Starting phenix.real_space_refine on Wed Mar 4 16:44:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7uze_26886/03_2026/7uze_26886_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7uze_26886/03_2026/7uze_26886.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7uze_26886/03_2026/7uze_26886.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7uze_26886/03_2026/7uze_26886.map" model { file = "/net/cci-nas-00/data/ceres_data/7uze_26886/03_2026/7uze_26886_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7uze_26886/03_2026/7uze_26886_trim.cif" } resolution = 2.4 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= 0.006 sd= 0.357 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: 5 Type Number sf(0) Gaussians S 20 5.16 5 C 4884 2.51 5 N 1264 2.21 5 O 1409 1.98 5 H 7528 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15105 Number of models: 1 Model: "" Number of chains: 12 Chain: "D" Number of atoms: 3720 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 247, 3695 Classifications: {'peptide': 247} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 240} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'P1L:plan-1': 1, 'ASP:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 11 Conformer: "B" Number of residues, atoms: 247, 3695 Classifications: {'peptide': 247} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 240} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'P1L:plan-1': 1, 'ASP:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 11 bond proxies already assigned to first conformer: 3704 Chain: "B" Number of atoms: 3720 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 247, 3695 Classifications: {'peptide': 247} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 240} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'P1L:plan-1': 1, 'ASP:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 11 Conformer: "B" Number of residues, atoms: 247, 3695 Classifications: {'peptide': 247} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 240} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'P1L:plan-1': 1, 'ASP:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 11 bond proxies already assigned to first conformer: 3704 Chain: "C" Number of atoms: 3720 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 247, 3695 Classifications: {'peptide': 247} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 240} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'P1L:plan-1': 1, 'ASP:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 11 Conformer: "B" Number of residues, atoms: 247, 3695 Classifications: {'peptide': 247} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 240} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'P1L:plan-1': 1, 'ASP:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 11 bond proxies already assigned to first conformer: 3704 Chain: "A" Number of atoms: 3720 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 247, 3695 Classifications: {'peptide': 247} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 240} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'P1L:plan-1': 1, 'ASP:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 11 Conformer: "B" Number of residues, atoms: 247, 3695 Classifications: {'peptide': 247} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 240} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'P1L:plan-1': 1, 'ASP:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 11 bond proxies already assigned to first conformer: 3704 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 28 Classifications: {'water': 28} Link IDs: {None: 27} Chain: "B" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 29 Classifications: {'water': 29} Link IDs: {None: 28} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 28 Classifications: {'water': 28} Link IDs: {None: 27} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 28 Classifications: {'water': 28} Link IDs: {None: 27} Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N AARG D 234 " occ=0.48 ... (46 atoms not shown) pdb="HH22BARG D 234 " occ=0.52 residue: pdb=" N AARG B 234 " occ=0.50 ... (46 atoms not shown) pdb="HH22BARG B 234 " occ=0.50 residue: pdb=" N AARG C 234 " occ=0.50 ... (46 atoms not shown) pdb="HH22BARG C 234 " occ=0.50 residue: pdb=" N AARG A 234 " occ=0.51 ... (46 atoms not shown) pdb="HH22BARG A 234 " occ=0.49 Time building chain proxies: 4.60, per 1000 atoms: 0.30 Number of scatterers: 15105 At special positions: 0 Unit cell: (70.55, 90.885, 90.885, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 20 16.00 O 1409 8.00 N 1264 7.00 C 4884 6.00 H 7528 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.10 Conformation dependent library (CDL) restraints added in 632.8 milliseconds 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1768 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 0 sheets defined 76.9% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.33 Creating SS restraints... Processing helix chain 'D' and resid 3 through 6 Processing helix chain 'D' and resid 7 through 33 removed outlier: 3.508A pdb=" N TRP D 11 " --> pdb=" O LYS D 7 " (cutoff:3.500A) Processing helix chain 'D' and resid 34 through 37 Processing helix chain 'D' and resid 48 through 72 removed outlier: 5.737A pdb=" N HIS D 69 " --> pdb=" O GLN D 65 " (cutoff:3.500A) removed outlier: 5.816A pdb=" N ILE D 70 " --> pdb=" O SER D 66 " (cutoff:3.500A) Processing helix chain 'D' and resid 76 through 86 Processing helix chain 'D' and resid 90 through 116 Processing helix chain 'D' and resid 134 through 157 Processing helix chain 'D' and resid 167 through 188 removed outlier: 5.628A pdb=" N ASP D 185 " --> pdb=" O LEU D 181 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N TYR D 186 " --> pdb=" O LEU D 182 " (cutoff:3.500A) Processing helix chain 'D' and resid 192 through 204 removed outlier: 3.699A pdb=" N SER D 199 " --> pdb=" O ARG D 195 " (cutoff:3.500A) Processing helix chain 'D' and resid 210 through 230 Proline residue: D 216 - end of helix Processing helix chain 'D' and resid 237 through 248 removed outlier: 3.611A pdb=" N LYS D 243 " --> pdb=" O THR D 239 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N VAL D 244 " --> pdb=" O ASP D 240 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N TRP D 245 " --> pdb=" O ARG D 241 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N THR D 246 " --> pdb=" O VAL D 242 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 6 Processing helix chain 'B' and resid 7 through 33 removed outlier: 3.509A pdb=" N TRP B 11 " --> pdb=" O LYS B 7 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 37 Processing helix chain 'B' and resid 48 through 72 removed outlier: 5.686A pdb=" N HIS B 69 " --> pdb=" O GLN B 65 " (cutoff:3.500A) removed outlier: 5.796A pdb=" N ILE B 70 " --> pdb=" O SER B 66 " (cutoff:3.500A) Processing helix chain 'B' and resid 76 through 86 Processing helix chain 'B' and resid 90 through 116 Processing helix chain 'B' and resid 134 through 157 Processing helix chain 'B' and resid 167 through 188 removed outlier: 5.611A pdb=" N ASP B 185 " --> pdb=" O LEU B 181 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N TYR B 186 " --> pdb=" O LEU B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 192 through 204 removed outlier: 3.694A pdb=" N SER B 199 " --> pdb=" O ARG B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 210 through 230 Proline residue: B 216 - end of helix Processing helix chain 'B' and resid 237 through 248 removed outlier: 3.610A pdb=" N LYS B 243 " --> pdb=" O THR B 239 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N VAL B 244 " --> pdb=" O ASP B 240 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N TRP B 245 " --> pdb=" O ARG B 241 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N THR B 246 " --> pdb=" O VAL B 242 " (cutoff:3.500A) Processing helix chain 'C' and resid 3 through 6 Processing helix chain 'C' and resid 7 through 33 removed outlier: 3.514A pdb=" N TRP C 11 " --> pdb=" O LYS C 7 " (cutoff:3.500A) Processing helix chain 'C' and resid 34 through 37 Processing helix chain 'C' and resid 48 through 72 removed outlier: 5.736A pdb=" N HIS C 69 " --> pdb=" O GLN C 65 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N ILE C 70 " --> pdb=" O SER C 66 " (cutoff:3.500A) Processing helix chain 'C' and resid 76 through 86 Processing helix chain 'C' and resid 90 through 116 Processing helix chain 'C' and resid 134 through 157 Processing helix chain 'C' and resid 167 through 188 removed outlier: 5.633A pdb=" N ASP C 185 " --> pdb=" O LEU C 181 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N TYR C 186 " --> pdb=" O LEU C 182 " (cutoff:3.500A) Processing helix chain 'C' and resid 192 through 204 removed outlier: 3.707A pdb=" N SER C 199 " --> pdb=" O ARG C 195 " (cutoff:3.500A) Processing helix chain 'C' and resid 210 through 230 Proline residue: C 216 - end of helix Processing helix chain 'C' and resid 237 through 248 removed outlier: 3.626A pdb=" N LYS C 243 " --> pdb=" O THR C 239 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N VAL C 244 " --> pdb=" O ASP C 240 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N TRP C 245 " --> pdb=" O ARG C 241 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N THR C 246 " --> pdb=" O VAL C 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 3 through 6 Processing helix chain 'A' and resid 7 through 33 removed outlier: 3.509A pdb=" N TRP A 11 " --> pdb=" O LYS A 7 " (cutoff:3.500A) Processing helix chain 'A' and resid 34 through 37 Processing helix chain 'A' and resid 48 through 72 removed outlier: 5.726A pdb=" N HIS A 69 " --> pdb=" O GLN A 65 " (cutoff:3.500A) removed outlier: 5.800A pdb=" N ILE A 70 " --> pdb=" O SER A 66 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 86 Processing helix chain 'A' and resid 90 through 116 Processing helix chain 'A' and resid 134 through 157 Processing helix chain 'A' and resid 167 through 188 removed outlier: 5.618A pdb=" N ASP A 185 " --> pdb=" O LEU A 181 " (cutoff:3.500A) removed outlier: 4.894A pdb=" N TYR A 186 " --> pdb=" O LEU A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 204 removed outlier: 3.690A pdb=" N SER A 199 " --> pdb=" O ARG A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 230 Proline residue: A 216 - end of helix Processing helix chain 'A' and resid 237 through 248 removed outlier: 3.612A pdb=" N LYS A 243 " --> pdb=" O THR A 239 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N VAL A 244 " --> pdb=" O ASP A 240 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N TRP A 245 " --> pdb=" O ARG A 241 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N THR A 246 " --> pdb=" O VAL A 242 " (cutoff:3.500A) 540 hydrogen bonds defined for protein. 1596 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: 3.57 Time building geometry restraints manager: 1.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 7380 1.03 - 1.23: 162 1.23 - 1.42: 3074 1.42 - 1.62: 4504 1.62 - 1.81: 28 Bond restraints: 15148 Sorted by residual: bond pdb=" CA CYS C 189 " pdb=" C CYS C 189 " ideal model delta sigma weight residual 1.532 1.520 0.012 9.60e-03 1.09e+04 1.68e+00 bond pdb=" CA CYS A 189 " pdb=" C CYS A 189 " ideal model delta sigma weight residual 1.532 1.521 0.012 9.60e-03 1.09e+04 1.52e+00 bond pdb=" CA CYS B 189 " pdb=" C CYS B 189 " ideal model delta sigma weight residual 1.532 1.521 0.011 9.60e-03 1.09e+04 1.37e+00 bond pdb=" CG PRO D 38 " pdb=" CD PRO D 38 " ideal model delta sigma weight residual 1.512 1.492 0.020 2.70e-02 1.37e+03 5.60e-01 bond pdb=" CA ILE D 191 " pdb=" CB ILE D 191 " ideal model delta sigma weight residual 1.540 1.550 -0.010 1.36e-02 5.41e+03 5.21e-01 ... (remaining 15143 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.47: 26731 1.47 - 2.93: 563 2.93 - 4.40: 52 4.40 - 5.87: 16 5.87 - 7.33: 2 Bond angle restraints: 27364 Sorted by residual: angle pdb=" CA CYS D 189 " pdb=" CB CYS D 189 " pdb=" SG CYS D 189 " ideal model delta sigma weight residual 114.40 107.07 7.33 2.30e+00 1.89e-01 1.02e+01 angle pdb=" N GLY D 190 " pdb=" CA GLY D 190 " pdb=" C GLY D 190 " ideal model delta sigma weight residual 113.18 107.15 6.03 2.37e+00 1.78e-01 6.47e+00 angle pdb=" CA CYS A 189 " pdb=" C CYS A 189 " pdb=" N GLY A 190 " ideal model delta sigma weight residual 114.17 117.70 -3.53 1.45e+00 4.76e-01 5.92e+00 angle pdb=" CA CYS B 189 " pdb=" C CYS B 189 " pdb=" N GLY B 190 " ideal model delta sigma weight residual 114.17 117.63 -3.46 1.45e+00 4.76e-01 5.70e+00 angle pdb=" CA CYS C 189 " pdb=" C CYS C 189 " pdb=" N GLY C 190 " ideal model delta sigma weight residual 114.17 117.63 -3.46 1.45e+00 4.76e-01 5.68e+00 ... (remaining 27359 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.78: 6836 26.78 - 53.56: 346 53.56 - 80.35: 79 80.35 - 107.13: 7 107.13 - 133.91: 4 Dihedral angle restraints: 7272 sinusoidal: 4016 harmonic: 3256 Sorted by residual: dihedral pdb=" CA LEU B 182 " pdb=" C LEU B 182 " pdb=" N ALA B 183 " pdb=" CA ALA B 183 " ideal model delta harmonic sigma weight residual -180.00 -157.21 -22.79 0 5.00e+00 4.00e-02 2.08e+01 dihedral pdb=" CA LEU A 182 " pdb=" C LEU A 182 " pdb=" N ALA A 183 " pdb=" CA ALA A 183 " ideal model delta harmonic sigma weight residual -180.00 -157.53 -22.47 0 5.00e+00 4.00e-02 2.02e+01 dihedral pdb=" CA LEU C 182 " pdb=" C LEU C 182 " pdb=" N ALA C 183 " pdb=" CA ALA C 183 " ideal model delta harmonic sigma weight residual -180.00 -157.83 -22.17 0 5.00e+00 4.00e-02 1.97e+01 ... (remaining 7269 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 828 0.031 - 0.061: 313 0.061 - 0.092: 101 0.092 - 0.123: 21 0.123 - 0.153: 5 Chirality restraints: 1268 Sorted by residual: chirality pdb=" CA CYS D 189 " pdb=" N CYS D 189 " pdb=" C CYS D 189 " pdb=" CB CYS D 189 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.88e-01 chirality pdb=" CA VAL B 133 " pdb=" N VAL B 133 " pdb=" C VAL B 133 " pdb=" CB VAL B 133 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 3.99e-01 chirality pdb=" CA VAL D 133 " pdb=" N VAL D 133 " pdb=" C VAL D 133 " pdb=" CB VAL D 133 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 3.99e-01 ... (remaining 1265 not shown) Planarity restraints: 2236 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE A 191 " 0.006 2.00e-02 2.50e+03 1.16e-02 1.34e+00 pdb=" C ILE A 191 " -0.020 2.00e-02 2.50e+03 pdb=" O ILE A 191 " 0.008 2.00e-02 2.50e+03 pdb=" N ASN A 192 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN B 76 " 0.019 5.00e-02 4.00e+02 2.88e-02 1.33e+00 pdb=" N PRO B 77 " -0.050 5.00e-02 4.00e+02 pdb=" CA PRO B 77 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO B 77 " 0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU C 225 " 0.006 2.00e-02 2.50e+03 1.15e-02 1.31e+00 pdb=" C LEU C 225 " -0.020 2.00e-02 2.50e+03 pdb=" O LEU C 225 " 0.007 2.00e-02 2.50e+03 pdb=" N ILE C 226 " 0.007 2.00e-02 2.50e+03 ... (remaining 2233 not shown) Histogram of nonbonded interaction distances: 1.66 - 2.25: 1833 2.25 - 2.84: 34939 2.84 - 3.42: 44117 3.42 - 4.01: 61072 4.01 - 4.60: 92691 Nonbonded interactions: 234652 Sorted by model distance: nonbonded pdb=" HH TYR D 186 " pdb=" O GLY C 30 " model vdw 1.661 2.450 nonbonded pdb=" HH TYR C 186 " pdb=" O GLY A 30 " model vdw 1.664 2.450 nonbonded pdb=" O GLY D 30 " pdb=" HH TYR B 186 " model vdw 1.671 2.450 nonbonded pdb=" O GLY B 30 " pdb=" HH TYR A 186 " model vdw 1.674 2.450 nonbonded pdb=" HE ARG B 195 " pdb=" O HOH B 406 " model vdw 1.742 2.450 ... (remaining 234647 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 Found NCS groups: ncs_group { reference = chain 'D' selection = chain 'B' selection = chain 'C' selection = chain 'A' } 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=0.48 max=1.00 mean=0.99 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: 0.770 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.070 Extract box with map and model: 0.300 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 17.190 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:5.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8695 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 : 0.003 0.022 7620 Z= 0.156 Angle : 0.584 7.334 10392 Z= 0.313 Chirality : 0.037 0.153 1268 Planarity : 0.003 0.029 1272 Dihedral : 14.965 89.846 2816 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.41 % Allowed : 3.00 % Favored : 96.59 % Rotamer: Outliers : 0.68 % Allowed : 14.86 % Favored : 84.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 1.69 (0.26), residues: 980 helix: 1.85 (0.19), residues: 644 sheet: None (None), residues: 0 loop : -0.25 (0.36), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 161 TYR 0.010 0.002 TYR D 227 PHE 0.018 0.002 PHE D 212 TRP 0.004 0.001 TRP C 11 HIS 0.004 0.001 HIS B 180 Details of bonding type rmsd covalent geometry : bond 0.00315 ( 7620) covalent geometry : angle 0.58386 (10392) hydrogen bonds : bond 0.09906 ( 540) hydrogen bonds : angle 6.24330 ( 1596) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 3 is missing expected H atoms. Skipping. Residue LYS 6 is missing expected H atoms. Skipping. Residue SER 236 is missing expected H atoms. Skipping. Residue THR 239 is missing expected H atoms. Skipping. Residue LYS 243 is missing expected H atoms. Skipping. Residue SER 247 is missing expected H atoms. Skipping. Residue SER 3 is missing expected H atoms. Skipping. Residue LYS 6 is missing expected H atoms. Skipping. Residue SER 236 is missing expected H atoms. Skipping. Residue THR 239 is missing expected H atoms. Skipping. Residue LYS 243 is missing expected H atoms. Skipping. Residue SER 247 is missing expected H atoms. Skipping. Residue SER 3 is missing expected H atoms. Skipping. Residue LYS 6 is missing expected H atoms. Skipping. Residue SER 236 is missing expected H atoms. Skipping. Residue THR 239 is missing expected H atoms. Skipping. Residue LYS 243 is missing expected H atoms. Skipping. Residue SER 247 is missing expected H atoms. Skipping. Residue SER 3 is missing expected H atoms. Skipping. Residue LYS 6 is missing expected H atoms. Skipping. Residue SER 236 is missing expected H atoms. Skipping. Residue THR 239 is missing expected H atoms. Skipping. Residue LYS 243 is missing expected H atoms. Skipping. Residue SER 247 is missing expected H atoms. Skipping. Evaluate side-chains 76 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 71 time to evaluate : 0.381 Fit side-chains outliers start: 5 outliers final: 4 residues processed: 76 average time/residue: 1.1248 time to fit residues: 90.7281 Evaluate side-chains 72 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 68 time to evaluate : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 242 VAL Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain A residue 242 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 49 optimal weight: 10.0000 chunk 53 optimal weight: 10.0000 chunk 5 optimal weight: 10.0000 chunk 33 optimal weight: 8.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 5.9990 chunk 38 optimal weight: 0.9980 chunk 61 optimal weight: 2.9990 chunk 45 optimal weight: 0.9990 chunk 74 optimal weight: 7.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 88 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.113575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.096847 restraints weight = 49247.283| |-----------------------------------------------------------------------------| r_work (start): 0.2978 rms_B_bonded: 1.82 r_work: 0.2906 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2804 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.2804 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2800 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2800 r_free = 0.2800 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2800 r_free = 0.2800 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2800 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8687 moved from start: 0.0475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 7620 Z= 0.138 Angle : 0.537 7.306 10392 Z= 0.289 Chirality : 0.037 0.148 1268 Planarity : 0.004 0.031 1272 Dihedral : 7.980 52.209 1376 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.41 % Allowed : 2.69 % Favored : 96.90 % Rotamer: Outliers : 2.30 % Allowed : 13.38 % Favored : 84.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 1.97 (0.26), residues: 980 helix: 2.15 (0.19), residues: 644 sheet: None (None), residues: 0 loop : -0.36 (0.35), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 161 TYR 0.009 0.001 TYR D 227 PHE 0.016 0.001 PHE A 212 TRP 0.004 0.001 TRP A 11 HIS 0.004 0.001 HIS C 180 Details of bonding type rmsd covalent geometry : bond 0.00275 ( 7620) covalent geometry : angle 0.53663 (10392) hydrogen bonds : bond 0.04640 ( 540) hydrogen bonds : angle 5.39703 ( 1596) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 3 is missing expected H atoms. Skipping. Residue LYS 6 is missing expected H atoms. Skipping. Residue SER 236 is missing expected H atoms. Skipping. Residue THR 239 is missing expected H atoms. Skipping. Residue LYS 243 is missing expected H atoms. Skipping. Residue SER 247 is missing expected H atoms. Skipping. Residue SER 3 is missing expected H atoms. Skipping. Residue LYS 6 is missing expected H atoms. Skipping. Residue SER 236 is missing expected H atoms. Skipping. Residue THR 239 is missing expected H atoms. Skipping. Residue LYS 243 is missing expected H atoms. Skipping. Residue SER 247 is missing expected H atoms. Skipping. Residue SER 3 is missing expected H atoms. Skipping. Residue LYS 6 is missing expected H atoms. Skipping. Residue SER 236 is missing expected H atoms. Skipping. Residue THR 239 is missing expected H atoms. Skipping. Residue LYS 243 is missing expected H atoms. Skipping. Residue SER 247 is missing expected H atoms. Skipping. Residue SER 3 is missing expected H atoms. Skipping. Residue LYS 6 is missing expected H atoms. Skipping. Residue SER 236 is missing expected H atoms. Skipping. Residue THR 239 is missing expected H atoms. Skipping. Residue LYS 243 is missing expected H atoms. Skipping. Residue SER 247 is missing expected H atoms. Skipping. Evaluate side-chains 96 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 79 time to evaluate : 0.321 Fit side-chains revert: symmetry clash REVERT: D 191 ILE cc_start: 0.8281 (OUTLIER) cc_final: 0.7894 (mp) REVERT: D 225 LEU cc_start: 0.8661 (OUTLIER) cc_final: 0.8099 (tm) REVERT: B 36 LYS cc_start: 0.8906 (OUTLIER) cc_final: 0.8659 (mttm) REVERT: C 225 LEU cc_start: 0.8653 (OUTLIER) cc_final: 0.8082 (tm) outliers start: 17 outliers final: 9 residues processed: 91 average time/residue: 1.1227 time to fit residues: 108.9478 Evaluate side-chains 86 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 73 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 115 ILE Chi-restraints excluded: chain D residue 191 ILE Chi-restraints excluded: chain D residue 225 LEU Chi-restraints excluded: chain D residue 242 VAL Chi-restraints excluded: chain B residue 36 LYS Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain C residue 51 LYS Chi-restraints excluded: chain C residue 115 ILE Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 242 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 51 optimal weight: 10.0000 chunk 15 optimal weight: 10.0000 chunk 25 optimal weight: 8.9990 chunk 21 optimal weight: 6.9990 chunk 66 optimal weight: 10.0000 chunk 71 optimal weight: 0.9980 chunk 78 optimal weight: 10.0000 chunk 52 optimal weight: 2.9990 chunk 74 optimal weight: 6.9990 chunk 8 optimal weight: 0.9980 chunk 58 optimal weight: 10.0000 overall best weight: 3.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 88 GLN B 88 GLN A 43 GLN A 88 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.113040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.096427 restraints weight = 51901.223| |-----------------------------------------------------------------------------| r_work (start): 0.3013 rms_B_bonded: 1.83 r_work: 0.2942 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2838 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2780 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2780 r_free = 0.2780 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2780 r_free = 0.2780 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2780 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8710 moved from start: 0.0531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7620 Z= 0.164 Angle : 0.556 7.297 10392 Z= 0.301 Chirality : 0.038 0.150 1268 Planarity : 0.004 0.031 1272 Dihedral : 8.319 52.090 1376 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.41 % Allowed : 3.31 % Favored : 96.28 % Rotamer: Outliers : 1.62 % Allowed : 13.24 % Favored : 85.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 1.94 (0.27), residues: 980 helix: 2.11 (0.19), residues: 644 sheet: None (None), residues: 0 loop : -0.32 (0.36), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 161 TYR 0.010 0.002 TYR D 227 PHE 0.018 0.002 PHE B 212 TRP 0.004 0.001 TRP D 245 HIS 0.004 0.001 HIS A 69 Details of bonding type rmsd covalent geometry : bond 0.00344 ( 7620) covalent geometry : angle 0.55590 (10392) hydrogen bonds : bond 0.04958 ( 540) hydrogen bonds : angle 5.35393 ( 1596) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 3 is missing expected H atoms. Skipping. Residue LYS 6 is missing expected H atoms. Skipping. Residue SER 236 is missing expected H atoms. Skipping. Residue THR 239 is missing expected H atoms. Skipping. Residue LYS 243 is missing expected H atoms. Skipping. Residue SER 247 is missing expected H atoms. Skipping. Residue SER 3 is missing expected H atoms. Skipping. Residue LYS 6 is missing expected H atoms. Skipping. Residue SER 236 is missing expected H atoms. Skipping. Residue THR 239 is missing expected H atoms. Skipping. Residue LYS 243 is missing expected H atoms. Skipping. Residue SER 247 is missing expected H atoms. Skipping. Residue SER 3 is missing expected H atoms. Skipping. Residue LYS 6 is missing expected H atoms. Skipping. Residue SER 236 is missing expected H atoms. Skipping. Residue THR 239 is missing expected H atoms. Skipping. Residue LYS 243 is missing expected H atoms. Skipping. Residue SER 247 is missing expected H atoms. Skipping. Residue SER 3 is missing expected H atoms. Skipping. Residue LYS 6 is missing expected H atoms. Skipping. Residue SER 236 is missing expected H atoms. Skipping. Residue THR 239 is missing expected H atoms. Skipping. Residue LYS 243 is missing expected H atoms. Skipping. Residue SER 247 is missing expected H atoms. Skipping. Evaluate side-chains 89 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 77 time to evaluate : 0.378 Fit side-chains REVERT: D 191 ILE cc_start: 0.8304 (OUTLIER) cc_final: 0.7924 (mp) REVERT: D 225 LEU cc_start: 0.8694 (OUTLIER) cc_final: 0.8122 (tm) REVERT: B 36 LYS cc_start: 0.8921 (OUTLIER) cc_final: 0.8680 (mttm) REVERT: B 225 LEU cc_start: 0.8692 (OUTLIER) cc_final: 0.8126 (tm) REVERT: C 51 LYS cc_start: 0.8869 (OUTLIER) cc_final: 0.8311 (tttt) REVERT: C 225 LEU cc_start: 0.8689 (OUTLIER) cc_final: 0.8122 (tm) REVERT: A 225 LEU cc_start: 0.8685 (OUTLIER) cc_final: 0.8115 (tm) outliers start: 12 outliers final: 3 residues processed: 88 average time/residue: 1.1515 time to fit residues: 107.7975 Evaluate side-chains 83 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 73 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 191 ILE Chi-restraints excluded: chain D residue 225 LEU Chi-restraints excluded: chain B residue 36 LYS Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain C residue 51 LYS Chi-restraints excluded: chain C residue 115 ILE Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 225 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 25 optimal weight: 8.9990 chunk 7 optimal weight: 3.9990 chunk 72 optimal weight: 10.0000 chunk 93 optimal weight: 6.9990 chunk 76 optimal weight: 2.9990 chunk 45 optimal weight: 6.9990 chunk 37 optimal weight: 6.9990 chunk 83 optimal weight: 6.9990 chunk 11 optimal weight: 1.9990 chunk 65 optimal weight: 8.9990 chunk 30 optimal weight: 1.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 88 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.113693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.097176 restraints weight = 52244.901| |-----------------------------------------------------------------------------| r_work (start): 0.3043 rms_B_bonded: 1.82 r_work: 0.2972 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.2869 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2802 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2802 r_free = 0.2802 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2802 r_free = 0.2802 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2802 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8709 moved from start: 0.0609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 7620 Z= 0.156 Angle : 0.544 7.331 10392 Z= 0.294 Chirality : 0.037 0.149 1268 Planarity : 0.004 0.031 1272 Dihedral : 8.099 51.049 1372 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.41 % Allowed : 3.72 % Favored : 95.87 % Rotamer: Outliers : 1.89 % Allowed : 12.70 % Favored : 85.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 1.99 (0.27), residues: 980 helix: 2.15 (0.19), residues: 644 sheet: None (None), residues: 0 loop : -0.31 (0.36), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 161 TYR 0.009 0.002 TYR D 227 PHE 0.016 0.002 PHE A 212 TRP 0.003 0.001 TRP C 245 HIS 0.004 0.001 HIS D 180 Details of bonding type rmsd covalent geometry : bond 0.00324 ( 7620) covalent geometry : angle 0.54381 (10392) hydrogen bonds : bond 0.04814 ( 540) hydrogen bonds : angle 5.25979 ( 1596) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 3 is missing expected H atoms. Skipping. Residue LYS 6 is missing expected H atoms. Skipping. Residue SER 236 is missing expected H atoms. Skipping. Residue THR 239 is missing expected H atoms. Skipping. Residue LYS 243 is missing expected H atoms. Skipping. Residue SER 247 is missing expected H atoms. Skipping. Residue SER 3 is missing expected H atoms. Skipping. Residue LYS 6 is missing expected H atoms. Skipping. Residue SER 236 is missing expected H atoms. Skipping. Residue THR 239 is missing expected H atoms. Skipping. Residue LYS 243 is missing expected H atoms. Skipping. Residue SER 247 is missing expected H atoms. Skipping. Residue SER 3 is missing expected H atoms. Skipping. Residue LYS 6 is missing expected H atoms. Skipping. Residue SER 236 is missing expected H atoms. Skipping. Residue THR 239 is missing expected H atoms. Skipping. Residue LYS 243 is missing expected H atoms. Skipping. Residue SER 247 is missing expected H atoms. Skipping. Residue SER 3 is missing expected H atoms. Skipping. Residue LYS 6 is missing expected H atoms. Skipping. Residue SER 236 is missing expected H atoms. Skipping. Residue THR 239 is missing expected H atoms. Skipping. Residue LYS 243 is missing expected H atoms. Skipping. Residue SER 247 is missing expected H atoms. Skipping. Evaluate side-chains 91 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 77 time to evaluate : 0.395 Fit side-chains REVERT: D 191 ILE cc_start: 0.8300 (OUTLIER) cc_final: 0.7917 (mp) REVERT: D 225 LEU cc_start: 0.8696 (OUTLIER) cc_final: 0.8118 (tm) REVERT: B 36 LYS cc_start: 0.8925 (OUTLIER) cc_final: 0.8692 (mttm) REVERT: B 225 LEU cc_start: 0.8681 (OUTLIER) cc_final: 0.8104 (tm) REVERT: C 51 LYS cc_start: 0.8868 (OUTLIER) cc_final: 0.8313 (tttt) REVERT: C 225 LEU cc_start: 0.8687 (OUTLIER) cc_final: 0.8116 (tm) REVERT: A 225 LEU cc_start: 0.8678 (OUTLIER) cc_final: 0.8109 (tm) outliers start: 14 outliers final: 4 residues processed: 87 average time/residue: 1.1156 time to fit residues: 103.4250 Evaluate side-chains 85 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 74 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 115 ILE Chi-restraints excluded: chain D residue 191 ILE Chi-restraints excluded: chain D residue 225 LEU Chi-restraints excluded: chain B residue 36 LYS Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain C residue 51 LYS Chi-restraints excluded: chain C residue 115 ILE Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 225 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 39 optimal weight: 10.0000 chunk 33 optimal weight: 8.9990 chunk 20 optimal weight: 7.9990 chunk 87 optimal weight: 10.0000 chunk 68 optimal weight: 7.9990 chunk 35 optimal weight: 7.9990 chunk 88 optimal weight: 5.9990 chunk 21 optimal weight: 2.9990 chunk 82 optimal weight: 10.0000 chunk 11 optimal weight: 0.9980 chunk 78 optimal weight: 7.9990 overall best weight: 5.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 88 GLN A 88 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.111094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.093588 restraints weight = 53789.594| |-----------------------------------------------------------------------------| r_work (start): 0.2993 rms_B_bonded: 1.92 r_work: 0.2921 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.2816 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2753 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2753 r_free = 0.2753 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2753 r_free = 0.2753 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2753 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8729 moved from start: 0.0643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 7620 Z= 0.197 Angle : 0.583 7.349 10392 Z= 0.315 Chirality : 0.039 0.155 1268 Planarity : 0.004 0.033 1272 Dihedral : 8.490 52.007 1372 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.41 % Allowed : 3.82 % Favored : 95.76 % Rotamer: Outliers : 2.03 % Allowed : 12.57 % Favored : 85.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 1.78 (0.27), residues: 980 helix: 1.94 (0.19), residues: 644 sheet: None (None), residues: 0 loop : -0.28 (0.37), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 161 TYR 0.010 0.002 TYR D 227 PHE 0.018 0.002 PHE A 212 TRP 0.005 0.001 TRP C 213 HIS 0.005 0.002 HIS D 180 Details of bonding type rmsd covalent geometry : bond 0.00427 ( 7620) covalent geometry : angle 0.58292 (10392) hydrogen bonds : bond 0.05248 ( 540) hydrogen bonds : angle 5.38566 ( 1596) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 3 is missing expected H atoms. Skipping. Residue LYS 6 is missing expected H atoms. Skipping. Residue SER 236 is missing expected H atoms. Skipping. Residue THR 239 is missing expected H atoms. Skipping. Residue LYS 243 is missing expected H atoms. Skipping. Residue SER 247 is missing expected H atoms. Skipping. Residue SER 3 is missing expected H atoms. Skipping. Residue LYS 6 is missing expected H atoms. Skipping. Residue SER 236 is missing expected H atoms. Skipping. Residue THR 239 is missing expected H atoms. Skipping. Residue LYS 243 is missing expected H atoms. Skipping. Residue SER 247 is missing expected H atoms. Skipping. Residue SER 3 is missing expected H atoms. Skipping. Residue LYS 6 is missing expected H atoms. Skipping. Residue SER 236 is missing expected H atoms. Skipping. Residue THR 239 is missing expected H atoms. Skipping. Residue LYS 243 is missing expected H atoms. Skipping. Residue SER 247 is missing expected H atoms. Skipping. Residue SER 3 is missing expected H atoms. Skipping. Residue LYS 6 is missing expected H atoms. Skipping. Residue SER 236 is missing expected H atoms. Skipping. Residue THR 239 is missing expected H atoms. Skipping. Residue LYS 243 is missing expected H atoms. Skipping. Residue SER 247 is missing expected H atoms. Skipping. Evaluate side-chains 89 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 74 time to evaluate : 0.364 Fit side-chains REVERT: D 191 ILE cc_start: 0.8360 (OUTLIER) cc_final: 0.8041 (mp) REVERT: D 225 LEU cc_start: 0.8714 (OUTLIER) cc_final: 0.8141 (tm) REVERT: B 36 LYS cc_start: 0.8915 (OUTLIER) cc_final: 0.8685 (mttm) REVERT: B 225 LEU cc_start: 0.8717 (OUTLIER) cc_final: 0.8145 (tm) REVERT: C 51 LYS cc_start: 0.8877 (OUTLIER) cc_final: 0.8336 (tttt) REVERT: C 225 LEU cc_start: 0.8718 (OUTLIER) cc_final: 0.8155 (tm) REVERT: A 225 LEU cc_start: 0.8717 (OUTLIER) cc_final: 0.8146 (tm) outliers start: 15 outliers final: 7 residues processed: 88 average time/residue: 1.0439 time to fit residues: 98.2446 Evaluate side-chains 83 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 69 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 115 ILE Chi-restraints excluded: chain D residue 191 ILE Chi-restraints excluded: chain D residue 225 LEU Chi-restraints excluded: chain D residue 242 VAL Chi-restraints excluded: chain B residue 36 LYS Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain C residue 51 LYS Chi-restraints excluded: chain C residue 115 ILE Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 225 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 54 optimal weight: 9.9990 chunk 67 optimal weight: 0.4980 chunk 59 optimal weight: 9.9990 chunk 23 optimal weight: 2.9990 chunk 57 optimal weight: 6.9990 chunk 84 optimal weight: 0.6980 chunk 27 optimal weight: 0.9980 chunk 2 optimal weight: 8.9990 chunk 30 optimal weight: 3.9990 chunk 36 optimal weight: 9.9990 chunk 17 optimal weight: 10.0000 overall best weight: 1.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 88 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.115507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.098933 restraints weight = 53229.662| |-----------------------------------------------------------------------------| r_work (start): 0.2993 rms_B_bonded: 1.86 r_work: 0.2918 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.2812 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.2812 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2806 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2806 r_free = 0.2806 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2806 r_free = 0.2806 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2806 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8678 moved from start: 0.0789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 7620 Z= 0.119 Angle : 0.509 7.349 10392 Z= 0.274 Chirality : 0.036 0.143 1268 Planarity : 0.003 0.031 1272 Dihedral : 7.680 49.357 1372 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.41 % Allowed : 3.10 % Favored : 96.49 % Rotamer: Outliers : 1.89 % Allowed : 13.11 % Favored : 85.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 2.30 (0.27), residues: 980 helix: 2.40 (0.20), residues: 644 sheet: None (None), residues: 0 loop : -0.20 (0.37), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 161 TYR 0.007 0.001 TYR D 227 PHE 0.011 0.001 PHE A 212 TRP 0.006 0.001 TRP A 11 HIS 0.003 0.001 HIS D 180 Details of bonding type rmsd covalent geometry : bond 0.00234 ( 7620) covalent geometry : angle 0.50893 (10392) hydrogen bonds : bond 0.04236 ( 540) hydrogen bonds : angle 5.07076 ( 1596) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 3 is missing expected H atoms. Skipping. Residue LYS 6 is missing expected H atoms. Skipping. Residue SER 236 is missing expected H atoms. Skipping. Residue THR 239 is missing expected H atoms. Skipping. Residue LYS 243 is missing expected H atoms. Skipping. Residue SER 247 is missing expected H atoms. Skipping. Residue SER 3 is missing expected H atoms. Skipping. Residue LYS 6 is missing expected H atoms. Skipping. Residue SER 236 is missing expected H atoms. Skipping. Residue THR 239 is missing expected H atoms. Skipping. Residue LYS 243 is missing expected H atoms. Skipping. Residue SER 247 is missing expected H atoms. Skipping. Residue SER 3 is missing expected H atoms. Skipping. Residue LYS 6 is missing expected H atoms. Skipping. Residue SER 236 is missing expected H atoms. Skipping. Residue THR 239 is missing expected H atoms. Skipping. Residue LYS 243 is missing expected H atoms. Skipping. Residue SER 247 is missing expected H atoms. Skipping. Residue SER 3 is missing expected H atoms. Skipping. Residue LYS 6 is missing expected H atoms. Skipping. Residue SER 236 is missing expected H atoms. Skipping. Residue THR 239 is missing expected H atoms. Skipping. Residue LYS 243 is missing expected H atoms. Skipping. Residue SER 247 is missing expected H atoms. Skipping. Evaluate side-chains 94 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 80 time to evaluate : 0.405 Fit side-chains REVERT: D 191 ILE cc_start: 0.8217 (OUTLIER) cc_final: 0.7824 (mp) REVERT: D 225 LEU cc_start: 0.8604 (OUTLIER) cc_final: 0.8056 (tm) REVERT: B 36 LYS cc_start: 0.8877 (OUTLIER) cc_final: 0.8630 (mttm) REVERT: B 225 LEU cc_start: 0.8607 (OUTLIER) cc_final: 0.8055 (tm) REVERT: C 225 LEU cc_start: 0.8609 (OUTLIER) cc_final: 0.8061 (tm) REVERT: A 225 LEU cc_start: 0.8590 (OUTLIER) cc_final: 0.8045 (tm) outliers start: 14 outliers final: 0 residues processed: 90 average time/residue: 1.0751 time to fit residues: 103.3083 Evaluate side-chains 82 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 76 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 191 ILE Chi-restraints excluded: chain D residue 225 LEU Chi-restraints excluded: chain B residue 36 LYS Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain A residue 225 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 48 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 67 optimal weight: 5.9990 chunk 79 optimal weight: 6.9990 chunk 94 optimal weight: 8.9990 chunk 27 optimal weight: 0.0470 chunk 10 optimal weight: 10.0000 chunk 49 optimal weight: 10.0000 chunk 9 optimal weight: 4.9990 chunk 47 optimal weight: 5.9990 chunk 54 optimal weight: 4.9990 overall best weight: 4.4086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 88 GLN A 88 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.111563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.094734 restraints weight = 43437.106| |-----------------------------------------------------------------------------| r_work (start): 0.2955 rms_B_bonded: 1.76 r_work: 0.2883 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.2779 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.2779 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2774 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2774 r_free = 0.2774 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2774 r_free = 0.2774 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2774 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8700 moved from start: 0.0710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 7620 Z= 0.176 Angle : 0.564 7.346 10392 Z= 0.305 Chirality : 0.038 0.152 1268 Planarity : 0.004 0.032 1272 Dihedral : 8.322 51.834 1372 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.41 % Allowed : 3.82 % Favored : 95.76 % Rotamer: Outliers : 1.35 % Allowed : 13.11 % Favored : 85.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 1.97 (0.27), residues: 980 helix: 2.10 (0.19), residues: 644 sheet: None (None), residues: 0 loop : -0.22 (0.37), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 161 TYR 0.010 0.002 TYR D 227 PHE 0.019 0.002 PHE A 212 TRP 0.005 0.001 TRP C 213 HIS 0.005 0.001 HIS D 180 Details of bonding type rmsd covalent geometry : bond 0.00374 ( 7620) covalent geometry : angle 0.56422 (10392) hydrogen bonds : bond 0.05029 ( 540) hydrogen bonds : angle 5.26919 ( 1596) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 3 is missing expected H atoms. Skipping. Residue LYS 6 is missing expected H atoms. Skipping. Residue SER 236 is missing expected H atoms. Skipping. Residue THR 239 is missing expected H atoms. Skipping. Residue LYS 243 is missing expected H atoms. Skipping. Residue SER 247 is missing expected H atoms. Skipping. Residue SER 3 is missing expected H atoms. Skipping. Residue LYS 6 is missing expected H atoms. Skipping. Residue SER 236 is missing expected H atoms. Skipping. Residue THR 239 is missing expected H atoms. Skipping. Residue LYS 243 is missing expected H atoms. Skipping. Residue SER 247 is missing expected H atoms. Skipping. Residue SER 3 is missing expected H atoms. Skipping. Residue LYS 6 is missing expected H atoms. Skipping. Residue SER 236 is missing expected H atoms. Skipping. Residue THR 239 is missing expected H atoms. Skipping. Residue LYS 243 is missing expected H atoms. Skipping. Residue SER 247 is missing expected H atoms. Skipping. Residue SER 3 is missing expected H atoms. Skipping. Residue LYS 6 is missing expected H atoms. Skipping. Residue SER 236 is missing expected H atoms. Skipping. Residue THR 239 is missing expected H atoms. Skipping. Residue LYS 243 is missing expected H atoms. Skipping. Residue SER 247 is missing expected H atoms. Skipping. Evaluate side-chains 83 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 73 time to evaluate : 0.415 Fit side-chains REVERT: D 191 ILE cc_start: 0.8299 (OUTLIER) cc_final: 0.7970 (mp) REVERT: D 225 LEU cc_start: 0.8676 (OUTLIER) cc_final: 0.8106 (tm) REVERT: B 36 LYS cc_start: 0.8886 (OUTLIER) cc_final: 0.8655 (mttm) REVERT: B 225 LEU cc_start: 0.8672 (OUTLIER) cc_final: 0.8093 (tm) REVERT: C 225 LEU cc_start: 0.8679 (OUTLIER) cc_final: 0.8111 (tm) REVERT: A 225 LEU cc_start: 0.8667 (OUTLIER) cc_final: 0.8105 (tm) outliers start: 10 outliers final: 4 residues processed: 82 average time/residue: 1.1160 time to fit residues: 97.4491 Evaluate side-chains 81 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 71 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 115 ILE Chi-restraints excluded: chain D residue 191 ILE Chi-restraints excluded: chain D residue 225 LEU Chi-restraints excluded: chain B residue 36 LYS Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain C residue 115 ILE Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 225 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 68 optimal weight: 0.9990 chunk 83 optimal weight: 6.9990 chunk 43 optimal weight: 8.9990 chunk 85 optimal weight: 9.9990 chunk 62 optimal weight: 5.9990 chunk 80 optimal weight: 0.7980 chunk 4 optimal weight: 10.0000 chunk 94 optimal weight: 5.9990 chunk 29 optimal weight: 7.9990 chunk 33 optimal weight: 6.9990 chunk 78 optimal weight: 6.9990 overall best weight: 4.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.112853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.095505 restraints weight = 50317.890| |-----------------------------------------------------------------------------| r_work (start): 0.2945 rms_B_bonded: 1.91 r_work: 0.2867 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2759 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.2759 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2758 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2758 r_free = 0.2758 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2758 r_free = 0.2758 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2758 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8696 moved from start: 0.0716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 7620 Z= 0.169 Angle : 0.556 7.353 10392 Z= 0.300 Chirality : 0.038 0.151 1268 Planarity : 0.004 0.032 1272 Dihedral : 8.258 52.575 1372 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.41 % Allowed : 4.03 % Favored : 95.56 % Rotamer: Outliers : 1.49 % Allowed : 12.97 % Favored : 85.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 1.94 (0.27), residues: 980 helix: 2.06 (0.19), residues: 644 sheet: None (None), residues: 0 loop : -0.21 (0.37), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 161 TYR 0.010 0.002 TYR D 227 PHE 0.016 0.002 PHE A 212 TRP 0.004 0.001 TRP C 213 HIS 0.005 0.001 HIS D 180 Details of bonding type rmsd covalent geometry : bond 0.00357 ( 7620) covalent geometry : angle 0.55577 (10392) hydrogen bonds : bond 0.04948 ( 540) hydrogen bonds : angle 5.25395 ( 1596) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 3 is missing expected H atoms. Skipping. Residue LYS 6 is missing expected H atoms. Skipping. Residue SER 236 is missing expected H atoms. Skipping. Residue THR 239 is missing expected H atoms. Skipping. Residue LYS 243 is missing expected H atoms. Skipping. Residue SER 247 is missing expected H atoms. Skipping. Residue SER 3 is missing expected H atoms. Skipping. Residue LYS 6 is missing expected H atoms. Skipping. Residue SER 236 is missing expected H atoms. Skipping. Residue THR 239 is missing expected H atoms. Skipping. Residue LYS 243 is missing expected H atoms. Skipping. Residue SER 247 is missing expected H atoms. Skipping. Residue SER 3 is missing expected H atoms. Skipping. Residue LYS 6 is missing expected H atoms. Skipping. Residue SER 236 is missing expected H atoms. Skipping. Residue THR 239 is missing expected H atoms. Skipping. Residue LYS 243 is missing expected H atoms. Skipping. Residue SER 247 is missing expected H atoms. Skipping. Residue SER 3 is missing expected H atoms. Skipping. Residue LYS 6 is missing expected H atoms. Skipping. Residue SER 236 is missing expected H atoms. Skipping. Residue THR 239 is missing expected H atoms. Skipping. Residue LYS 243 is missing expected H atoms. Skipping. Residue SER 247 is missing expected H atoms. Skipping. Evaluate side-chains 84 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 73 time to evaluate : 0.371 Fit side-chains REVERT: D 191 ILE cc_start: 0.8315 (OUTLIER) cc_final: 0.7985 (mp) REVERT: D 225 LEU cc_start: 0.8672 (OUTLIER) cc_final: 0.8107 (tm) REVERT: B 225 LEU cc_start: 0.8661 (OUTLIER) cc_final: 0.8096 (tm) REVERT: C 225 LEU cc_start: 0.8662 (OUTLIER) cc_final: 0.8103 (tm) REVERT: A 225 LEU cc_start: 0.8660 (OUTLIER) cc_final: 0.8101 (tm) outliers start: 11 outliers final: 3 residues processed: 82 average time/residue: 1.0885 time to fit residues: 95.1022 Evaluate side-chains 80 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 72 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 115 ILE Chi-restraints excluded: chain D residue 191 ILE Chi-restraints excluded: chain D residue 225 LEU Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain C residue 115 ILE Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain A residue 225 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 35 optimal weight: 5.9990 chunk 86 optimal weight: 10.0000 chunk 5 optimal weight: 8.9990 chunk 92 optimal weight: 6.9990 chunk 64 optimal weight: 6.9990 chunk 84 optimal weight: 8.9990 chunk 94 optimal weight: 0.9980 chunk 29 optimal weight: 7.9990 chunk 38 optimal weight: 9.9990 chunk 11 optimal weight: 0.1980 chunk 30 optimal weight: 1.9990 overall best weight: 3.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.116368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.099599 restraints weight = 55662.015| |-----------------------------------------------------------------------------| r_work (start): 0.2958 rms_B_bonded: 1.90 r_work: 0.2881 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2775 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.2775 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2772 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2772 r_free = 0.2772 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2772 r_free = 0.2772 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2772 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8706 moved from start: 0.0750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 7620 Z= 0.149 Angle : 0.537 7.325 10392 Z= 0.290 Chirality : 0.037 0.148 1268 Planarity : 0.004 0.032 1272 Dihedral : 8.067 51.610 1372 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.41 % Allowed : 3.93 % Favored : 95.66 % Rotamer: Outliers : 1.22 % Allowed : 13.11 % Favored : 85.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 2.05 (0.27), residues: 980 helix: 2.17 (0.19), residues: 644 sheet: None (None), residues: 0 loop : -0.22 (0.37), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 161 TYR 0.009 0.002 TYR D 227 PHE 0.015 0.002 PHE A 212 TRP 0.003 0.001 TRP C 213 HIS 0.004 0.001 HIS D 180 Details of bonding type rmsd covalent geometry : bond 0.00307 ( 7620) covalent geometry : angle 0.53701 (10392) hydrogen bonds : bond 0.04710 ( 540) hydrogen bonds : angle 5.17113 ( 1596) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 3 is missing expected H atoms. Skipping. Residue LYS 6 is missing expected H atoms. Skipping. Residue SER 236 is missing expected H atoms. Skipping. Residue THR 239 is missing expected H atoms. Skipping. Residue LYS 243 is missing expected H atoms. Skipping. Residue SER 247 is missing expected H atoms. Skipping. Residue SER 3 is missing expected H atoms. Skipping. Residue LYS 6 is missing expected H atoms. Skipping. Residue SER 236 is missing expected H atoms. Skipping. Residue THR 239 is missing expected H atoms. Skipping. Residue LYS 243 is missing expected H atoms. Skipping. Residue SER 247 is missing expected H atoms. Skipping. Residue SER 3 is missing expected H atoms. Skipping. Residue LYS 6 is missing expected H atoms. Skipping. Residue SER 236 is missing expected H atoms. Skipping. Residue THR 239 is missing expected H atoms. Skipping. Residue LYS 243 is missing expected H atoms. Skipping. Residue SER 247 is missing expected H atoms. Skipping. Residue SER 3 is missing expected H atoms. Skipping. Residue LYS 6 is missing expected H atoms. Skipping. Residue SER 236 is missing expected H atoms. Skipping. Residue THR 239 is missing expected H atoms. Skipping. Residue LYS 243 is missing expected H atoms. Skipping. Residue SER 247 is missing expected H atoms. Skipping. Evaluate side-chains 84 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 75 time to evaluate : 0.482 Fit side-chains REVERT: D 191 ILE cc_start: 0.8295 (OUTLIER) cc_final: 0.7953 (mp) REVERT: D 225 LEU cc_start: 0.8668 (OUTLIER) cc_final: 0.8110 (tm) REVERT: B 225 LEU cc_start: 0.8661 (OUTLIER) cc_final: 0.8105 (tm) REVERT: C 225 LEU cc_start: 0.8671 (OUTLIER) cc_final: 0.8120 (tm) REVERT: A 225 LEU cc_start: 0.8655 (OUTLIER) cc_final: 0.8106 (tm) outliers start: 9 outliers final: 4 residues processed: 83 average time/residue: 1.0824 time to fit residues: 96.2113 Evaluate side-chains 78 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 69 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 115 ILE Chi-restraints excluded: chain D residue 191 ILE Chi-restraints excluded: chain D residue 225 LEU Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain C residue 115 ILE Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 225 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 53 optimal weight: 8.9990 chunk 85 optimal weight: 9.9990 chunk 80 optimal weight: 1.9990 chunk 81 optimal weight: 0.9990 chunk 34 optimal weight: 10.0000 chunk 91 optimal weight: 7.9990 chunk 66 optimal weight: 5.9990 chunk 40 optimal weight: 5.9990 chunk 62 optimal weight: 2.9990 chunk 28 optimal weight: 10.0000 chunk 6 optimal weight: 4.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 88 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.114272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.096904 restraints weight = 51295.502| |-----------------------------------------------------------------------------| r_work (start): 0.2955 rms_B_bonded: 1.94 r_work: 0.2879 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2771 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.2771 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2768 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2768 r_free = 0.2768 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2768 r_free = 0.2768 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2768 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8690 moved from start: 0.0753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 7620 Z= 0.152 Angle : 0.543 7.314 10392 Z= 0.293 Chirality : 0.037 0.148 1268 Planarity : 0.004 0.032 1272 Dihedral : 8.085 51.675 1372 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.41 % Allowed : 3.93 % Favored : 95.66 % Rotamer: Outliers : 1.49 % Allowed : 12.97 % Favored : 85.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 2.03 (0.27), residues: 980 helix: 2.16 (0.19), residues: 644 sheet: None (None), residues: 0 loop : -0.24 (0.37), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 161 TYR 0.009 0.002 TYR D 227 PHE 0.015 0.002 PHE A 212 TRP 0.003 0.001 TRP C 213 HIS 0.005 0.001 HIS D 180 Details of bonding type rmsd covalent geometry : bond 0.00315 ( 7620) covalent geometry : angle 0.54311 (10392) hydrogen bonds : bond 0.04740 ( 540) hydrogen bonds : angle 5.17642 ( 1596) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 3 is missing expected H atoms. Skipping. Residue LYS 6 is missing expected H atoms. Skipping. Residue SER 236 is missing expected H atoms. Skipping. Residue THR 239 is missing expected H atoms. Skipping. Residue LYS 243 is missing expected H atoms. Skipping. Residue SER 247 is missing expected H atoms. Skipping. Residue SER 3 is missing expected H atoms. Skipping. Residue LYS 6 is missing expected H atoms. Skipping. Residue SER 236 is missing expected H atoms. Skipping. Residue THR 239 is missing expected H atoms. Skipping. Residue LYS 243 is missing expected H atoms. Skipping. Residue SER 247 is missing expected H atoms. Skipping. Residue SER 3 is missing expected H atoms. Skipping. Residue LYS 6 is missing expected H atoms. Skipping. Residue SER 236 is missing expected H atoms. Skipping. Residue THR 239 is missing expected H atoms. Skipping. Residue LYS 243 is missing expected H atoms. Skipping. Residue SER 247 is missing expected H atoms. Skipping. Residue SER 3 is missing expected H atoms. Skipping. Residue LYS 6 is missing expected H atoms. Skipping. Residue SER 236 is missing expected H atoms. Skipping. Residue THR 239 is missing expected H atoms. Skipping. Residue LYS 243 is missing expected H atoms. Skipping. Residue SER 247 is missing expected H atoms. Skipping. Evaluate side-chains 81 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 70 time to evaluate : 0.459 Fit side-chains REVERT: D 191 ILE cc_start: 0.8298 (OUTLIER) cc_final: 0.7951 (mp) REVERT: D 225 LEU cc_start: 0.8651 (OUTLIER) cc_final: 0.8092 (tm) REVERT: B 225 LEU cc_start: 0.8647 (OUTLIER) cc_final: 0.8088 (tm) REVERT: C 225 LEU cc_start: 0.8651 (OUTLIER) cc_final: 0.8096 (tm) REVERT: A 225 LEU cc_start: 0.8637 (OUTLIER) cc_final: 0.8084 (tm) outliers start: 11 outliers final: 4 residues processed: 79 average time/residue: 1.1508 time to fit residues: 96.5756 Evaluate side-chains 78 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 69 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 115 ILE Chi-restraints excluded: chain D residue 191 ILE Chi-restraints excluded: chain D residue 225 LEU Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain C residue 115 ILE Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 225 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 27 optimal weight: 0.0060 chunk 65 optimal weight: 10.0000 chunk 22 optimal weight: 3.9990 chunk 9 optimal weight: 8.9990 chunk 47 optimal weight: 0.9990 chunk 71 optimal weight: 1.9990 chunk 57 optimal weight: 8.9990 chunk 53 optimal weight: 0.8980 chunk 8 optimal weight: 4.9990 chunk 12 optimal weight: 8.9990 chunk 6 optimal weight: 2.9990 overall best weight: 1.3802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.115193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.098377 restraints weight = 45687.589| |-----------------------------------------------------------------------------| r_work (start): 0.3009 rms_B_bonded: 1.82 r_work: 0.2938 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.2832 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.2832 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2827 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2827 r_free = 0.2827 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2827 r_free = 0.2827 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2827 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8656 moved from start: 0.0924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 7620 Z= 0.111 Angle : 0.504 7.088 10392 Z= 0.270 Chirality : 0.036 0.140 1268 Planarity : 0.003 0.031 1272 Dihedral : 7.593 47.707 1372 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.41 % Allowed : 3.00 % Favored : 96.59 % Rotamer: Outliers : 1.35 % Allowed : 13.24 % Favored : 85.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 2.48 (0.28), residues: 980 helix: 2.53 (0.20), residues: 644 sheet: None (None), residues: 0 loop : -0.11 (0.37), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 161 TYR 0.007 0.001 TYR D 227 PHE 0.010 0.001 PHE B 212 TRP 0.007 0.001 TRP C 11 HIS 0.004 0.001 HIS D 180 Details of bonding type rmsd covalent geometry : bond 0.00216 ( 7620) covalent geometry : angle 0.50370 (10392) hydrogen bonds : bond 0.04081 ( 540) hydrogen bonds : angle 4.97856 ( 1596) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5366.01 seconds wall clock time: 91 minutes 16.49 seconds (5476.49 seconds total)