Starting phenix.real_space_refine on Fri Aug 7 01:43:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9tg6_55892/08_2026/9tg6_55892_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9tg6_55892/08_2026/9tg6_55892.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.29 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9tg6_55892/08_2026/9tg6_55892.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9tg6_55892/08_2026/9tg6_55892.map" model { file = "/net/cci-nas-00/data/ceres_data/9tg6_55892/08_2026/9tg6_55892_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9tg6_55892/08_2026/9tg6_55892_trim.cif" } resolution = 3.29 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.035 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: 7 Type Number sf(0) Gaussians K 4 8.98 5 P 12 5.49 5 S 68 5.16 5 C 5936 2.51 5 N 1492 2.21 5 O 1731 1.98 5 H 8740 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 32 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 17983 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4470 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 4470 Classifications: {'peptide': 298} Link IDs: {'PTRANS': 15, 'TRANS': 282} Chain breaks: 1 Unresolved non-hydrogen bonds: 88 Unresolved non-hydrogen angles: 109 Unresolved non-hydrogen dihedrals: 77 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 5, 'ASP:plan': 1, 'TRP:plan': 1, 'GLU:plan': 2, 'ASN:plan1': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 59 Chain: "B" Number of atoms: 4470 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 4470 Classifications: {'peptide': 298} Link IDs: {'PTRANS': 15, 'TRANS': 282} Chain breaks: 1 Unresolved non-hydrogen bonds: 88 Unresolved non-hydrogen angles: 109 Unresolved non-hydrogen dihedrals: 77 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 5, 'ASP:plan': 1, 'TRP:plan': 1, 'GLU:plan': 2, 'ASN:plan1': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 59 Chain: "D" Number of atoms: 4470 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 4470 Classifications: {'peptide': 298} Link IDs: {'PTRANS': 15, 'TRANS': 282} Chain breaks: 1 Unresolved non-hydrogen bonds: 88 Unresolved non-hydrogen angles: 109 Unresolved non-hydrogen dihedrals: 77 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 5, 'ASP:plan': 1, 'TRP:plan': 1, 'GLU:plan': 2, 'ASN:plan1': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 59 Chain: "C" Number of atoms: 4470 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 4470 Classifications: {'peptide': 298} Link IDs: {'PTRANS': 15, 'TRANS': 282} Chain breaks: 1 Unresolved non-hydrogen bonds: 88 Unresolved non-hydrogen angles: 109 Unresolved non-hydrogen dihedrals: 77 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 5, 'ASP:plan': 1, 'TRP:plan': 1, 'GLU:plan': 2, 'ASN:plan1': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 59 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 28 Unusual residues: {' K': 3, 'PIO': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PIO:plan-1': 1, 'PIO:plan-2': 1} Unresolved non-hydrogen planarities: 8 Chain: "B" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 26 Unusual residues: {' K': 1, 'PIO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PIO:plan-1': 1, 'PIO:plan-2': 1} Unresolved non-hydrogen planarities: 8 Chain: "D" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 25 Unusual residues: {'PIO': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PIO:plan-1': 1, 'PIO:plan-2': 1} Unresolved non-hydrogen planarities: 8 Chain: "C" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 24 Unusual residues: {'PIO': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PIO:plan-1': 1, 'PIO:plan-2': 1} Unresolved non-hydrogen planarities: 8 Time building chain proxies: 3.78, per 1000 atoms: 0.21 Number of scatterers: 17983 At special positions: 0 Unit cell: (95.55, 95.55, 120.9, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) K 4 19.00 S 68 16.00 P 12 15.00 O 1731 8.00 N 1492 7.00 C 5936 6.00 H 8740 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 99 " - pdb=" SG CYS A 131 " distance=2.04 Simple disulfide: pdb=" SG CYS B 99 " - pdb=" SG CYS B 131 " distance=2.04 Simple disulfide: pdb=" SG CYS D 99 " - pdb=" SG CYS D 131 " distance=2.04 Simple disulfide: pdb=" SG CYS C 99 " - pdb=" SG CYS C 131 " distance=2.04 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=3, symmetry=0 Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.45 Conformation dependent library (CDL) restraints added in 645.9 milliseconds 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2264 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 24 sheets defined 33.9% alpha, 28.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.38 Creating SS restraints... Processing helix chain 'A' and resid 40 through 51 Processing helix chain 'A' and resid 55 through 83 removed outlier: 3.729A pdb=" N LEU A 74 " --> pdb=" O VAL A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 87 removed outlier: 3.571A pdb=" N LEU A 87 " --> pdb=" O ASP A 84 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 84 through 87' Processing helix chain 'A' and resid 105 through 118 Processing helix chain 'A' and resid 131 through 157 Processing helix chain 'A' and resid 251 through 258 removed outlier: 4.492A pdb=" N THR A 255 " --> pdb=" O PRO A 252 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU A 257 " --> pdb=" O ALA A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 291 No H-bonds generated for 'chain 'A' and resid 289 through 291' Processing helix chain 'A' and resid 315 through 318 Processing helix chain 'B' and resid 40 through 51 Processing helix chain 'B' and resid 55 through 83 removed outlier: 3.730A pdb=" N LEU B 74 " --> pdb=" O VAL B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 84 through 87 removed outlier: 3.571A pdb=" N LEU B 87 " --> pdb=" O ASP B 84 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 84 through 87' Processing helix chain 'B' and resid 105 through 118 Processing helix chain 'B' and resid 131 through 157 Processing helix chain 'B' and resid 251 through 258 removed outlier: 4.492A pdb=" N THR B 255 " --> pdb=" O PRO B 252 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU B 257 " --> pdb=" O ALA B 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 289 through 291 No H-bonds generated for 'chain 'B' and resid 289 through 291' Processing helix chain 'B' and resid 315 through 318 Processing helix chain 'D' and resid 40 through 51 Processing helix chain 'D' and resid 55 through 83 removed outlier: 3.729A pdb=" N LEU D 74 " --> pdb=" O VAL D 70 " (cutoff:3.500A) Processing helix chain 'D' and resid 84 through 87 removed outlier: 3.571A pdb=" N LEU D 87 " --> pdb=" O ASP D 84 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 84 through 87' Processing helix chain 'D' and resid 105 through 118 Processing helix chain 'D' and resid 131 through 157 Processing helix chain 'D' and resid 251 through 258 removed outlier: 4.492A pdb=" N THR D 255 " --> pdb=" O PRO D 252 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU D 257 " --> pdb=" O ALA D 254 " (cutoff:3.500A) Processing helix chain 'D' and resid 289 through 291 No H-bonds generated for 'chain 'D' and resid 289 through 291' Processing helix chain 'D' and resid 315 through 318 Processing helix chain 'C' and resid 40 through 51 Processing helix chain 'C' and resid 55 through 83 removed outlier: 3.729A pdb=" N LEU C 74 " --> pdb=" O VAL C 70 " (cutoff:3.500A) Processing helix chain 'C' and resid 84 through 87 removed outlier: 3.571A pdb=" N LEU C 87 " --> pdb=" O ASP C 84 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 84 through 87' Processing helix chain 'C' and resid 105 through 118 Processing helix chain 'C' and resid 131 through 157 Processing helix chain 'C' and resid 251 through 258 removed outlier: 4.492A pdb=" N THR C 255 " --> pdb=" O PRO C 252 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU C 257 " --> pdb=" O ALA C 254 " (cutoff:3.500A) Processing helix chain 'C' and resid 289 through 291 No H-bonds generated for 'chain 'C' and resid 289 through 291' Processing helix chain 'C' and resid 315 through 318 Processing sheet with id=AA1, first strand: chain 'A' and resid 170 through 172 Processing sheet with id=AA2, first strand: chain 'A' and resid 170 through 172 Processing sheet with id=AA3, first strand: chain 'A' and resid 217 through 218 removed outlier: 6.498A pdb=" N THR A 200 " --> pdb=" O PHE A 236 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N PHE A 236 " --> pdb=" O THR A 200 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 221 through 222 removed outlier: 5.592A pdb=" N SER A 201 " --> pdb=" O MET A 274 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N MET A 274 " --> pdb=" O SER A 201 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 297 through 299 Processing sheet with id=AA6, first strand: chain 'A' and resid 303 through 304 Processing sheet with id=AA7, first strand: chain 'B' and resid 170 through 172 Processing sheet with id=AA8, first strand: chain 'B' and resid 170 through 172 Processing sheet with id=AA9, first strand: chain 'B' and resid 217 through 218 removed outlier: 6.498A pdb=" N THR B 200 " --> pdb=" O PHE B 236 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N PHE B 236 " --> pdb=" O THR B 200 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 221 through 222 removed outlier: 5.592A pdb=" N SER B 201 " --> pdb=" O MET B 274 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N MET B 274 " --> pdb=" O SER B 201 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 297 through 299 Processing sheet with id=AB3, first strand: chain 'B' and resid 303 through 304 Processing sheet with id=AB4, first strand: chain 'D' and resid 170 through 172 Processing sheet with id=AB5, first strand: chain 'D' and resid 170 through 172 Processing sheet with id=AB6, first strand: chain 'D' and resid 217 through 218 removed outlier: 6.498A pdb=" N THR D 200 " --> pdb=" O PHE D 236 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N PHE D 236 " --> pdb=" O THR D 200 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 221 through 222 removed outlier: 5.592A pdb=" N SER D 201 " --> pdb=" O MET D 274 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N MET D 274 " --> pdb=" O SER D 201 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 297 through 299 Processing sheet with id=AB9, first strand: chain 'D' and resid 303 through 304 Processing sheet with id=AC1, first strand: chain 'C' and resid 170 through 172 Processing sheet with id=AC2, first strand: chain 'C' and resid 170 through 172 Processing sheet with id=AC3, first strand: chain 'C' and resid 217 through 218 removed outlier: 6.499A pdb=" N THR C 200 " --> pdb=" O PHE C 236 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N PHE C 236 " --> pdb=" O THR C 200 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 221 through 222 removed outlier: 5.593A pdb=" N SER C 201 " --> pdb=" O MET C 274 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N MET C 274 " --> pdb=" O SER C 201 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 297 through 299 Processing sheet with id=AC6, first strand: chain 'C' and resid 303 through 304 460 hydrogen bonds defined for protein. 1260 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.43 Time building geometry restraints manager: 2.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.95 - 1.12: 8728 1.12 - 1.30: 1472 1.30 - 1.47: 3545 1.47 - 1.64: 4346 1.64 - 1.82: 132 Bond restraints: 18223 Sorted by residual: bond pdb=" CD2 TYR D 288 " pdb=" HD2 TYR D 288 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.69e+01 bond pdb=" CD2 HIS D 259 " pdb=" HD2 HIS D 259 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.69e+01 bond pdb=" CD1 TYR D 288 " pdb=" HD1 TYR D 288 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.69e+01 bond pdb=" N ALA B 44 " pdb=" H ALA B 44 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.69e+01 bond pdb=" N LEU C 58 " pdb=" H LEU C 58 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.68e+01 ... (remaining 18218 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.74: 28194 2.74 - 5.48: 3540 5.48 - 8.22: 1047 8.22 - 10.96: 8 10.96 - 13.70: 20 Bond angle restraints: 32809 Sorted by residual: angle pdb=" CA PHE C 237 " pdb=" CB PHE C 237 " pdb=" CG PHE C 237 " ideal model delta sigma weight residual 113.80 119.97 -6.17 1.00e+00 1.00e+00 3.81e+01 angle pdb=" CA PHE A 237 " pdb=" CB PHE A 237 " pdb=" CG PHE A 237 " ideal model delta sigma weight residual 113.80 119.97 -6.17 1.00e+00 1.00e+00 3.80e+01 angle pdb=" CA PHE B 237 " pdb=" CB PHE B 237 " pdb=" CG PHE B 237 " ideal model delta sigma weight residual 113.80 119.96 -6.16 1.00e+00 1.00e+00 3.80e+01 angle pdb=" CA PHE D 237 " pdb=" CB PHE D 237 " pdb=" CG PHE D 237 " ideal model delta sigma weight residual 113.80 119.96 -6.16 1.00e+00 1.00e+00 3.79e+01 angle pdb=" CB HIS C 25 " pdb=" CG HIS C 25 " pdb=" CD2 HIS C 25 " ideal model delta sigma weight residual 131.20 124.81 6.39 1.30e+00 5.92e-01 2.42e+01 ... (remaining 32804 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.60: 8010 16.60 - 33.20: 451 33.20 - 49.80: 145 49.80 - 66.39: 117 66.39 - 82.99: 4 Dihedral angle restraints: 8727 sinusoidal: 4471 harmonic: 4256 Sorted by residual: dihedral pdb=" CA TYR D 311 " pdb=" C TYR D 311 " pdb=" N GLN D 312 " pdb=" CA GLN D 312 " ideal model delta harmonic sigma weight residual 180.00 151.95 28.05 0 5.00e+00 4.00e-02 3.15e+01 dihedral pdb=" CA TYR B 311 " pdb=" C TYR B 311 " pdb=" N GLN B 312 " pdb=" CA GLN B 312 " ideal model delta harmonic sigma weight residual 180.00 151.99 28.01 0 5.00e+00 4.00e-02 3.14e+01 dihedral pdb=" CA TYR A 311 " pdb=" C TYR A 311 " pdb=" N GLN A 312 " pdb=" CA GLN A 312 " ideal model delta harmonic sigma weight residual 180.00 151.99 28.01 0 5.00e+00 4.00e-02 3.14e+01 ... (remaining 8724 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.081: 1006 0.081 - 0.161: 377 0.161 - 0.241: 69 0.241 - 0.322: 36 0.322 - 0.402: 8 Chirality restraints: 1496 Sorted by residual: chirality pdb=" CA TYR D 102 " pdb=" N TYR D 102 " pdb=" C TYR D 102 " pdb=" CB TYR D 102 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 4.04e+00 chirality pdb=" CA TYR A 102 " pdb=" N TYR A 102 " pdb=" C TYR A 102 " pdb=" CB TYR A 102 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 4.01e+00 chirality pdb=" CA TYR C 102 " pdb=" N TYR C 102 " pdb=" C TYR C 102 " pdb=" CB TYR C 102 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 3.99e+00 ... (remaining 1493 not shown) Planarity restraints: 2744 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE C 270 " 0.107 2.00e-02 2.50e+03 4.59e-02 6.33e+01 pdb=" CG PHE C 270 " -0.010 2.00e-02 2.50e+03 pdb=" CD1 PHE C 270 " -0.038 2.00e-02 2.50e+03 pdb=" CD2 PHE C 270 " -0.024 2.00e-02 2.50e+03 pdb=" CE1 PHE C 270 " 0.016 2.00e-02 2.50e+03 pdb=" CE2 PHE C 270 " -0.022 2.00e-02 2.50e+03 pdb=" CZ PHE C 270 " 0.006 2.00e-02 2.50e+03 pdb=" HD1 PHE C 270 " -0.087 2.00e-02 2.50e+03 pdb=" HD2 PHE C 270 " -0.015 2.00e-02 2.50e+03 pdb=" HE1 PHE C 270 " 0.046 2.00e-02 2.50e+03 pdb=" HE2 PHE C 270 " -0.013 2.00e-02 2.50e+03 pdb=" HZ PHE C 270 " 0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 270 " -0.107 2.00e-02 2.50e+03 4.59e-02 6.32e+01 pdb=" CG PHE B 270 " 0.010 2.00e-02 2.50e+03 pdb=" CD1 PHE B 270 " 0.038 2.00e-02 2.50e+03 pdb=" CD2 PHE B 270 " 0.025 2.00e-02 2.50e+03 pdb=" CE1 PHE B 270 " -0.016 2.00e-02 2.50e+03 pdb=" CE2 PHE B 270 " 0.021 2.00e-02 2.50e+03 pdb=" CZ PHE B 270 " -0.005 2.00e-02 2.50e+03 pdb=" HD1 PHE B 270 " 0.086 2.00e-02 2.50e+03 pdb=" HD2 PHE B 270 " 0.014 2.00e-02 2.50e+03 pdb=" HE1 PHE B 270 " -0.046 2.00e-02 2.50e+03 pdb=" HE2 PHE B 270 " 0.012 2.00e-02 2.50e+03 pdb=" HZ PHE B 270 " -0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 270 " -0.106 2.00e-02 2.50e+03 4.58e-02 6.30e+01 pdb=" CG PHE A 270 " 0.010 2.00e-02 2.50e+03 pdb=" CD1 PHE A 270 " 0.038 2.00e-02 2.50e+03 pdb=" CD2 PHE A 270 " 0.025 2.00e-02 2.50e+03 pdb=" CE1 PHE A 270 " -0.016 2.00e-02 2.50e+03 pdb=" CE2 PHE A 270 " 0.021 2.00e-02 2.50e+03 pdb=" CZ PHE A 270 " -0.005 2.00e-02 2.50e+03 pdb=" HD1 PHE A 270 " 0.086 2.00e-02 2.50e+03 pdb=" HD2 PHE A 270 " 0.014 2.00e-02 2.50e+03 pdb=" HE1 PHE A 270 " -0.046 2.00e-02 2.50e+03 pdb=" HE2 PHE A 270 " 0.012 2.00e-02 2.50e+03 pdb=" HZ PHE A 270 " -0.033 2.00e-02 2.50e+03 ... (remaining 2741 not shown) Histogram of nonbonded interaction distances: 1.44 - 2.18: 974 2.18 - 2.92: 41307 2.92 - 3.66: 66109 3.66 - 4.40: 99371 4.40 - 5.14: 157526 Nonbonded interactions: 365287 Sorted by model distance: nonbonded pdb=" HZ3 LYS A 164 " pdb=" O GLY D 277 " model vdw 1.443 2.450 nonbonded pdb=" HZ3 LYS D 164 " pdb=" O GLY C 277 " model vdw 1.553 2.450 nonbonded pdb=" O GLY B 277 " pdb=" HZ3 LYS C 164 " model vdw 1.559 2.450 nonbonded pdb=" HE1 MET A 19 " pdb=" HE2 PHE D 239 " model vdw 1.577 2.270 nonbonded pdb=" OE2 GLU B 266 " pdb=" HG SER B 287 " model vdw 1.606 2.450 ... (remaining 365282 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 17 through 324) selection = (chain 'B' and resid 17 through 324) selection = (chain 'C' and resid 17 through 324) selection = (chain 'D' and resid 17 through 324) } 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: 8.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.120 Extract box with map and model: 0.310 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 17.300 Find NCS groups from input model: 0.340 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: 0.010 Load rotamer database and sin/cos tables:0.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 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 : 0.015 0.534 9490 Z= 1.076 Angle : 1.871 13.699 12953 Z= 1.243 Chirality : 0.093 0.402 1496 Planarity : 0.011 0.057 1620 Dihedral : 12.414 82.992 3247 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 1.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Cbeta Deviations : 0.88 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.37 (0.23), residues: 1176 helix: -0.11 (0.23), residues: 344 sheet: -0.63 (0.31), residues: 248 loop : 0.04 (0.26), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C 203 TYR 0.045 0.011 TYR D 209 PHE 0.067 0.014 PHE D 60 TRP 0.033 0.011 TRP D 75 HIS 0.008 0.003 HIS C 225 Details of bonding type rmsd/Z covalent geometry : bond 0.01266 / 0.78 ( 9483) covalent geometry : angle 1.87050 / 1.24 (12945) SS BOND : bond 0.00713 / 0.36 ( 4) SS BOND : angle 2.22164 / 1.57 ( 8) hydrogen bonds : bond 0.13573 / 9.42 ( 452) hydrogen bonds : angle 6.45409 / 4.76 ( 1260) Misc. bond : bond 0.41844 / 21.50 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 40 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue ILE 47 is missing expected H atoms. Skipping. Residue LEU 48 is missing expected H atoms. Skipping. Residue MET 51 is missing expected H atoms. Skipping. Residue LYS 216 is missing expected H atoms. Skipping. Residue SER 307 is missing expected H atoms. Skipping. Residue LYS 308 is missing expected H atoms. Skipping. Residue TYR 40 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue ILE 47 is missing expected H atoms. Skipping. Residue LEU 48 is missing expected H atoms. Skipping. Residue MET 51 is missing expected H atoms. Skipping. Residue LYS 216 is missing expected H atoms. Skipping. Residue SER 307 is missing expected H atoms. Skipping. Residue LYS 308 is missing expected H atoms. Skipping. Residue TYR 40 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue ILE 47 is missing expected H atoms. Skipping. Residue LEU 48 is missing expected H atoms. Skipping. Residue MET 51 is missing expected H atoms. Skipping. Residue LYS 216 is missing expected H atoms. Skipping. Residue SER 307 is missing expected H atoms. Skipping. Residue LYS 308 is missing expected H atoms. Skipping. Residue TYR 40 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue ILE 47 is missing expected H atoms. Skipping. Residue LEU 48 is missing expected H atoms. Skipping. Residue MET 51 is missing expected H atoms. Skipping. Residue LYS 216 is missing expected H atoms. Skipping. Residue SER 307 is missing expected H atoms. Skipping. Residue LYS 308 is missing expected H atoms. Skipping. Evaluate side-chains 196 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 196 time to evaluate : 0.606 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 ASN cc_start: 0.5879 (t0) cc_final: 0.5466 (t0) REVERT: A 230 SER cc_start: 0.9277 (p) cc_final: 0.8856 (m) REVERT: B 105 SER cc_start: 0.7660 (t) cc_final: 0.7330 (p) REVERT: B 230 SER cc_start: 0.9218 (p) cc_final: 0.8870 (m) REVERT: B 266 GLU cc_start: 0.8709 (tt0) cc_final: 0.8351 (tt0) REVERT: D 105 SER cc_start: 0.7631 (t) cc_final: 0.7299 (p) REVERT: D 230 SER cc_start: 0.9251 (p) cc_final: 0.8888 (m) REVERT: D 233 GLU cc_start: 0.7700 (mt-10) cc_final: 0.7456 (mp0) REVERT: D 266 GLU cc_start: 0.8707 (tt0) cc_final: 0.8352 (tt0) REVERT: C 105 SER cc_start: 0.7647 (t) cc_final: 0.7341 (p) REVERT: C 230 SER cc_start: 0.9222 (p) cc_final: 0.8858 (m) REVERT: C 233 GLU cc_start: 0.7690 (mt-10) cc_final: 0.7478 (mp0) REVERT: C 266 GLU cc_start: 0.8710 (tt0) cc_final: 0.8352 (tt0) outliers start: 0 outliers final: 0 residues processed: 196 average time/residue: 0.2046 time to fit residues: 55.9795 Evaluate side-chains 154 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 154 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 108 optimal weight: 0.6980 chunk 49 optimal weight: 0.5980 chunk 97 optimal weight: 0.9980 chunk 113 optimal weight: 0.5980 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 0.9990 chunk 100 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.202140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.165304 restraints weight = 22351.450| |-----------------------------------------------------------------------------| r_work (start): 0.3777 rms_B_bonded: 1.62 r_work: 0.3320 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.2167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 9490 Z= 0.171 Angle : 0.646 7.187 12953 Z= 0.344 Chirality : 0.043 0.179 1496 Planarity : 0.005 0.049 1620 Dihedral : 6.617 54.528 1267 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 0.73 % Allowed : 6.33 % Favored : 92.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.72 (0.25), residues: 1176 helix: 1.97 (0.26), residues: 344 sheet: -0.80 (0.32), residues: 248 loop : 0.28 (0.27), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 195 TYR 0.014 0.002 TYR A 218 PHE 0.019 0.002 PHE D 60 TRP 0.010 0.001 TRP C 55 HIS 0.006 0.001 HIS A 264 Details of bonding type rmsd/Z covalent geometry : bond 0.00395 / 0.17 ( 9483) covalent geometry : angle 0.64604 / 0.34 (12945) SS BOND : bond 0.00100 / 0.05 ( 4) SS BOND : angle 0.84392 / 0.58 ( 8) hydrogen bonds : bond 0.04991 / 3.46 ( 452) hydrogen bonds : angle 5.37371 / 3.94 ( 1260) Misc. bond : bond 0.00117 / 0.06 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 40 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue ILE 47 is missing expected H atoms. Skipping. Residue LEU 48 is missing expected H atoms. Skipping. Residue MET 51 is missing expected H atoms. Skipping. Residue LYS 216 is missing expected H atoms. Skipping. Residue SER 307 is missing expected H atoms. Skipping. Residue LYS 308 is missing expected H atoms. Skipping. Residue TYR 40 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue ILE 47 is missing expected H atoms. Skipping. Residue LEU 48 is missing expected H atoms. Skipping. Residue MET 51 is missing expected H atoms. Skipping. Residue LYS 216 is missing expected H atoms. Skipping. Residue SER 307 is missing expected H atoms. Skipping. Residue LYS 308 is missing expected H atoms. Skipping. Residue TYR 40 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue ILE 47 is missing expected H atoms. Skipping. Residue LEU 48 is missing expected H atoms. Skipping. Residue MET 51 is missing expected H atoms. Skipping. Residue LYS 216 is missing expected H atoms. Skipping. Residue SER 307 is missing expected H atoms. Skipping. Residue LYS 308 is missing expected H atoms. Skipping. Residue TYR 40 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue ILE 47 is missing expected H atoms. Skipping. Residue LEU 48 is missing expected H atoms. Skipping. Residue MET 51 is missing expected H atoms. Skipping. Residue LYS 216 is missing expected H atoms. Skipping. Residue SER 307 is missing expected H atoms. Skipping. Residue LYS 308 is missing expected H atoms. Skipping. Evaluate side-chains 147 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 140 time to evaluate : 0.332 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 ASN cc_start: 0.6558 (t0) cc_final: 0.6358 (t0) REVERT: B 230 SER cc_start: 0.9228 (p) cc_final: 0.8843 (m) REVERT: D 230 SER cc_start: 0.9242 (p) cc_final: 0.8863 (m) REVERT: C 230 SER cc_start: 0.9217 (p) cc_final: 0.8845 (m) REVERT: C 285 ARG cc_start: 0.8143 (mtm-85) cc_final: 0.7843 (ttp-110) outliers start: 7 outliers final: 5 residues processed: 147 average time/residue: 0.2054 time to fit residues: 42.5930 Evaluate side-chains 131 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 126 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 281 ILE Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain D residue 281 ILE Chi-restraints excluded: chain C residue 281 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 92 optimal weight: 3.9990 chunk 99 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 106 optimal weight: 0.9990 chunk 78 optimal weight: 0.9980 chunk 4 optimal weight: 2.9990 chunk 1 optimal weight: 6.9990 chunk 70 optimal weight: 3.9990 chunk 76 optimal weight: 0.7980 chunk 95 optimal weight: 1.9990 chunk 3 optimal weight: 0.9980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.199455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.162965 restraints weight = 22380.883| |-----------------------------------------------------------------------------| r_work (start): 0.3749 rms_B_bonded: 1.59 r_work: 0.3248 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.2692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 9490 Z= 0.172 Angle : 0.548 6.626 12953 Z= 0.296 Chirality : 0.043 0.190 1496 Planarity : 0.005 0.041 1620 Dihedral : 5.810 46.564 1267 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 0.41 % Allowed : 8.61 % Favored : 90.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.97 (0.26), residues: 1176 helix: 2.45 (0.28), residues: 348 sheet: -0.85 (0.32), residues: 248 loop : 0.33 (0.27), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 284 TYR 0.011 0.001 TYR A 218 PHE 0.022 0.002 PHE A 60 TRP 0.007 0.001 TRP A 55 HIS 0.006 0.001 HIS A 264 Details of bonding type rmsd/Z covalent geometry : bond 0.00404 / 0.17 ( 9483) covalent geometry : angle 0.54778 / 0.30 (12945) SS BOND : bond 0.00013 / 0.01 ( 4) SS BOND : angle 0.63670 / 0.44 ( 8) hydrogen bonds : bond 0.04066 / 2.84 ( 452) hydrogen bonds : angle 5.08032 / 3.72 ( 1260) Misc. bond : bond 0.00070 / 0.03 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 40 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue ILE 47 is missing expected H atoms. Skipping. Residue LEU 48 is missing expected H atoms. Skipping. Residue MET 51 is missing expected H atoms. Skipping. Residue LYS 216 is missing expected H atoms. Skipping. Residue SER 307 is missing expected H atoms. Skipping. Residue LYS 308 is missing expected H atoms. Skipping. Residue TYR 40 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue ILE 47 is missing expected H atoms. Skipping. Residue LEU 48 is missing expected H atoms. Skipping. Residue MET 51 is missing expected H atoms. Skipping. Residue LYS 216 is missing expected H atoms. Skipping. Residue SER 307 is missing expected H atoms. Skipping. Residue LYS 308 is missing expected H atoms. Skipping. Residue TYR 40 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue ILE 47 is missing expected H atoms. Skipping. Residue LEU 48 is missing expected H atoms. Skipping. Residue MET 51 is missing expected H atoms. Skipping. Residue LYS 216 is missing expected H atoms. Skipping. Residue SER 307 is missing expected H atoms. Skipping. Residue LYS 308 is missing expected H atoms. Skipping. Residue TYR 40 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue ILE 47 is missing expected H atoms. Skipping. Residue LEU 48 is missing expected H atoms. Skipping. Residue MET 51 is missing expected H atoms. Skipping. Residue LYS 216 is missing expected H atoms. Skipping. Residue SER 307 is missing expected H atoms. Skipping. Residue LYS 308 is missing expected H atoms. Skipping. Evaluate side-chains 141 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 137 time to evaluate : 0.505 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 ASN cc_start: 0.6813 (t0) cc_final: 0.6532 (t0) REVERT: A 96 HIS cc_start: 0.7459 (t70) cc_final: 0.7154 (t-170) outliers start: 4 outliers final: 4 residues processed: 140 average time/residue: 0.1838 time to fit residues: 37.9979 Evaluate side-chains 127 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 123 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 SER Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain C residue 74 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 11 optimal weight: 1.9990 chunk 84 optimal weight: 0.2980 chunk 13 optimal weight: 1.9990 chunk 95 optimal weight: 1.9990 chunk 76 optimal weight: 0.9980 chunk 0 optimal weight: 1.9990 chunk 29 optimal weight: 0.8980 chunk 20 optimal weight: 0.5980 chunk 64 optimal weight: 3.9990 chunk 105 optimal weight: 0.9980 chunk 43 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 82 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.199018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.163570 restraints weight = 22301.897| |-----------------------------------------------------------------------------| r_work (start): 0.3757 rms_B_bonded: 1.51 r_work: 0.3279 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.2963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 9490 Z= 0.140 Angle : 0.515 6.211 12953 Z= 0.275 Chirality : 0.041 0.179 1496 Planarity : 0.004 0.034 1620 Dihedral : 5.472 44.636 1267 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 0.52 % Allowed : 9.13 % Favored : 90.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.15 (0.26), residues: 1176 helix: 2.70 (0.28), residues: 348 sheet: -0.89 (0.33), residues: 248 loop : 0.45 (0.28), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 285 TYR 0.009 0.001 TYR A 218 PHE 0.020 0.002 PHE A 60 TRP 0.005 0.001 TRP C 53 HIS 0.006 0.001 HIS B 264 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.14 ( 9483) covalent geometry : angle 0.51474 / 0.27 (12945) SS BOND : bond 0.00042 / 0.02 ( 4) SS BOND : angle 0.89892 / 0.62 ( 8) hydrogen bonds : bond 0.03871 / 2.70 ( 452) hydrogen bonds : angle 4.93274 / 3.62 ( 1260) Misc. bond : bond 0.00052 / 0.03 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 40 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue ILE 47 is missing expected H atoms. Skipping. Residue LEU 48 is missing expected H atoms. Skipping. Residue MET 51 is missing expected H atoms. Skipping. Residue LYS 216 is missing expected H atoms. Skipping. Residue SER 307 is missing expected H atoms. Skipping. Residue LYS 308 is missing expected H atoms. Skipping. Residue TYR 40 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue ILE 47 is missing expected H atoms. Skipping. Residue LEU 48 is missing expected H atoms. Skipping. Residue MET 51 is missing expected H atoms. Skipping. Residue LYS 216 is missing expected H atoms. Skipping. Residue SER 307 is missing expected H atoms. Skipping. Residue LYS 308 is missing expected H atoms. Skipping. Residue TYR 40 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue ILE 47 is missing expected H atoms. Skipping. Residue LEU 48 is missing expected H atoms. Skipping. Residue MET 51 is missing expected H atoms. Skipping. Residue LYS 216 is missing expected H atoms. Skipping. Residue SER 307 is missing expected H atoms. Skipping. Residue LYS 308 is missing expected H atoms. Skipping. Residue TYR 40 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue ILE 47 is missing expected H atoms. Skipping. Residue LEU 48 is missing expected H atoms. Skipping. Residue MET 51 is missing expected H atoms. Skipping. Residue LYS 216 is missing expected H atoms. Skipping. Residue SER 307 is missing expected H atoms. Skipping. Residue LYS 308 is missing expected H atoms. Skipping. Evaluate side-chains 130 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 125 time to evaluate : 0.495 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 ASN cc_start: 0.6846 (t0) cc_final: 0.6605 (t0) REVERT: A 96 HIS cc_start: 0.7436 (t70) cc_final: 0.7063 (t-170) REVERT: B 233 GLU cc_start: 0.8053 (OUTLIER) cc_final: 0.7184 (mt-10) REVERT: C 285 ARG cc_start: 0.8529 (mtm-85) cc_final: 0.8125 (ttp-110) outliers start: 5 outliers final: 4 residues processed: 128 average time/residue: 0.1876 time to fit residues: 35.7717 Evaluate side-chains 126 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 121 time to evaluate : 0.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 233 GLU Chi-restraints excluded: chain D residue 49 MET Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain C residue 74 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 32 optimal weight: 3.9990 chunk 99 optimal weight: 0.8980 chunk 35 optimal weight: 4.9990 chunk 59 optimal weight: 4.9990 chunk 103 optimal weight: 0.9980 chunk 4 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 50 optimal weight: 0.7980 chunk 57 optimal weight: 3.9990 chunk 3 optimal weight: 0.6980 chunk 39 optimal weight: 0.0470 overall best weight: 0.6878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.198526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.166749 restraints weight = 22274.734| |-----------------------------------------------------------------------------| r_work (start): 0.3796 rms_B_bonded: 1.43 r_work: 0.3347 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.3176 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.3162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 9490 Z= 0.132 Angle : 0.495 5.831 12953 Z= 0.263 Chirality : 0.041 0.173 1496 Planarity : 0.004 0.031 1620 Dihedral : 5.270 45.164 1267 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 1.04 % Allowed : 9.75 % Favored : 89.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.24 (0.26), residues: 1176 helix: 2.78 (0.28), residues: 348 sheet: -0.89 (0.33), residues: 248 loop : 0.53 (0.28), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 284 TYR 0.008 0.001 TYR B 218 PHE 0.020 0.002 PHE A 60 TRP 0.005 0.001 TRP C 53 HIS 0.003 0.001 HIS B 264 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.13 ( 9483) covalent geometry : angle 0.49514 / 0.26 (12945) SS BOND : bond 0.00021 / 0.01 ( 4) SS BOND : angle 0.77276 / 0.54 ( 8) hydrogen bonds : bond 0.03702 / 2.59 ( 452) hydrogen bonds : angle 4.82337 / 3.53 ( 1260) Misc. bond : bond 0.00046 / 0.02 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 40 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue ILE 47 is missing expected H atoms. Skipping. Residue LEU 48 is missing expected H atoms. Skipping. Residue MET 51 is missing expected H atoms. Skipping. Residue LYS 216 is missing expected H atoms. Skipping. Residue SER 307 is missing expected H atoms. Skipping. Residue LYS 308 is missing expected H atoms. Skipping. Residue TYR 40 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue ILE 47 is missing expected H atoms. Skipping. Residue LEU 48 is missing expected H atoms. Skipping. Residue MET 51 is missing expected H atoms. Skipping. Residue LYS 216 is missing expected H atoms. Skipping. Residue SER 307 is missing expected H atoms. Skipping. Residue LYS 308 is missing expected H atoms. Skipping. Residue TYR 40 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue ILE 47 is missing expected H atoms. Skipping. Residue LEU 48 is missing expected H atoms. Skipping. Residue MET 51 is missing expected H atoms. Skipping. Residue LYS 216 is missing expected H atoms. Skipping. Residue SER 307 is missing expected H atoms. Skipping. Residue LYS 308 is missing expected H atoms. Skipping. Residue TYR 40 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue ILE 47 is missing expected H atoms. Skipping. Residue LEU 48 is missing expected H atoms. Skipping. Residue MET 51 is missing expected H atoms. Skipping. Residue LYS 216 is missing expected H atoms. Skipping. Residue SER 307 is missing expected H atoms. Skipping. Residue LYS 308 is missing expected H atoms. Skipping. Evaluate side-chains 134 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 124 time to evaluate : 0.493 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 ASN cc_start: 0.6814 (t0) cc_final: 0.6476 (t0) REVERT: B 233 GLU cc_start: 0.8158 (OUTLIER) cc_final: 0.7347 (mt-10) outliers start: 10 outliers final: 9 residues processed: 129 average time/residue: 0.1814 time to fit residues: 35.2144 Evaluate side-chains 131 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 121 time to evaluate : 0.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 169 SER Chi-restraints excluded: chain B residue 21 THR Chi-restraints excluded: chain B residue 23 ASP Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 233 GLU Chi-restraints excluded: chain D residue 21 THR Chi-restraints excluded: chain D residue 23 ASP Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain C residue 74 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 3 optimal weight: 1.9990 chunk 53 optimal weight: 0.9980 chunk 78 optimal weight: 0.9990 chunk 105 optimal weight: 0.7980 chunk 86 optimal weight: 0.0670 chunk 46 optimal weight: 0.6980 chunk 13 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 115 optimal weight: 0.7980 chunk 69 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 overall best weight: 0.6718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 82 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.199211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.154130 restraints weight = 22307.190| |-----------------------------------------------------------------------------| r_work (start): 0.3652 rms_B_bonded: 1.89 r_work: 0.3287 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3092 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.3333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 9490 Z= 0.129 Angle : 0.489 5.473 12953 Z= 0.258 Chirality : 0.041 0.164 1496 Planarity : 0.004 0.033 1620 Dihedral : 5.129 45.473 1267 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 2.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 1.14 % Allowed : 10.37 % Favored : 88.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.31 (0.26), residues: 1176 helix: 2.86 (0.28), residues: 348 sheet: -0.76 (0.34), residues: 228 loop : 0.45 (0.28), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 284 TYR 0.007 0.001 TYR D 218 PHE 0.019 0.002 PHE A 60 TRP 0.004 0.001 TRP C 53 HIS 0.003 0.001 HIS A 264 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.13 ( 9483) covalent geometry : angle 0.48879 / 0.26 (12945) SS BOND : bond 0.00041 / 0.02 ( 4) SS BOND : angle 0.80791 / 0.56 ( 8) hydrogen bonds : bond 0.03596 / 2.52 ( 452) hydrogen bonds : angle 4.75118 / 3.48 ( 1260) Misc. bond : bond 0.00041 / 0.02 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 40 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue ILE 47 is missing expected H atoms. Skipping. Residue LEU 48 is missing expected H atoms. Skipping. Residue MET 51 is missing expected H atoms. Skipping. Residue LYS 216 is missing expected H atoms. Skipping. Residue SER 307 is missing expected H atoms. Skipping. Residue LYS 308 is missing expected H atoms. Skipping. Residue TYR 40 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue ILE 47 is missing expected H atoms. Skipping. Residue LEU 48 is missing expected H atoms. Skipping. Residue MET 51 is missing expected H atoms. Skipping. Residue LYS 216 is missing expected H atoms. Skipping. Residue SER 307 is missing expected H atoms. Skipping. Residue LYS 308 is missing expected H atoms. Skipping. Residue TYR 40 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue ILE 47 is missing expected H atoms. Skipping. Residue LEU 48 is missing expected H atoms. Skipping. Residue MET 51 is missing expected H atoms. Skipping. Residue LYS 216 is missing expected H atoms. Skipping. Residue SER 307 is missing expected H atoms. Skipping. Residue LYS 308 is missing expected H atoms. Skipping. Residue TYR 40 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue ILE 47 is missing expected H atoms. Skipping. Residue LEU 48 is missing expected H atoms. Skipping. Residue MET 51 is missing expected H atoms. Skipping. Residue LYS 216 is missing expected H atoms. Skipping. Residue SER 307 is missing expected H atoms. Skipping. Residue LYS 308 is missing expected H atoms. Skipping. Evaluate side-chains 142 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 131 time to evaluate : 0.533 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 ASN cc_start: 0.6727 (t0) cc_final: 0.6313 (t0) REVERT: B 233 GLU cc_start: 0.8104 (OUTLIER) cc_final: 0.7293 (mt-10) outliers start: 11 outliers final: 9 residues processed: 136 average time/residue: 0.1786 time to fit residues: 36.1753 Evaluate side-chains 132 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 122 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ASP Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 113 SER Chi-restraints excluded: chain A residue 169 SER Chi-restraints excluded: chain B residue 21 THR Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 233 GLU Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain C residue 23 ASP Chi-restraints excluded: chain C residue 74 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 82 optimal weight: 0.9980 chunk 77 optimal weight: 0.9990 chunk 5 optimal weight: 3.9990 chunk 3 optimal weight: 1.9990 chunk 81 optimal weight: 3.9990 chunk 88 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 114 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 1 optimal weight: 6.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.194159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.153039 restraints weight = 22897.401| |-----------------------------------------------------------------------------| r_work (start): 0.3635 rms_B_bonded: 1.74 r_work: 0.3242 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.3550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.049 9490 Z= 0.298 Angle : 0.609 5.315 12953 Z= 0.326 Chirality : 0.045 0.160 1496 Planarity : 0.005 0.043 1620 Dihedral : 5.572 45.016 1267 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 1.66 % Allowed : 10.37 % Favored : 87.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.95 (0.26), residues: 1176 helix: 2.60 (0.28), residues: 348 sheet: -0.80 (0.36), residues: 228 loop : 0.12 (0.28), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 284 TYR 0.008 0.002 TYR B 218 PHE 0.023 0.003 PHE A 60 TRP 0.005 0.001 TRP C 53 HIS 0.005 0.001 HIS A 245 Details of bonding type rmsd/Z covalent geometry : bond 0.00726 / 0.30 ( 9483) covalent geometry : angle 0.60883 / 0.33 (12945) SS BOND : bond 0.00095 / 0.05 ( 4) SS BOND : angle 1.13883 / 0.78 ( 8) hydrogen bonds : bond 0.04146 / 2.89 ( 452) hydrogen bonds : angle 5.07673 / 3.72 ( 1260) Misc. bond : bond 0.00045 / 0.02 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 40 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue ILE 47 is missing expected H atoms. Skipping. Residue LEU 48 is missing expected H atoms. Skipping. Residue MET 51 is missing expected H atoms. Skipping. Residue LYS 216 is missing expected H atoms. Skipping. Residue SER 307 is missing expected H atoms. Skipping. Residue LYS 308 is missing expected H atoms. Skipping. Residue TYR 40 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue ILE 47 is missing expected H atoms. Skipping. Residue LEU 48 is missing expected H atoms. Skipping. Residue MET 51 is missing expected H atoms. Skipping. Residue LYS 216 is missing expected H atoms. Skipping. Residue SER 307 is missing expected H atoms. Skipping. Residue LYS 308 is missing expected H atoms. Skipping. Residue TYR 40 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue ILE 47 is missing expected H atoms. Skipping. Residue LEU 48 is missing expected H atoms. Skipping. Residue MET 51 is missing expected H atoms. Skipping. Residue LYS 216 is missing expected H atoms. Skipping. Residue SER 307 is missing expected H atoms. Skipping. Residue LYS 308 is missing expected H atoms. Skipping. Residue TYR 40 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue ILE 47 is missing expected H atoms. Skipping. Residue LEU 48 is missing expected H atoms. Skipping. Residue MET 51 is missing expected H atoms. Skipping. Residue LYS 216 is missing expected H atoms. Skipping. Residue SER 307 is missing expected H atoms. Skipping. Residue LYS 308 is missing expected H atoms. Skipping. Evaluate side-chains 137 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 121 time to evaluate : 0.514 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 ASN cc_start: 0.7054 (t0) cc_final: 0.6628 (t0) REVERT: A 283 GLN cc_start: 0.7359 (mt0) cc_final: 0.6810 (tt0) REVERT: B 233 GLU cc_start: 0.8063 (OUTLIER) cc_final: 0.7192 (mt-10) REVERT: C 82 ASN cc_start: 0.6885 (t0) cc_final: 0.6675 (t0) outliers start: 16 outliers final: 11 residues processed: 129 average time/residue: 0.1626 time to fit residues: 31.8970 Evaluate side-chains 132 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 120 time to evaluate : 0.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 113 SER Chi-restraints excluded: chain A residue 169 SER Chi-restraints excluded: chain A residue 239 PHE Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 169 SER Chi-restraints excluded: chain B residue 233 GLU Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain D residue 169 SER Chi-restraints excluded: chain D residue 239 PHE Chi-restraints excluded: chain C residue 169 SER Chi-restraints excluded: chain C residue 239 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 78 optimal weight: 0.0370 chunk 87 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 chunk 67 optimal weight: 0.9980 chunk 90 optimal weight: 1.9990 chunk 57 optimal weight: 3.9990 chunk 10 optimal weight: 0.6980 chunk 95 optimal weight: 0.6980 chunk 16 optimal weight: 0.6980 chunk 37 optimal weight: 0.9980 chunk 100 optimal weight: 0.3980 overall best weight: 0.5058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.198375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.154054 restraints weight = 22534.379| |-----------------------------------------------------------------------------| r_work (start): 0.3644 rms_B_bonded: 1.99 r_work: 0.3258 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.3596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 9490 Z= 0.123 Angle : 0.499 5.101 12953 Z= 0.264 Chirality : 0.041 0.153 1496 Planarity : 0.004 0.037 1620 Dihedral : 5.177 45.208 1267 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 0.73 % Allowed : 11.41 % Favored : 87.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.15 (0.27), residues: 1176 helix: 2.85 (0.28), residues: 348 sheet: -0.84 (0.35), residues: 236 loop : 0.28 (0.29), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 18 TYR 0.009 0.001 TYR D 218 PHE 0.018 0.002 PHE A 60 TRP 0.004 0.001 TRP A 55 HIS 0.004 0.001 HIS D 245 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.12 ( 9483) covalent geometry : angle 0.49872 / 0.26 (12945) SS BOND : bond 0.00043 / 0.02 ( 4) SS BOND : angle 0.73158 / 0.52 ( 8) hydrogen bonds : bond 0.03596 / 2.51 ( 452) hydrogen bonds : angle 4.87247 / 3.57 ( 1260) Misc. bond : bond 0.00046 / 0.02 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 40 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue ILE 47 is missing expected H atoms. Skipping. Residue LEU 48 is missing expected H atoms. Skipping. Residue MET 51 is missing expected H atoms. Skipping. Residue LYS 216 is missing expected H atoms. Skipping. Residue SER 307 is missing expected H atoms. Skipping. Residue LYS 308 is missing expected H atoms. Skipping. Residue TYR 40 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue ILE 47 is missing expected H atoms. Skipping. Residue LEU 48 is missing expected H atoms. Skipping. Residue MET 51 is missing expected H atoms. Skipping. Residue LYS 216 is missing expected H atoms. Skipping. Residue SER 307 is missing expected H atoms. Skipping. Residue LYS 308 is missing expected H atoms. Skipping. Residue TYR 40 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue ILE 47 is missing expected H atoms. Skipping. Residue LEU 48 is missing expected H atoms. Skipping. Residue MET 51 is missing expected H atoms. Skipping. Residue LYS 216 is missing expected H atoms. Skipping. Residue SER 307 is missing expected H atoms. Skipping. Residue LYS 308 is missing expected H atoms. Skipping. Residue TYR 40 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue ILE 47 is missing expected H atoms. Skipping. Residue LEU 48 is missing expected H atoms. Skipping. Residue MET 51 is missing expected H atoms. Skipping. Residue LYS 216 is missing expected H atoms. Skipping. Residue SER 307 is missing expected H atoms. Skipping. Residue LYS 308 is missing expected H atoms. Skipping. Evaluate side-chains 122 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 115 time to evaluate : 0.492 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 ASN cc_start: 0.6982 (t0) cc_final: 0.6511 (t0) REVERT: A 96 HIS cc_start: 0.7321 (t-170) cc_final: 0.6804 (t-170) REVERT: B 233 GLU cc_start: 0.7943 (OUTLIER) cc_final: 0.7075 (mt-10) outliers start: 7 outliers final: 4 residues processed: 119 average time/residue: 0.1895 time to fit residues: 33.2197 Evaluate side-chains 116 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 111 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 113 SER Chi-restraints excluded: chain A residue 239 PHE Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 233 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 23 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 87 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 113 optimal weight: 0.9990 chunk 77 optimal weight: 0.2980 chunk 16 optimal weight: 0.4980 chunk 72 optimal weight: 1.9990 chunk 73 optimal weight: 0.9990 overall best weight: 0.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 82 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.197604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.153476 restraints weight = 22557.681| |-----------------------------------------------------------------------------| r_work (start): 0.3647 rms_B_bonded: 1.85 r_work: 0.3258 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.3699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 9490 Z= 0.145 Angle : 0.504 5.036 12953 Z= 0.266 Chirality : 0.041 0.149 1496 Planarity : 0.004 0.035 1620 Dihedral : 5.059 45.802 1267 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.04 % Allowed : 11.41 % Favored : 87.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.18 (0.27), residues: 1176 helix: 2.90 (0.28), residues: 348 sheet: -0.82 (0.35), residues: 236 loop : 0.27 (0.29), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 18 TYR 0.006 0.001 TYR D 218 PHE 0.019 0.002 PHE A 60 TRP 0.003 0.001 TRP C 53 HIS 0.003 0.001 HIS C 245 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.15 ( 9483) covalent geometry : angle 0.50406 / 0.27 (12945) SS BOND : bond 0.00070 / 0.04 ( 4) SS BOND : angle 0.87599 / 0.61 ( 8) hydrogen bonds : bond 0.03570 / 2.50 ( 452) hydrogen bonds : angle 4.80971 / 3.52 ( 1260) Misc. bond : bond 0.00039 / 0.02 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 40 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue ILE 47 is missing expected H atoms. Skipping. Residue LEU 48 is missing expected H atoms. Skipping. Residue MET 51 is missing expected H atoms. Skipping. Residue LYS 216 is missing expected H atoms. Skipping. Residue SER 307 is missing expected H atoms. Skipping. Residue LYS 308 is missing expected H atoms. Skipping. Residue TYR 40 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue ILE 47 is missing expected H atoms. Skipping. Residue LEU 48 is missing expected H atoms. Skipping. Residue MET 51 is missing expected H atoms. Skipping. Residue LYS 216 is missing expected H atoms. Skipping. Residue SER 307 is missing expected H atoms. Skipping. Residue LYS 308 is missing expected H atoms. Skipping. Residue TYR 40 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue ILE 47 is missing expected H atoms. Skipping. Residue LEU 48 is missing expected H atoms. Skipping. Residue MET 51 is missing expected H atoms. Skipping. Residue LYS 216 is missing expected H atoms. Skipping. Residue SER 307 is missing expected H atoms. Skipping. Residue LYS 308 is missing expected H atoms. Skipping. Residue TYR 40 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue ILE 47 is missing expected H atoms. Skipping. Residue LEU 48 is missing expected H atoms. Skipping. Residue MET 51 is missing expected H atoms. Skipping. Residue LYS 216 is missing expected H atoms. Skipping. Residue SER 307 is missing expected H atoms. Skipping. Residue LYS 308 is missing expected H atoms. Skipping. Evaluate side-chains 126 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 116 time to evaluate : 0.519 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 ASN cc_start: 0.7089 (t0) cc_final: 0.6609 (t0) REVERT: A 96 HIS cc_start: 0.7310 (t-170) cc_final: 0.6848 (t-170) REVERT: B 233 GLU cc_start: 0.8022 (OUTLIER) cc_final: 0.7178 (mt-10) outliers start: 10 outliers final: 8 residues processed: 119 average time/residue: 0.1762 time to fit residues: 30.8721 Evaluate side-chains 125 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 116 time to evaluate : 0.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 113 SER Chi-restraints excluded: chain A residue 169 SER Chi-restraints excluded: chain A residue 239 PHE Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 233 GLU Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain D residue 239 PHE Chi-restraints excluded: chain C residue 239 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 62 optimal weight: 2.9990 chunk 63 optimal weight: 0.9980 chunk 4 optimal weight: 1.9990 chunk 31 optimal weight: 7.9990 chunk 75 optimal weight: 0.9990 chunk 38 optimal weight: 0.8980 chunk 36 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 chunk 35 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 96 optimal weight: 0.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 82 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.195944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.150685 restraints weight = 22581.021| |-----------------------------------------------------------------------------| r_work (start): 0.3613 rms_B_bonded: 1.86 r_work: 0.3245 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.3813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 9490 Z= 0.167 Angle : 0.526 6.550 12953 Z= 0.275 Chirality : 0.041 0.138 1496 Planarity : 0.004 0.035 1620 Dihedral : 5.071 45.505 1267 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 0.93 % Allowed : 11.62 % Favored : 87.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.10 (0.27), residues: 1176 helix: 2.89 (0.28), residues: 348 sheet: -0.82 (0.35), residues: 236 loop : 0.16 (0.28), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 18 TYR 0.007 0.001 TYR D 218 PHE 0.019 0.002 PHE C 60 TRP 0.003 0.001 TRP A 55 HIS 0.003 0.001 HIS D 245 Details of bonding type rmsd/Z covalent geometry : bond 0.00404 / 0.17 ( 9483) covalent geometry : angle 0.52584 / 0.27 (12945) SS BOND : bond 0.00068 / 0.03 ( 4) SS BOND : angle 0.92612 / 0.64 ( 8) hydrogen bonds : bond 0.03619 / 2.53 ( 452) hydrogen bonds : angle 4.83325 / 3.54 ( 1260) Misc. bond : bond 0.00041 / 0.02 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 40 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue ILE 47 is missing expected H atoms. Skipping. Residue LEU 48 is missing expected H atoms. Skipping. Residue MET 51 is missing expected H atoms. Skipping. Residue LYS 216 is missing expected H atoms. Skipping. Residue SER 307 is missing expected H atoms. Skipping. Residue LYS 308 is missing expected H atoms. Skipping. Residue TYR 40 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue ILE 47 is missing expected H atoms. Skipping. Residue LEU 48 is missing expected H atoms. Skipping. Residue MET 51 is missing expected H atoms. Skipping. Residue LYS 216 is missing expected H atoms. Skipping. Residue SER 307 is missing expected H atoms. Skipping. Residue LYS 308 is missing expected H atoms. Skipping. Residue TYR 40 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue ILE 47 is missing expected H atoms. Skipping. Residue LEU 48 is missing expected H atoms. Skipping. Residue MET 51 is missing expected H atoms. Skipping. Residue LYS 216 is missing expected H atoms. Skipping. Residue SER 307 is missing expected H atoms. Skipping. Residue LYS 308 is missing expected H atoms. Skipping. Residue TYR 40 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue ILE 47 is missing expected H atoms. Skipping. Residue LEU 48 is missing expected H atoms. Skipping. Residue MET 51 is missing expected H atoms. Skipping. Residue LYS 216 is missing expected H atoms. Skipping. Residue SER 307 is missing expected H atoms. Skipping. Residue LYS 308 is missing expected H atoms. Skipping. Evaluate side-chains 125 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 116 time to evaluate : 0.421 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 ASN cc_start: 0.7111 (t0) cc_final: 0.6648 (t0) REVERT: A 96 HIS cc_start: 0.7265 (t-170) cc_final: 0.6856 (t-170) REVERT: B 233 GLU cc_start: 0.8048 (OUTLIER) cc_final: 0.7205 (mt-10) REVERT: C 82 ASN cc_start: 0.6870 (t0) cc_final: 0.6453 (t0) outliers start: 9 outliers final: 8 residues processed: 119 average time/residue: 0.1690 time to fit residues: 29.3340 Evaluate side-chains 124 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 115 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 113 SER Chi-restraints excluded: chain A residue 169 SER Chi-restraints excluded: chain A residue 239 PHE Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 233 GLU Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain D residue 239 PHE Chi-restraints excluded: chain C residue 239 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 96 optimal weight: 1.9990 chunk 47 optimal weight: 0.9990 chunk 40 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 92 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 104 optimal weight: 0.5980 chunk 57 optimal weight: 0.0470 chunk 14 optimal weight: 1.9990 chunk 24 optimal weight: 0.6980 chunk 21 optimal weight: 0.8980 overall best weight: 0.6480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.200108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.151081 restraints weight = 22477.873| |-----------------------------------------------------------------------------| r_work (start): 0.3652 rms_B_bonded: 2.05 r_work: 0.3293 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.3874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 9490 Z= 0.127 Angle : 0.492 5.671 12953 Z= 0.256 Chirality : 0.041 0.130 1496 Planarity : 0.004 0.035 1620 Dihedral : 4.881 45.369 1267 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 0.83 % Allowed : 11.72 % Favored : 87.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.22 (0.27), residues: 1176 helix: 2.98 (0.28), residues: 348 sheet: -0.81 (0.34), residues: 236 loop : 0.27 (0.28), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 285 TYR 0.007 0.001 TYR B 218 PHE 0.018 0.001 PHE A 60 TRP 0.004 0.001 TRP D 55 HIS 0.003 0.001 HIS B 245 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.13 ( 9483) covalent geometry : angle 0.49172 / 0.26 (12945) SS BOND : bond 0.00056 / 0.03 ( 4) SS BOND : angle 0.80109 / 0.55 ( 8) hydrogen bonds : bond 0.03428 / 2.41 ( 452) hydrogen bonds : angle 4.73248 / 3.46 ( 1260) Misc. bond : bond 0.00040 / 0.02 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3971.48 seconds wall clock time: 68 minutes 7.69 seconds (4087.69 seconds total)