { file = "/net/cci-nas-00/data/ceres_data/8z7l_39819/03_2025/8z7l_39819.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8z7l_39819/03_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-5624/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: 5.22, per 1000 atoms: 0.77 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: 1.59 Conformation dependent library (CDL) restraints added in 978.8 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: 0.84 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: 1.94 Time building geometry restraints manager: 1.93 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: 2.550 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: 0.010 Extract box with map and model: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 20.080 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:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.880 ------------------------------------------------------------------------------- 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 : 0.766 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: 0.2090 time to fit residues: 50.9396 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 : 0.716 ------------------------------------------------------------------------------- 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 = 0.2496 r_free = 0.2496 target = 0.043505 restraints weight = 21232.544| |-----------------------------------------------------------------------------| r_work (start): 0.2492 rms_B_bonded: 2.35 r_work: 0.2385 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2277 rms_B_bonded: 4.49 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 : 0.717 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 319 ARG cc_start: 0.8934 (mtp85) cc_final: 0.8652 (mtp85) REVERT: A 592 PHE cc_start: 0.8641 (t80) cc_final: 0.8357 (t80) REVERT: A 654 GLU cc_start: 0.8731 (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: 0.1535 time to fit residues: 30.5171 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 : 0.722 ------------------------------------------------------------------------------- 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: 0.0870 chunk 14 optimal weight: 0.0070 chunk 35 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 75 optimal weight: 1.9990 chunk 24 optimal weight: 0.4980 chunk 68 optimal weight: 0.5980 chunk 55 optimal weight: 0.0870 overall best weight: 0.2554 ------------------------------------------------------------------------------- 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 = 0.2749 r_free = 0.2749 target = 0.052475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2522 r_free = 0.2522 target = 0.044414 restraints weight = 21358.826| |-----------------------------------------------------------------------------| r_work (start): 0.2520 rms_B_bonded: 2.35 r_work: 0.2416 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2308 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8823 moved from start: 0.2645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 6909 Z= 0.192 Angle : 0.552 6.567 9381 Z= 0.292 Chirality : 0.045 0.232 1122 Planarity : 0.004 0.032 1185 Dihedral : 6.697 53.847 1157 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 4.12 % Allowed : 12.88 % Favored : 83.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.81 (0.28), residues: 795 helix: 0.31 (1.18), residues: 27 sheet: -0.41 (0.29), residues: 252 loop : -1.79 (0.26), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 64 HIS 0.001 0.000 HIS C 655 PHE 0.026 0.001 PHE B 643 TYR 0.036 0.001 TYR C 660 ARG 0.003 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: 31 poor density : 95 time to evaluate : 0.828 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 319 ARG cc_start: 0.8923 (mtp85) cc_final: 0.8669 (mtp85) REVERT: A 592 PHE cc_start: 0.8637 (t80) cc_final: 0.8411 (t80) REVERT: A 654 GLU cc_start: 0.8679 (mm-30) cc_final: 0.8401 (mm-30) REVERT: B 281 GLU cc_start: 0.8192 (pm20) cc_final: 0.7976 (pm20) REVERT: B 675 GLN cc_start: 0.8207 (tp40) cc_final: 0.7968 (pp30) REVERT: C 571 ASP cc_start: 0.8775 (m-30) cc_final: 0.8566 (m-30) outliers start: 31 outliers final: 21 residues processed: 121 average time/residue: 0.1556 time to fit residues: 26.4218 Evaluate side-chains 109 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 88 time to evaluate : 0.689 ------------------------------------------------------------------------------- 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 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 54 optimal weight: 1.9990 chunk 57 optimal weight: 0.8980 chunk 2 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 52 optimal weight: 0.8980 chunk 18 optimal weight: 0.6980 chunk 12 optimal weight: 2.9990 chunk 70 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- 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 = 0.2646 r_free = 0.2646 target = 0.048651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2408 r_free = 0.2408 target = 0.040603 restraints weight = 21916.644| |-----------------------------------------------------------------------------| r_work (start): 0.2404 rms_B_bonded: 2.35 r_work: 0.2298 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2189 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8908 moved from start: 0.3234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.075 6909 Z= 0.419 Angle : 0.654 5.682 9381 Z= 0.351 Chirality : 0.048 0.241 1122 Planarity : 0.005 0.036 1185 Dihedral : 7.138 59.590 1156 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.54 % Favored : 93.46 % Rotamer: Outliers : 5.98 % Allowed : 11.29 % Favored : 82.74 % 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: -1.79 (0.28), residues: 795 helix: 1.47 (1.24), residues: 24 sheet: -0.17 (0.29), residues: 252 loop : -1.97 (0.25), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 64 HIS 0.002 0.001 HIS A 49 PHE 0.026 0.002 PHE B 643 TYR 0.024 0.002 TYR C 660 ARG 0.003 0.000 ARG A 273 *********************** 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 142 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 97 time to evaluate : 0.720 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 319 ARG cc_start: 0.8957 (mtp85) cc_final: 0.8669 (mtp85) REVERT: A 592 PHE cc_start: 0.8674 (t80) cc_final: 0.8452 (t80) REVERT: A 643 PHE cc_start: 0.8081 (p90) cc_final: 0.7683 (p90) outliers start: 45 outliers final: 28 residues processed: 135 average time/residue: 0.1477 time to fit residues: 28.0014 Evaluate side-chains 111 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 83 time to evaluate : 0.757 ------------------------------------------------------------------------------- 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 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 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 301 CYS Chi-restraints excluded: chain C residue 544 ASN Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 580 GLN Chi-restraints excluded: chain C residue 618 THR 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: 0.9990 chunk 31 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 52 optimal weight: 0.5980 chunk 0 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 55 optimal weight: 1.9990 chunk 64 optimal weight: 0.9990 chunk 79 optimal weight: 0.1980 chunk 67 optimal weight: 0.9990 chunk 80 optimal weight: 0.7980 overall best weight: 0.7182 ------------------------------------------------------------------------------- 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 = 0.2653 r_free = 0.2653 target = 0.048886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2417 r_free = 0.2417 target = 0.040898 restraints weight = 21423.068| |-----------------------------------------------------------------------------| r_work (start): 0.2413 rms_B_bonded: 2.33 r_work: 0.2308 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2199 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8900 moved from start: 0.3425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 6909 Z= 0.298 Angle : 0.606 6.820 9381 Z= 0.325 Chirality : 0.047 0.223 1122 Planarity : 0.005 0.034 1185 Dihedral : 7.132 59.658 1156 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 5.18 % Allowed : 12.88 % Favored : 81.94 % 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: -1.66 (0.28), residues: 795 helix: 1.55 (1.24), residues: 24 sheet: -0.10 (0.29), residues: 252 loop : -1.87 (0.26), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 64 HIS 0.002 0.001 HIS A 655 PHE 0.023 0.002 PHE B 643 TYR 0.027 0.001 TYR C 660 ARG 0.002 0.000 ARG C 319 *********************** 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 128 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 89 time to evaluate : 0.823 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 319 ARG cc_start: 0.8952 (mtp85) cc_final: 0.8685 (mtp85) REVERT: A 592 PHE cc_start: 0.8661 (t80) cc_final: 0.8444 (t80) REVERT: A 643 PHE cc_start: 0.8058 (p90) cc_final: 0.7683 (p90) outliers start: 39 outliers final: 31 residues processed: 123 average time/residue: 0.1588 time to fit residues: 27.6657 Evaluate side-chains 115 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 84 time to evaluate : 0.684 ------------------------------------------------------------------------------- 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 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 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 301 CYS 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 658 ASN 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: 0.8980 chunk 78 optimal weight: 1.9990 chunk 34 optimal weight: 0.2980 chunk 4 optimal weight: 0.9990 chunk 39 optimal weight: 0.9990 chunk 56 optimal weight: 2.9990 chunk 17 optimal weight: 0.9990 chunk 58 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 6 optimal weight: 0.1980 overall best weight: 0.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 211 ASN A 580 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2648 r_free = 0.2648 target = 0.048638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2411 r_free = 0.2411 target = 0.040636 restraints weight = 21476.019| |-----------------------------------------------------------------------------| r_work (start): 0.2406 rms_B_bonded: 2.35 r_work: 0.2302 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2193 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8906 moved from start: 0.3556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 6909 Z= 0.282 Angle : 0.590 7.802 9381 Z= 0.316 Chirality : 0.046 0.187 1122 Planarity : 0.005 0.036 1185 Dihedral : 7.053 59.423 1156 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 5.44 % Allowed : 13.55 % Favored : 81.01 % 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: -1.48 (0.28), residues: 795 helix: 1.53 (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 TRP 0.011 0.002 TRP A 64 HIS 0.003 0.000 HIS A 655 PHE 0.023 0.002 PHE B 643 TYR 0.026 0.001 TYR C 660 ARG 0.004 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 133 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 92 time to evaluate : 0.721 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 319 ARG cc_start: 0.8955 (mtp85) cc_final: 0.8700 (mtp85) REVERT: A 643 PHE cc_start: 0.8065 (p90) cc_final: 0.7769 (p90) REVERT: C 319 ARG cc_start: 0.8883 (mtp85) cc_final: 0.8350 (mtp85) outliers start: 41 outliers final: 35 residues processed: 125 average time/residue: 0.1533 time to fit residues: 26.8716 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 : 0.694 ------------------------------------------------------------------------------- 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 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 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 301 CYS 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 658 ASN 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: 0.9980 chunk 21 optimal weight: 0.1980 chunk 50 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 11 optimal weight: 0.9990 chunk 59 optimal weight: 1.9990 chunk 75 optimal weight: 0.8980 chunk 77 optimal weight: 0.9990 chunk 20 optimal weight: 0.7980 chunk 38 optimal weight: 1.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 211 ASN A 580 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2636 r_free = 0.2636 target = 0.048259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2401 r_free = 0.2401 target = 0.040343 restraints weight = 21306.122| |-----------------------------------------------------------------------------| r_work (start): 0.2396 rms_B_bonded: 2.31 r_work: 0.2291 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2183 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8914 moved from start: 0.3681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 6909 Z= 0.317 Angle : 0.623 11.836 9381 Z= 0.332 Chirality : 0.046 0.179 1122 Planarity : 0.005 0.035 1185 Dihedral : 7.101 59.897 1156 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 5.31 % Allowed : 14.48 % 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: -1.39 (0.29), residues: 795 helix: 1.51 (1.22), residues: 24 sheet: 0.01 (0.29), residues: 282 loop : -1.71 (0.27), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 64 HIS 0.001 0.001 HIS A 207 PHE 0.027 0.002 PHE A 592 TYR 0.026 0.001 TYR C 660 ARG 0.003 0.000 ARG A 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 132 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 92 time to evaluate : 0.775 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 319 ARG cc_start: 0.8964 (mtp85) cc_final: 0.8747 (mtp85) REVERT: A 643 PHE cc_start: 0.8064 (p90) cc_final: 0.7821 (p90) REVERT: C 661 GLU cc_start: 0.8935 (pm20) cc_final: 0.8724 (pm20) outliers start: 40 outliers final: 33 residues processed: 125 average time/residue: 0.1564 time to fit residues: 27.3677 Evaluate side-chains 118 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 85 time to evaluate : 0.783 ------------------------------------------------------------------------------- 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 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 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 301 CYS 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: 1.9990 chunk 22 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 6 optimal weight: 5.9990 chunk 4 optimal weight: 0.2980 chunk 46 optimal weight: 0.7980 chunk 54 optimal weight: 0.6980 overall best weight: 1.1584 ------------------------------------------------------------------------------- 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 = 0.2601 r_free = 0.2601 target = 0.047009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2361 r_free = 0.2361 target = 0.039049 restraints weight = 21948.931| |-----------------------------------------------------------------------------| r_work (start): 0.2357 rms_B_bonded: 2.34 r_work: 0.2250 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2140 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8945 moved from start: 0.3911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.057 6909 Z= 0.443 Angle : 0.699 13.615 9381 Z= 0.374 Chirality : 0.048 0.188 1122 Planarity : 0.005 0.036 1185 Dihedral : 7.440 58.403 1156 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.04 % Favored : 92.96 % Rotamer: Outliers : 4.91 % Allowed : 15.80 % Favored : 79.28 % 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: -1.46 (0.29), residues: 795 helix: 1.32 (1.17), residues: 24 sheet: 0.09 (0.29), residues: 297 loop : -1.90 (0.27), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP A 64 HIS 0.002 0.001 HIS B 207 PHE 0.025 0.002 PHE A 592 TYR 0.023 0.002 TYR C 660 ARG 0.002 0.000 ARG A 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: 37 poor density : 90 time to evaluate : 0.806 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 643 PHE cc_start: 0.8074 (p90) cc_final: 0.7833 (p90) REVERT: C 215 ASP cc_start: 0.7793 (m-30) cc_final: 0.7456 (m-30) outliers start: 37 outliers final: 35 residues processed: 120 average time/residue: 0.1573 time to fit residues: 26.7625 Evaluate side-chains 124 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 89 time to evaluate : 0.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 ILE 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 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 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 301 CYS Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 580 GLN 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: 0.7980 chunk 12 optimal weight: 1.9990 chunk 47 optimal weight: 0.7980 chunk 42 optimal weight: 0.7980 chunk 14 optimal weight: 0.8980 chunk 64 optimal weight: 0.9980 chunk 73 optimal weight: 0.9980 chunk 50 optimal weight: 0.6980 chunk 80 optimal weight: 0.9990 chunk 48 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.2624 r_free = 0.2624 target = 0.047811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2386 r_free = 0.2386 target = 0.039832 restraints weight = 21839.921| |-----------------------------------------------------------------------------| r_work (start): 0.2381 rms_B_bonded: 2.34 r_work: 0.2275 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2166 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8927 moved from start: 0.3922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 6909 Z= 0.320 Angle : 0.645 11.784 9381 Z= 0.345 Chirality : 0.046 0.175 1122 Planarity : 0.005 0.038 1185 Dihedral : 7.294 59.938 1156 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 4.78 % Allowed : 16.73 % Favored : 78.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.34 (0.29), residues: 795 helix: 1.55 (1.21), residues: 24 sheet: 0.12 (0.29), residues: 297 loop : -1.78 (0.27), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP B 64 HIS 0.001 0.000 HIS A 49 PHE 0.024 0.002 PHE A 592 TYR 0.023 0.001 TYR C 660 ARG 0.004 0.000 ARG C 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 129 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 93 time to evaluate : 0.913 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 592 PHE cc_start: 0.8427 (t80) cc_final: 0.7455 (t80) REVERT: A 643 PHE cc_start: 0.8043 (p90) cc_final: 0.7806 (p90) REVERT: C 661 GLU cc_start: 0.8888 (pm20) cc_final: 0.8643 (pm20) outliers start: 36 outliers final: 33 residues processed: 122 average time/residue: 0.1572 time to fit residues: 26.9227 Evaluate side-chains 121 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 88 time to evaluate : 0.700 ------------------------------------------------------------------------------- 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 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 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 301 CYS Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 580 GLN 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 81 optimal weight: 0.9980 chunk 72 optimal weight: 0.8980 chunk 77 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 79 optimal weight: 0.9990 chunk 71 optimal weight: 0.6980 chunk 36 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 chunk 39 optimal weight: 0.9980 overall best weight: 0.9180 ------------------------------------------------------------------------------- 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 = 0.2615 r_free = 0.2615 target = 0.047525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.2373 r_free = 0.2373 target = 0.039513 restraints weight = 22513.095| |-----------------------------------------------------------------------------| r_work (start): 0.2368 rms_B_bonded: 2.37 r_work: 0.2261 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2151 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8936 moved from start: 0.3992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 6909 Z= 0.365 Angle : 0.675 10.887 9381 Z= 0.362 Chirality : 0.047 0.181 1122 Planarity : 0.005 0.039 1185 Dihedral : 7.329 59.315 1156 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.92 % Favored : 93.08 % Rotamer: Outliers : 4.38 % Allowed : 17.13 % Favored : 78.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.35 (0.29), residues: 795 helix: 1.48 (1.20), residues: 24 sheet: 0.13 (0.29), residues: 297 loop : -1.81 (0.27), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP B 64 HIS 0.001 0.001 HIS A 655 PHE 0.024 0.002 PHE A 592 TYR 0.023 0.002 TYR C 660 ARG 0.007 0.000 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 120 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 87 time to evaluate : 0.808 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: 0.8021 (p90) cc_final: 0.7774 (p90) REVERT: C 319 ARG cc_start: 0.8872 (mtp85) cc_final: 0.8036 (mtp85) outliers start: 33 outliers final: 33 residues processed: 114 average time/residue: 0.1513 time to fit residues: 24.4038 Evaluate side-chains 117 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 84 time to evaluate : 0.777 ------------------------------------------------------------------------------- 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 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 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 301 CYS Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 580 GLN 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 67 optimal weight: 0.6980 chunk 37 optimal weight: 0.6980 chunk 72 optimal weight: 0.9990 chunk 77 optimal weight: 1.9990 chunk 47 optimal weight: 0.9980 chunk 15 optimal weight: 0.9980 chunk 75 optimal weight: 0.6980 chunk 19 optimal weight: 0.5980 chunk 11 optimal weight: 0.5980 chunk 12 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 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 = 0.2631 r_free = 0.2631 target = 0.048060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2391 r_free = 0.2391 target = 0.040043 restraints weight = 22289.547| |-----------------------------------------------------------------------------| r_work (start): 0.2386 rms_B_bonded: 2.36 r_work: 0.2280 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2169 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8923 moved from start: 0.3997 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= 0.290 Angle : 0.651 10.774 9381 Z= 0.349 Chirality : 0.046 0.170 1122 Planarity : 0.005 0.039 1185 Dihedral : 7.244 59.560 1156 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 4.38 % Allowed : 16.87 % Favored : 78.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.30 (0.29), residues: 795 helix: 1.61 (1.22), residues: 24 sheet: 0.10 (0.29), residues: 297 loop : -1.73 (0.28), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.003 TRP B 64 HIS 0.001 0.000 HIS A 49 PHE 0.018 0.002 PHE B 643 TYR 0.022 0.001 TYR C 660 ARG 0.009 0.001 ARG A 319 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3453.28 seconds wall clock time: 60 minutes 11.14 seconds (3611.14 seconds total)