Starting phenix.real_space_refine on Fri Jul 3 16:02:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7uze_26886/07_2026/7uze_26886_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7uze_26886/07_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 { model { file = "/net/cci-nas-00/data/ceres_data/7uze_26886/07_2026/7uze_26886_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7uze_26886/07_2026/7uze_26886_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7uze_26886/07_2026/7uze_26886.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7uze_26886/07_2026/7uze_26886.map" } 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-6108/lib/python3.11/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: 21 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: 21 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: 21 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: 21 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: 21 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: 21 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: 21 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: 21 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: 4.86, per 1000 atoms: 0.32 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: 1.48 Conformation dependent library (CDL) restraints added in 747.6 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: 3.58 Time building geometry restraints manager: 2.00 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 P1L C 87 " pdb=" H4 P1L C 87 " ideal model delta sigma weight residual 0.970 1.137 -0.167 2.00e-02 2.50e+03 7.01e+01 bond pdb=" CA P1L A 87 " pdb=" H4 P1L A 87 " ideal model delta sigma weight residual 0.970 1.137 -0.167 2.00e-02 2.50e+03 6.98e+01 bond pdb=" CA P1L D 87 " pdb=" H4 P1L D 87 " ideal model delta sigma weight residual 0.970 1.137 -0.167 2.00e-02 2.50e+03 6.98e+01 bond pdb=" CA P1L B 87 " pdb=" H4 P1L B 87 " ideal model delta sigma weight residual 0.970 1.137 -0.167 2.00e-02 2.50e+03 6.95e+01 bond pdb=" C8 P1L A 87 " pdb="H8C2 P1L A 87 " ideal model delta sigma weight residual 0.970 1.125 -0.155 2.00e-02 2.50e+03 5.99e+01 ... (remaining 15143 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.47: 26685 1.47 - 2.93: 589 2.93 - 4.40: 72 4.40 - 5.87: 12 5.87 - 7.33: 6 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 - 17.97: 6577 17.97 - 35.94: 509 35.94 - 53.91: 247 53.91 - 71.88: 75 71.88 - 89.85: 12 Dihedral angle restraints: 7420 sinusoidal: 4164 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 7417 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 828 0.031 - 0.061: 317 0.061 - 0.092: 97 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: 2240 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" SG P1L D 87 " -0.017 2.00e-02 2.50e+03 3.72e-02 1.38e+01 pdb=" C7 P1L D 87 " 0.064 2.00e-02 2.50e+03 pdb=" C8 P1L D 87 " -0.019 2.00e-02 2.50e+03 pdb=" O7 P1L D 87 " -0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" SG P1L A 87 " -0.017 2.00e-02 2.50e+03 3.64e-02 1.32e+01 pdb=" C7 P1L A 87 " 0.063 2.00e-02 2.50e+03 pdb=" C8 P1L A 87 " -0.019 2.00e-02 2.50e+03 pdb=" O7 P1L A 87 " -0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" SG P1L B 87 " -0.016 2.00e-02 2.50e+03 3.54e-02 1.25e+01 pdb=" C7 P1L B 87 " 0.061 2.00e-02 2.50e+03 pdb=" C8 P1L B 87 " -0.018 2.00e-02 2.50e+03 pdb=" O7 P1L B 87 " -0.026 2.00e-02 2.50e+03 ... (remaining 2237 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: 0.03 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: 1.160 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: 0.120 Extract box with map and model: 0.440 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 18.460 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8747 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 : 0.004 0.051 7620 Z= 0.183 Angle : 0.612 7.334 10392 Z= 0.319 Chirality : 0.037 0.153 1268 Planarity : 0.004 0.037 1276 Dihedral : 15.413 89.846 2844 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/Z covalent geometry : bond 0.00368 / 0.18 ( 7620) covalent geometry : angle 0.61162 / 0.32 (10392) hydrogen bonds : bond 0.09906 / 6.72 ( 540) hydrogen bonds : angle 6.24330 / 4.46 ( 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 : 0.412 Fit side-chains outliers start: 5 outliers final: 4 residues processed: 76 average time/residue: 1.1259 time to fit residues: 91.7501 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 : 0.423 ------------------------------------------------------------------------------- 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: 2.9990 chunk 74 optimal weight: 7.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 88 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.113584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.096914 restraints weight = 49407.752| |-----------------------------------------------------------------------------| r_work (start): 0.2971 rms_B_bonded: 1.80 r_work: 0.2900 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.2797 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.2797 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2905 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2905 r_free = 0.2905 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2905 r_free = 0.2905 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.2905 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8754 moved from start: 0.0463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 7620 Z= 0.146 Angle : 0.535 7.307 10392 Z= 0.291 Chirality : 0.037 0.149 1268 Planarity : 0.004 0.031 1276 Dihedral : 9.141 58.129 1404 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.41 % Allowed : 2.89 % Favored : 96.69 % Rotamer: Outliers : 2.43 % Allowed : 13.11 % 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: 1.89 (0.26), residues: 980 helix: 2.08 (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 0.010 0.002 TYR D 227 PHE 0.016 0.002 PHE A 212 TRP 0.004 0.001 TRP A 11 HIS 0.004 0.001 HIS C 180 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.15 ( 7620) covalent geometry : angle 0.53521 / 0.29 (10392) hydrogen bonds : bond 0.04766 / 3.27 ( 540) hydrogen bonds : angle 5.44073 / 3.90 ( 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 97 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 79 time to evaluate : 0.453 Fit side-chains revert: symmetry clash REVERT: D 191 ILE cc_start: 0.8294 (OUTLIER) cc_final: 0.7930 (mp) REVERT: D 225 LEU cc_start: 0.8673 (OUTLIER) cc_final: 0.8110 (tm) REVERT: B 225 LEU cc_start: 0.8675 (OUTLIER) cc_final: 0.8100 (tm) REVERT: C 225 LEU cc_start: 0.8662 (OUTLIER) cc_final: 0.8091 (tm) outliers start: 18 outliers final: 8 residues processed: 92 average time/residue: 1.0613 time to fit residues: 104.9135 Evaluate side-chains 84 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 72 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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: 7.9990 chunk 66 optimal weight: 9.9990 chunk 71 optimal weight: 0.3980 chunk 78 optimal weight: 8.9990 chunk 52 optimal weight: 2.9990 chunk 74 optimal weight: 5.9990 chunk 8 optimal weight: 0.9980 chunk 58 optimal weight: 10.0000 overall best weight: 3.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 88 GLN B 88 GLN C 88 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 = 0.3227 r_free = 0.3227 target = 0.113601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.097013 restraints weight = 52162.157| |-----------------------------------------------------------------------------| r_work (start): 0.2972 rms_B_bonded: 1.84 r_work: 0.2902 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.2799 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.2799 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2781 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2781 r_free = 0.2781 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.43 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 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.2780 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8768 moved from start: 0.0539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7620 Z= 0.160 Angle : 0.543 7.328 10392 Z= 0.297 Chirality : 0.037 0.150 1268 Planarity : 0.004 0.031 1276 Dihedral : 9.178 58.531 1404 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.41 % Allowed : 3.10 % Favored : 96.49 % Rotamer: Outliers : 1.49 % Allowed : 13.51 % 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: 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 0.017 0.002 PHE A 212 TRP 0.003 0.001 TRP C 245 HIS 0.004 0.001 HIS A 69 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.16 ( 7620) covalent geometry : angle 0.54254 / 0.30 (10392) hydrogen bonds : bond 0.04909 / 3.36 ( 540) hydrogen bonds : angle 5.34882 / 3.84 ( 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 91 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 80 time to evaluate : 0.366 Fit side-chains REVERT: D 191 ILE cc_start: 0.8304 (OUTLIER) cc_final: 0.7933 (mp) REVERT: D 225 LEU cc_start: 0.8690 (OUTLIER) cc_final: 0.8117 (tm) REVERT: B 225 LEU cc_start: 0.8687 (OUTLIER) cc_final: 0.8119 (tm) REVERT: C 51 LYS cc_start: 0.8872 (OUTLIER) cc_final: 0.8314 (tttt) REVERT: C 225 LEU cc_start: 0.8686 (OUTLIER) cc_final: 0.8118 (tm) REVERT: A 225 LEU cc_start: 0.8682 (OUTLIER) cc_final: 0.8124 (tm) outliers start: 11 outliers final: 4 residues processed: 90 average time/residue: 1.0608 time to fit residues: 102.4920 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 : 0.404 ------------------------------------------------------------------------------- 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 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: 0.9990 chunk 72 optimal weight: 10.0000 chunk 93 optimal weight: 7.9990 chunk 76 optimal weight: 9.9990 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: 10.0000 chunk 30 optimal weight: 2.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 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 = 0.3216 r_free = 0.3216 target = 0.112921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.096268 restraints weight = 51921.586| |-----------------------------------------------------------------------------| r_work (start): 0.2955 rms_B_bonded: 1.83 r_work: 0.2880 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.2774 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.2774 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2809 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2809 r_free = 0.2809 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 = 0.2809 r_free = 0.2809 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2809 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8761 moved from start: 0.0606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7620 Z= 0.166 Angle : 0.545 7.330 10392 Z= 0.298 Chirality : 0.038 0.151 1268 Planarity : 0.004 0.032 1276 Dihedral : 8.979 58.516 1400 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.41 % Allowed : 3.82 % Favored : 95.76 % Rotamer: Outliers : 2.16 % Allowed : 12.57 % Favored : 85.27 % 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: 1.91 (0.27), residues: 980 helix: 2.08 (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 0.010 0.002 TYR D 227 PHE 0.017 0.002 PHE B 212 TRP 0.004 0.001 TRP C 245 HIS 0.004 0.001 HIS D 180 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.17 ( 7620) covalent geometry : angle 0.54509 / 0.30 (10392) hydrogen bonds : bond 0.04948 / 3.39 ( 540) hydrogen bonds : angle 5.30963 / 3.81 ( 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 90 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 74 time to evaluate : 0.416 Fit side-chains REVERT: D 191 ILE cc_start: 0.8308 (OUTLIER) cc_final: 0.7983 (mp) REVERT: D 225 LEU cc_start: 0.8682 (OUTLIER) cc_final: 0.8106 (tm) REVERT: B 225 LEU cc_start: 0.8678 (OUTLIER) cc_final: 0.8103 (tm) REVERT: C 51 LYS cc_start: 0.8873 (OUTLIER) cc_final: 0.8311 (tttt) REVERT: C 225 LEU cc_start: 0.8678 (OUTLIER) cc_final: 0.8112 (tm) REVERT: A 225 LEU cc_start: 0.8676 (OUTLIER) cc_final: 0.8109 (tm) outliers start: 16 outliers final: 7 residues processed: 86 average time/residue: 1.0327 time to fit residues: 95.6720 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 : 0.424 ------------------------------------------------------------------------------- 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 39 optimal weight: 9.9990 chunk 33 optimal weight: 8.9990 chunk 20 optimal weight: 7.9990 chunk 87 optimal weight: 8.9990 chunk 68 optimal weight: 7.9990 chunk 35 optimal weight: 7.9990 chunk 88 optimal weight: 5.9990 chunk 21 optimal weight: 1.9990 chunk 82 optimal weight: 10.0000 chunk 11 optimal weight: 2.9990 chunk 78 optimal weight: 6.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 88 GLN A 43 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.110911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.093271 restraints weight = 53662.454| |-----------------------------------------------------------------------------| r_work (start): 0.2932 rms_B_bonded: 1.95 r_work: 0.2854 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2746 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2746 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2880 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2880 r_free = 0.2880 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2880 r_free = 0.2880 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2880 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8775 moved from start: 0.0661 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 : 0.572 7.367 10392 Z= 0.313 Chirality : 0.039 0.155 1268 Planarity : 0.004 0.033 1276 Dihedral : 9.183 59.742 1400 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.41 % Allowed : 3.93 % Favored : 95.66 % 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: 1.74 (0.27), residues: 980 helix: 1.90 (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 0.019 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/Z covalent geometry : bond 0.00424 / 0.20 ( 7620) covalent geometry : angle 0.57192 / 0.31 (10392) hydrogen bonds : bond 0.05258 / 3.60 ( 540) hydrogen bonds : angle 5.39937 / 3.88 ( 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 : 0.475 Fit side-chains REVERT: D 191 ILE cc_start: 0.8377 (OUTLIER) cc_final: 0.8062 (mp) REVERT: D 225 LEU cc_start: 0.8704 (OUTLIER) cc_final: 0.8138 (tm) REVERT: B 225 LEU cc_start: 0.8704 (OUTLIER) cc_final: 0.8144 (tm) REVERT: C 51 LYS cc_start: 0.8874 (OUTLIER) cc_final: 0.8299 (tttt) REVERT: C 225 LEU cc_start: 0.8712 (OUTLIER) cc_final: 0.8154 (tm) REVERT: A 225 LEU cc_start: 0.8708 (OUTLIER) cc_final: 0.8142 (tm) outliers start: 15 outliers final: 7 residues processed: 87 average time/residue: 1.0292 time to fit residues: 96.4854 Evaluate side-chains 81 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 68 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 D residue 242 VAL 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: 3.9990 chunk 59 optimal weight: 5.9990 chunk 23 optimal weight: 1.9990 chunk 57 optimal weight: 6.9990 chunk 84 optimal weight: 10.0000 chunk 27 optimal weight: 7.9990 chunk 2 optimal weight: 8.9990 chunk 30 optimal weight: 4.9990 chunk 36 optimal weight: 10.0000 chunk 17 optimal weight: 9.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.111311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.093803 restraints weight = 51757.846| |-----------------------------------------------------------------------------| r_work (start): 0.2938 rms_B_bonded: 1.92 r_work: 0.2861 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2753 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.2753 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2865 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2865 r_free = 0.2865 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2865 r_free = 0.2865 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2865 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8771 moved from start: 0.0694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 7620 Z= 0.185 Angle : 0.561 7.383 10392 Z= 0.307 Chirality : 0.038 0.154 1268 Planarity : 0.004 0.033 1276 Dihedral : 9.047 58.263 1400 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.41 % Allowed : 3.93 % Favored : 95.66 % Rotamer: Outliers : 2.03 % Allowed : 12.70 % Favored : 85.27 % 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: 1.74 (0.27), residues: 980 helix: 1.89 (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 0.002 0.000 ARG A 161 TYR 0.010 0.002 TYR D 227 PHE 0.017 0.002 PHE A 212 TRP 0.004 0.001 TRP C 245 HIS 0.005 0.001 HIS D 180 Details of bonding type rmsd/Z covalent geometry : bond 0.00395 / 0.19 ( 7620) covalent geometry : angle 0.56130 / 0.31 (10392) hydrogen bonds : bond 0.05134 / 3.51 ( 540) hydrogen bonds : angle 5.36472 / 3.86 ( 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 86 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 71 time to evaluate : 0.413 Fit side-chains REVERT: D 191 ILE cc_start: 0.8371 (OUTLIER) cc_final: 0.8058 (mp) REVERT: D 225 LEU cc_start: 0.8691 (OUTLIER) cc_final: 0.8124 (tm) REVERT: B 225 LEU cc_start: 0.8699 (OUTLIER) cc_final: 0.8137 (tm) REVERT: C 51 LYS cc_start: 0.8870 (OUTLIER) cc_final: 0.8320 (tttt) REVERT: C 225 LEU cc_start: 0.8698 (OUTLIER) cc_final: 0.8142 (tm) REVERT: A 225 LEU cc_start: 0.8696 (OUTLIER) cc_final: 0.8130 (tm) outliers start: 15 outliers final: 7 residues processed: 83 average time/residue: 1.0610 time to fit residues: 94.6838 Evaluate side-chains 81 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 68 time to evaluate : 0.421 ------------------------------------------------------------------------------- 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 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=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: 4.9990 chunk 79 optimal weight: 4.9990 chunk 94 optimal weight: 5.9990 chunk 27 optimal weight: 3.9990 chunk 10 optimal weight: 9.9990 chunk 49 optimal weight: 6.9990 chunk 9 optimal weight: 5.9990 chunk 47 optimal weight: 0.6980 chunk 54 optimal weight: 6.9990 overall best weight: 4.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 88 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.111712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.094752 restraints weight = 44379.505| |-----------------------------------------------------------------------------| r_work (start): 0.2955 rms_B_bonded: 1.78 r_work: 0.2882 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.2776 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.2776 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2776 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2776 r_free = 0.2776 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 = 0.2776 r_free = 0.2776 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2776 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8758 moved from start: 0.0712 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= 0.170 Angle : 0.548 7.372 10392 Z= 0.299 Chirality : 0.038 0.152 1268 Planarity : 0.004 0.033 1276 Dihedral : 8.904 58.359 1400 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.41 % Allowed : 3.82 % Favored : 95.76 % Rotamer: Outliers : 1.76 % Allowed : 12.97 % Favored : 85.27 % 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: 1.83 (0.27), residues: 980 helix: 1.97 (0.19), residues: 644 sheet: None (None), residues: 0 loop : -0.23 (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 0.016 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/Z covalent geometry : bond 0.00357 / 0.17 ( 7620) covalent geometry : angle 0.54785 / 0.30 (10392) hydrogen bonds : bond 0.04960 / 3.40 ( 540) hydrogen bonds : angle 5.30167 / 3.81 ( 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 87 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 74 time to evaluate : 0.304 Fit side-chains REVERT: D 191 ILE cc_start: 0.8342 (OUTLIER) cc_final: 0.7969 (mp) REVERT: D 225 LEU cc_start: 0.8676 (OUTLIER) cc_final: 0.8103 (tm) REVERT: B 225 LEU cc_start: 0.8682 (OUTLIER) cc_final: 0.8112 (tm) REVERT: C 51 LYS cc_start: 0.8864 (OUTLIER) cc_final: 0.8311 (tttt) REVERT: C 225 LEU cc_start: 0.8677 (OUTLIER) cc_final: 0.8113 (tm) REVERT: A 225 LEU cc_start: 0.8670 (OUTLIER) cc_final: 0.8101 (tm) outliers start: 13 outliers final: 7 residues processed: 86 average time/residue: 1.0445 time to fit residues: 96.9286 Evaluate side-chains 82 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 69 time to evaluate : 0.414 ------------------------------------------------------------------------------- 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 68 optimal weight: 7.9990 chunk 83 optimal weight: 5.9990 chunk 43 optimal weight: 4.9990 chunk 85 optimal weight: 9.9990 chunk 62 optimal weight: 5.9990 chunk 80 optimal weight: 4.9990 chunk 4 optimal weight: 9.9990 chunk 94 optimal weight: 4.9990 chunk 29 optimal weight: 7.9990 chunk 33 optimal weight: 6.9990 chunk 78 optimal weight: 6.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 88 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.110965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.093746 restraints weight = 50293.980| |-----------------------------------------------------------------------------| r_work (start): 0.2934 rms_B_bonded: 1.86 r_work: 0.2859 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.2753 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.2753 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2748 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2748 r_free = 0.2748 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 = 0.2748 r_free = 0.2748 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2748 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8786 moved from start: 0.0742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 7620 Z= 0.201 Angle : 0.577 7.383 10392 Z= 0.315 Chirality : 0.039 0.157 1268 Planarity : 0.004 0.033 1276 Dihedral : 9.132 59.371 1400 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.41 % Allowed : 4.03 % Favored : 95.56 % Rotamer: Outliers : 2.16 % Allowed : 12.84 % 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: 1.63 (0.27), residues: 980 helix: 1.81 (0.19), residues: 644 sheet: None (None), residues: 0 loop : -0.29 (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 0.018 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/Z covalent geometry : bond 0.00436 / 0.20 ( 7620) covalent geometry : angle 0.57699 / 0.32 (10392) hydrogen bonds : bond 0.05284 / 3.61 ( 540) hydrogen bonds : angle 5.40385 / 3.89 ( 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 85 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 69 time to evaluate : 0.399 Fit side-chains REVERT: D 191 ILE cc_start: 0.8399 (OUTLIER) cc_final: 0.8090 (mp) REVERT: D 225 LEU cc_start: 0.8715 (OUTLIER) cc_final: 0.8153 (tm) REVERT: B 225 LEU cc_start: 0.8709 (OUTLIER) cc_final: 0.8153 (tm) REVERT: C 51 LYS cc_start: 0.8878 (OUTLIER) cc_final: 0.8289 (tttt) REVERT: C 225 LEU cc_start: 0.8720 (OUTLIER) cc_final: 0.8165 (tm) REVERT: A 225 LEU cc_start: 0.8721 (OUTLIER) cc_final: 0.8162 (tm) outliers start: 16 outliers final: 8 residues processed: 82 average time/residue: 0.9257 time to fit residues: 81.5127 Evaluate side-chains 82 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 68 time to evaluate : 0.296 ------------------------------------------------------------------------------- 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 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 Chi-restraints excluded: chain A residue 242 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 35 optimal weight: 0.9990 chunk 86 optimal weight: 7.9990 chunk 5 optimal weight: 7.9990 chunk 92 optimal weight: 6.9990 chunk 64 optimal weight: 6.9990 chunk 84 optimal weight: 10.0000 chunk 94 optimal weight: 1.9990 chunk 29 optimal weight: 7.9990 chunk 38 optimal weight: 7.9990 chunk 11 optimal weight: 0.0770 chunk 30 optimal weight: 1.9990 overall best weight: 2.4146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.113385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.095985 restraints weight = 55852.880| |-----------------------------------------------------------------------------| r_work (start): 0.2964 rms_B_bonded: 1.96 r_work: 0.2886 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2779 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.2779 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2776 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2776 r_free = 0.2776 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 = 0.2776 r_free = 0.2776 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2776 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8759 moved from start: 0.0777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 7620 Z= 0.132 Angle : 0.516 7.290 10392 Z= 0.281 Chirality : 0.036 0.147 1268 Planarity : 0.004 0.032 1276 Dihedral : 8.502 55.050 1400 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.41 % Allowed : 3.82 % Favored : 95.76 % Rotamer: Outliers : 1.62 % Allowed : 13.78 % Favored : 84.59 % 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: 2.09 (0.27), residues: 980 helix: 2.21 (0.20), 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 0.008 0.001 TYR D 227 PHE 0.013 0.001 PHE A 212 TRP 0.005 0.001 TRP C 11 HIS 0.004 0.001 HIS B 180 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.13 ( 7620) covalent geometry : angle 0.51563 / 0.28 (10392) hydrogen bonds : bond 0.04509 / 3.09 ( 540) hydrogen bonds : angle 5.15854 / 3.71 ( 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 89 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 77 time to evaluate : 0.244 Fit side-chains REVERT: D 191 ILE cc_start: 0.8300 (OUTLIER) cc_final: 0.7911 (mp) REVERT: D 225 LEU cc_start: 0.8659 (OUTLIER) cc_final: 0.8102 (tm) REVERT: B 225 LEU cc_start: 0.8654 (OUTLIER) cc_final: 0.8101 (tm) REVERT: C 51 LYS cc_start: 0.8865 (OUTLIER) cc_final: 0.8301 (tttt) REVERT: C 225 LEU cc_start: 0.8658 (OUTLIER) cc_final: 0.8109 (tm) REVERT: A 225 LEU cc_start: 0.8644 (OUTLIER) cc_final: 0.8098 (tm) outliers start: 12 outliers final: 4 residues processed: 87 average time/residue: 0.9400 time to fit residues: 87.8623 Evaluate side-chains 79 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 69 time to evaluate : 0.367 ------------------------------------------------------------------------------- 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 53 optimal weight: 8.9990 chunk 85 optimal weight: 10.0000 chunk 80 optimal weight: 2.9990 chunk 81 optimal weight: 0.8980 chunk 34 optimal weight: 9.9990 chunk 91 optimal weight: 7.9990 chunk 66 optimal weight: 6.9990 chunk 40 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 28 optimal weight: 10.0000 chunk 6 optimal weight: 3.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 88 GLN B 88 GLN C 88 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 = 0.3222 r_free = 0.3222 target = 0.113210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.096102 restraints weight = 51394.201| |-----------------------------------------------------------------------------| r_work (start): 0.2965 rms_B_bonded: 1.87 r_work: 0.2889 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.2783 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.2783 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2785 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2785 r_free = 0.2785 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2785 r_free = 0.2785 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2785 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8755 moved from start: 0.0816 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= 0.138 Angle : 0.526 7.338 10392 Z= 0.287 Chirality : 0.037 0.148 1268 Planarity : 0.004 0.032 1276 Dihedral : 8.551 55.722 1400 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.41 % Allowed : 3.82 % Favored : 95.76 % Rotamer: Outliers : 1.35 % Allowed : 13.51 % 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: 2.14 (0.27), residues: 980 helix: 2.25 (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 0.008 0.001 TYR D 227 PHE 0.015 0.001 PHE A 212 TRP 0.005 0.001 TRP C 11 HIS 0.004 0.001 HIS D 180 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.14 ( 7620) covalent geometry : angle 0.52623 / 0.29 (10392) hydrogen bonds : bond 0.04554 / 3.12 ( 540) hydrogen bonds : angle 5.13936 / 3.70 ( 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: 10 poor density : 71 time to evaluate : 0.419 Fit side-chains REVERT: D 191 ILE cc_start: 0.8274 (OUTLIER) cc_final: 0.7953 (mp) REVERT: D 225 LEU cc_start: 0.8650 (OUTLIER) cc_final: 0.8095 (tm) REVERT: B 225 LEU cc_start: 0.8649 (OUTLIER) cc_final: 0.8093 (tm) REVERT: C 51 LYS cc_start: 0.8864 (OUTLIER) cc_final: 0.8301 (tttt) REVERT: C 225 LEU cc_start: 0.8651 (OUTLIER) cc_final: 0.8103 (tm) REVERT: A 225 LEU cc_start: 0.8640 (OUTLIER) cc_final: 0.8098 (tm) outliers start: 10 outliers final: 3 residues processed: 80 average time/residue: 1.0570 time to fit residues: 91.0648 Evaluate side-chains 79 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 70 time to evaluate : 0.416 ------------------------------------------------------------------------------- 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 51 LYS 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 27 optimal weight: 0.0970 chunk 65 optimal weight: 9.9990 chunk 22 optimal weight: 6.9990 chunk 9 optimal weight: 7.9990 chunk 47 optimal weight: 2.9990 chunk 71 optimal weight: 0.2980 chunk 57 optimal weight: 8.9990 chunk 53 optimal weight: 0.9990 chunk 8 optimal weight: 3.9990 chunk 12 optimal weight: 10.0000 chunk 6 optimal weight: 2.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.115125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.098462 restraints weight = 45725.422| |-----------------------------------------------------------------------------| r_work (start): 0.3002 rms_B_bonded: 1.79 r_work: 0.2930 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.2825 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.2825 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2824 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2824 r_free = 0.2824 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2824 r_free = 0.2824 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2824 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8728 moved from start: 0.0935 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= 0.113 Angle : 0.495 7.171 10392 Z= 0.268 Chirality : 0.036 0.143 1268 Planarity : 0.003 0.031 1276 Dihedral : 8.137 51.376 1400 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.41 % Allowed : 3.00 % Favored : 96.59 % Rotamer: Outliers : 1.22 % Allowed : 13.51 % Favored : 85.27 % 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: 2.42 (0.27), residues: 980 helix: 2.49 (0.20), residues: 644 sheet: None (None), residues: 0 loop : -0.17 (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 0.007 0.001 TRP C 11 HIS 0.004 0.001 HIS D 180 Details of bonding type rmsd/Z covalent geometry : bond 0.00222 / 0.11 ( 7620) covalent geometry : angle 0.49504 / 0.27 (10392) hydrogen bonds : bond 0.04118 / 2.83 ( 540) hydrogen bonds : angle 5.00340 / 3.60 ( 1596) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5277.68 seconds wall clock time: 90 minutes 15.93 seconds (5415.93 seconds total)