Starting phenix.real_space_refine on Fri Jul 3 14:55:27 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cp3_45798/07_2026/9cp3_45798.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cp3_45798/07_2026/9cp3_45798.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.94 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9cp3_45798/07_2026/9cp3_45798.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cp3_45798/07_2026/9cp3_45798.map" model { file = "/net/cci-nas-00/data/ceres_data/9cp3_45798/07_2026/9cp3_45798.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cp3_45798/07_2026/9cp3_45798.cif" } resolution = 2.94 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= 0.000 sd= 0.024 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 474 atoms to isotropic. 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: 6 Type Number sf(0) Gaussians P 45 5.49 5 S 41 5.16 5 C 8718 2.51 5 N 2311 2.21 5 O 2749 1.98 5 H 110 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 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: 13974 Number of models: 1 Model: "" Number of chains: 10 Chain: "B" Number of atoms: 2458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2458 Classifications: {'peptide': 317} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 303} Chain breaks: 1 Chain: "C" Number of atoms: 2458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2458 Classifications: {'peptide': 317} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 303} Chain breaks: 1 Chain: "E" Number of atoms: 1424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1424 Classifications: {'peptide': 183} Link IDs: {'PTRANS': 7, 'TRANS': 175} Chain breaks: 3 Chain: "D" Number of atoms: 2421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 312, 2421 Classifications: {'peptide': 312} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 299} Chain breaks: 1 Chain: "A" Number of atoms: 2458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2458 Classifications: {'peptide': 317} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 303} Chain breaks: 1 Chain: "S" Number of atoms: 675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 675 Classifications: {'RNA': 32} Modifications used: {'5*END': 1, 'rna2p_pur': 7, 'rna2p_pyr': 10, 'rna3p_pur': 9, 'rna3p_pyr': 6} Link IDs: {'rna2p': 16, 'rna3p': 15} Chain: "G" Number of atoms: 1752 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1752 Classifications: {'peptide': 204} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 193} Chain breaks: 6 Chain: "M" Number of atoms: 288 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 288 Classifications: {'DNA': 14} Link IDs: {'rna3p': 13} Chain: "C" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'TRS': 1} Classifications: {'undetermined': 1} Chain: "S" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 32 Unusual residues: {'TRS': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 3.21, per 1000 atoms: 0.23 Number of scatterers: 13974 At special positions: 0 Unit cell: (83.78, 105.08, 166.14, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 41 16.00 P 45 15.00 O 2749 8.00 N 2311 7.00 C 8718 6.00 H 110 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: 1.23 Conformation dependent library (CDL) restraints added in 567.8 milliseconds 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3038 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 20 sheets defined 32.4% alpha, 17.0% beta 10 base pairs and 13 stacking pairs defined. Time for finding SS restraints: 1.35 Creating SS restraints... Processing helix chain 'B' and resid 49 through 69 removed outlier: 4.306A pdb=" N LEU B 53 " --> pdb=" O SER B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 78 removed outlier: 3.906A pdb=" N GLN B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 94 Processing helix chain 'B' and resid 103 through 115 Processing helix chain 'B' and resid 116 through 121 Processing helix chain 'B' and resid 207 through 225 removed outlier: 3.835A pdb=" N LEU B 211 " --> pdb=" O GLY B 207 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N ALA B 216 " --> pdb=" O GLU B 212 " (cutoff:3.500A) removed outlier: 5.147A pdb=" N LYS B 217 " --> pdb=" O ARG B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 225 through 232 removed outlier: 4.351A pdb=" N LEU B 229 " --> pdb=" O ALA B 225 " (cutoff:3.500A) Processing helix chain 'B' and resid 270 through 285 Processing helix chain 'B' and resid 310 through 321 removed outlier: 4.033A pdb=" N LEU B 314 " --> pdb=" O THR B 310 " (cutoff:3.500A) Processing helix chain 'C' and resid 50 through 69 Processing helix chain 'C' and resid 73 through 78 removed outlier: 3.899A pdb=" N GLN C 78 " --> pdb=" O SER C 74 " (cutoff:3.500A) Processing helix chain 'C' and resid 86 through 94 Processing helix chain 'C' and resid 103 through 113 Processing helix chain 'C' and resid 116 through 121 Processing helix chain 'C' and resid 207 through 225 removed outlier: 3.794A pdb=" N LEU C 211 " --> pdb=" O GLY C 207 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N ALA C 216 " --> pdb=" O GLU C 212 " (cutoff:3.500A) removed outlier: 5.133A pdb=" N LYS C 217 " --> pdb=" O ARG C 213 " (cutoff:3.500A) Processing helix chain 'C' and resid 225 through 232 removed outlier: 4.331A pdb=" N LEU C 229 " --> pdb=" O ALA C 225 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 285 Processing helix chain 'C' and resid 310 through 321 removed outlier: 4.029A pdb=" N LEU C 314 " --> pdb=" O THR C 310 " (cutoff:3.500A) Processing helix chain 'E' and resid 49 through 67 removed outlier: 4.184A pdb=" N LEU E 53 " --> pdb=" O SER E 49 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LYS E 67 " --> pdb=" O ASP E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 73 through 78 removed outlier: 4.350A pdb=" N GLN E 78 " --> pdb=" O SER E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 86 through 94 removed outlier: 3.631A pdb=" N LEU E 90 " --> pdb=" O THR E 86 " (cutoff:3.500A) Processing helix chain 'E' and resid 103 through 113 Processing helix chain 'E' and resid 116 through 122 Processing helix chain 'E' and resid 207 through 225 removed outlier: 3.583A pdb=" N LEU E 211 " --> pdb=" O GLY E 207 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N ALA E 216 " --> pdb=" O GLU E 212 " (cutoff:3.500A) removed outlier: 5.092A pdb=" N LYS E 217 " --> pdb=" O ARG E 213 " (cutoff:3.500A) Processing helix chain 'E' and resid 226 through 232 Processing helix chain 'D' and resid 49 through 69 removed outlier: 4.403A pdb=" N LEU D 53 " --> pdb=" O SER D 49 " (cutoff:3.500A) Processing helix chain 'D' and resid 73 through 78 removed outlier: 3.898A pdb=" N GLN D 78 " --> pdb=" O SER D 74 " (cutoff:3.500A) Processing helix chain 'D' and resid 86 through 94 Processing helix chain 'D' and resid 103 through 115 Processing helix chain 'D' and resid 116 through 121 Processing helix chain 'D' and resid 207 through 225 removed outlier: 3.762A pdb=" N LEU D 211 " --> pdb=" O GLY D 207 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N ALA D 216 " --> pdb=" O GLU D 212 " (cutoff:3.500A) removed outlier: 5.083A pdb=" N LYS D 217 " --> pdb=" O ARG D 213 " (cutoff:3.500A) Processing helix chain 'D' and resid 225 through 232 removed outlier: 4.349A pdb=" N LEU D 229 " --> pdb=" O ALA D 225 " (cutoff:3.500A) Processing helix chain 'D' and resid 270 through 285 Processing helix chain 'D' and resid 310 through 321 removed outlier: 4.059A pdb=" N LEU D 314 " --> pdb=" O THR D 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 49 through 69 removed outlier: 4.213A pdb=" N LEU A 53 " --> pdb=" O SER A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 94 removed outlier: 3.613A pdb=" N LEU A 90 " --> pdb=" O THR A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 115 Processing helix chain 'A' and resid 116 through 121 Processing helix chain 'A' and resid 192 through 195 Processing helix chain 'A' and resid 208 through 225 removed outlier: 4.805A pdb=" N ALA A 216 " --> pdb=" O GLU A 212 " (cutoff:3.500A) removed outlier: 4.959A pdb=" N LYS A 217 " --> pdb=" O ARG A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 232 removed outlier: 4.017A pdb=" N LEU A 229 " --> pdb=" O ALA A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 285 removed outlier: 3.793A pdb=" N THR A 273 " --> pdb=" O TYR A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 321 removed outlier: 4.067A pdb=" N LEU A 314 " --> pdb=" O THR A 310 " (cutoff:3.500A) Processing helix chain 'G' and resid 32 through 42 removed outlier: 3.588A pdb=" N LEU G 36 " --> pdb=" O PRO G 32 " (cutoff:3.500A) Processing helix chain 'G' and resid 129 through 138 removed outlier: 3.689A pdb=" N LEU G 133 " --> pdb=" O SER G 129 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N TRP G 138 " --> pdb=" O GLU G 134 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 2 through 13 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 2 through 13 current: chain 'B' and resid 174 through 190 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 174 through 190 current: chain 'B' and resid 289 through 295 removed outlier: 4.113A pdb=" N THR B 306 " --> pdb=" O ALA B 291 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 29 through 36 Processing sheet with id=AA3, first strand: chain 'B' and resid 123 through 125 Processing sheet with id=AA4, first strand: chain 'C' and resid 2 through 13 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 2 through 13 current: chain 'C' and resid 174 through 190 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 174 through 190 current: chain 'C' and resid 289 through 295 removed outlier: 3.983A pdb=" N THR C 306 " --> pdb=" O ALA C 291 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 29 through 36 Processing sheet with id=AA6, first strand: chain 'C' and resid 123 through 125 Processing sheet with id=AA7, first strand: chain 'E' and resid 137 through 138 removed outlier: 4.182A pdb=" N GLY E 4 " --> pdb=" O PHE E 188 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 29 through 36 Processing sheet with id=AA9, first strand: chain 'E' and resid 123 through 125 Processing sheet with id=AB1, first strand: chain 'D' and resid 2 through 13 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 2 through 13 current: chain 'D' and resid 174 through 190 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 174 through 190 current: chain 'D' and resid 289 through 295 removed outlier: 4.131A pdb=" N THR D 306 " --> pdb=" O ALA D 291 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 29 through 36 Processing sheet with id=AB3, first strand: chain 'D' and resid 123 through 125 Processing sheet with id=AB4, first strand: chain 'A' and resid 2 through 13 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 2 through 13 current: chain 'A' and resid 174 through 182 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 174 through 182 current: chain 'A' and resid 289 through 295 removed outlier: 8.870A pdb=" N THR A 306 " --> pdb=" O ALA A 289 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N ALA A 291 " --> pdb=" O THR A 306 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'A' and resid 29 through 35 Processing sheet with id=AB6, first strand: chain 'G' and resid 69 through 73 removed outlier: 4.036A pdb=" N GLY G 117 " --> pdb=" O LEU G 10 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LEU G 10 " --> pdb=" O GLY G 117 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ASN G 154 " --> pdb=" O PHE G 7 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'G' and resid 13 through 14 Processing sheet with id=AB8, first strand: chain 'G' and resid 161 through 163 removed outlier: 3.563A pdb=" N VAL G 163 " --> pdb=" O ALA G 229 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ALA G 229 " --> pdb=" O VAL G 163 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N GLU G 228 " --> pdb=" O PHE G 239 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N VAL G 232 " --> pdb=" O GLU G 235 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'G' and resid 167 through 169 Processing sheet with id=AC1, first strand: chain 'G' and resid 173 through 174 Processing sheet with id=AC2, first strand: chain 'G' and resid 212 through 213 removed outlier: 3.793A pdb=" N ALA G 218 " --> pdb=" O THR G 213 " (cutoff:3.500A) 426 hydrogen bonds defined for protein. 1206 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 24 hydrogen bonds 44 hydrogen bond angles 0 basepair planarities 10 basepair parallelities 13 stacking parallelities Total time for adding SS restraints: 2.21 Time building geometry restraints manager: 1.49 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: 110 1.03 - 1.23: 19 1.23 - 1.42: 5834 1.42 - 1.61: 8259 1.61 - 1.81: 81 Bond restraints: 14303 Sorted by residual: bond pdb=" N ILE G 209 " pdb=" CA ILE G 209 " ideal model delta sigma weight residual 1.459 1.500 -0.041 1.19e-02 7.06e+03 1.17e+01 bond pdb=" N GLU G 221 " pdb=" CA GLU G 221 " ideal model delta sigma weight residual 1.453 1.497 -0.044 1.31e-02 5.83e+03 1.13e+01 bond pdb=" N GLU G 221 " pdb=" H GLU G 221 " ideal model delta sigma weight residual 0.860 0.924 -0.064 2.00e-02 2.50e+03 1.03e+01 bond pdb=" N LEU G 210 " pdb=" H LEU G 210 " ideal model delta sigma weight residual 0.860 0.921 -0.061 2.00e-02 2.50e+03 9.39e+00 bond pdb=" N ILE G 209 " pdb=" H ILE G 209 " ideal model delta sigma weight residual 0.860 0.918 -0.058 2.00e-02 2.50e+03 8.33e+00 ... (remaining 14298 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.13: 18793 1.13 - 2.26: 599 2.26 - 3.39: 185 3.39 - 4.53: 19 4.53 - 5.66: 7 Bond angle restraints: 19603 Sorted by residual: angle pdb=" O4' DG M 23 " pdb=" C4' DG M 23 " pdb=" C3' DG M 23 " ideal model delta sigma weight residual 106.00 103.22 2.78 6.00e-01 2.78e+00 2.15e+01 angle pdb=" O4' DC M 21 " pdb=" C4' DC M 21 " pdb=" C3' DC M 21 " ideal model delta sigma weight residual 106.00 103.28 2.72 6.00e-01 2.78e+00 2.05e+01 angle pdb=" N3 DT M 16 " pdb=" C4 DT M 16 " pdb=" O4 DT M 16 " ideal model delta sigma weight residual 119.90 122.47 -2.57 6.00e-01 2.78e+00 1.83e+01 angle pdb=" N3 DT M 15 " pdb=" C4 DT M 15 " pdb=" O4 DT M 15 " ideal model delta sigma weight residual 119.90 122.37 -2.47 6.00e-01 2.78e+00 1.69e+01 angle pdb=" N3 DT M 20 " pdb=" C4 DT M 20 " pdb=" O4 DT M 20 " ideal model delta sigma weight residual 119.90 122.36 -2.46 6.00e-01 2.78e+00 1.68e+01 ... (remaining 19598 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.55: 8406 35.55 - 71.10: 186 71.10 - 106.65: 22 106.65 - 142.20: 0 142.20 - 177.76: 4 Dihedral angle restraints: 8618 sinusoidal: 3876 harmonic: 4742 Sorted by residual: dihedral pdb=" O4' U S 2 " pdb=" C1' U S 2 " pdb=" N1 U S 2 " pdb=" C2 U S 2 " ideal model delta sinusoidal sigma weight residual -128.00 49.76 -177.76 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' U S 32 " pdb=" C1' U S 32 " pdb=" N1 U S 32 " pdb=" C2 U S 32 " ideal model delta sinusoidal sigma weight residual 232.00 58.24 173.76 1 1.70e+01 3.46e-03 6.62e+01 dihedral pdb=" O4' C S 27 " pdb=" C1' C S 27 " pdb=" N1 C S 27 " pdb=" C2 C S 27 " ideal model delta sinusoidal sigma weight residual -128.00 -48.59 -79.41 1 1.70e+01 3.46e-03 2.71e+01 ... (remaining 8615 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 1637 0.042 - 0.084: 415 0.084 - 0.126: 160 0.126 - 0.168: 15 0.168 - 0.210: 4 Chirality restraints: 2231 Sorted by residual: chirality pdb=" CA LEU G 210 " pdb=" N LEU G 210 " pdb=" C LEU G 210 " pdb=" CB LEU G 210 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.11e+00 chirality pdb=" C1' U S 15 " pdb=" O4' U S 15 " pdb=" C2' U S 15 " pdb=" N1 U S 15 " both_signs ideal model delta sigma weight residual False 2.45 2.25 0.19 2.00e-01 2.50e+01 9.44e-01 chirality pdb=" CB ILE G 114 " pdb=" CA ILE G 114 " pdb=" CG1 ILE G 114 " pdb=" CG2 ILE G 114 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.18 2.00e-01 2.50e+01 7.79e-01 ... (remaining 2228 not shown) Planarity restraints: 2298 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' U S 15 " -0.018 2.00e-02 2.50e+03 2.49e-02 1.40e+01 pdb=" N1 U S 15 " 0.057 2.00e-02 2.50e+03 pdb=" C2 U S 15 " -0.041 2.00e-02 2.50e+03 pdb=" O2 U S 15 " 0.011 2.00e-02 2.50e+03 pdb=" N3 U S 15 " 0.006 2.00e-02 2.50e+03 pdb=" C4 U S 15 " -0.000 2.00e-02 2.50e+03 pdb=" O4 U S 15 " 0.002 2.00e-02 2.50e+03 pdb=" C5 U S 15 " -0.007 2.00e-02 2.50e+03 pdb=" C6 U S 15 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS G 220 " 0.016 2.00e-02 2.50e+03 3.23e-02 1.05e+01 pdb=" C LYS G 220 " -0.056 2.00e-02 2.50e+03 pdb=" O LYS G 220 " 0.021 2.00e-02 2.50e+03 pdb=" N GLU G 221 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DT M 20 " 0.020 2.00e-02 2.50e+03 1.93e-02 9.30e+00 pdb=" N1 DT M 20 " -0.050 2.00e-02 2.50e+03 pdb=" C2 DT M 20 " 0.027 2.00e-02 2.50e+03 pdb=" O2 DT M 20 " -0.004 2.00e-02 2.50e+03 pdb=" N3 DT M 20 " -0.002 2.00e-02 2.50e+03 pdb=" C4 DT M 20 " -0.001 2.00e-02 2.50e+03 pdb=" O4 DT M 20 " -0.001 2.00e-02 2.50e+03 pdb=" C5 DT M 20 " 0.003 2.00e-02 2.50e+03 pdb=" C7 DT M 20 " 0.005 2.00e-02 2.50e+03 pdb=" C6 DT M 20 " 0.003 2.00e-02 2.50e+03 ... (remaining 2295 not shown) Histogram of nonbonded interaction distances: 1.85 - 2.40: 114 2.40 - 2.95: 6402 2.95 - 3.50: 15235 3.50 - 4.05: 24417 4.05 - 4.60: 34936 Nonbonded interactions: 81104 Sorted by model distance: nonbonded pdb=" CE1 TYR G 29 " pdb="HD21 LEU G 217 " model vdw 1.847 2.970 nonbonded pdb=" CD1 TYR G 29 " pdb="HD21 LEU G 217 " model vdw 1.917 2.970 nonbonded pdb=" H THR G 214 " pdb="HG22 THR G 214 " model vdw 1.931 2.270 nonbonded pdb=" OE2 GLU G 187 " pdb=" HB ILE G 212 " model vdw 2.026 2.620 nonbonded pdb=" HA TYR G 215 " pdb=" HA PRO G 216 " model vdw 2.046 2.440 ... (remaining 81099 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 163 or resid 173 through 321)) selection = (chain 'B' and (resid 1 through 163 or resid 173 through 321)) selection = (chain 'C' and (resid 1 through 163 or resid 173 through 321)) selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.540 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.120 Extract box with map and model: 0.150 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 14.290 Find NCS groups from input model: 0.230 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:8.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 14193 Z= 0.173 Angle : 0.497 5.658 19350 Z= 0.319 Chirality : 0.043 0.210 2231 Planarity : 0.004 0.064 2287 Dihedral : 15.669 177.756 5543 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 0.21 % Allowed : 0.00 % Favored : 99.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.34 (0.21), residues: 1612 helix: 1.40 (0.25), residues: 472 sheet: 1.00 (0.27), residues: 364 loop : -0.92 (0.21), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 28 TYR 0.006 0.001 TYR C 141 PHE 0.014 0.001 PHE A 159 TRP 0.010 0.001 TRP G 12 HIS 0.003 0.001 HIS B 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.17 (14193) covalent geometry : angle 0.49700 / 0.32 (19350) hydrogen bonds : bond 0.14402 / 9.57 ( 450) hydrogen bonds : angle 6.02948 / 4.28 ( 1250) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 1397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 280 time to evaluate : 0.502 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 63 ASP cc_start: 0.8212 (m-30) cc_final: 0.7594 (t0) REVERT: E 78 GLN cc_start: 0.8426 (mp10) cc_final: 0.8218 (pm20) REVERT: E 190 LEU cc_start: 0.8602 (tp) cc_final: 0.8227 (tm) REVERT: A 132 ARG cc_start: 0.7051 (ttm170) cc_final: 0.6801 (mtt180) REVERT: G 129 SER cc_start: 0.7659 (t) cc_final: 0.7451 (t) REVERT: G 130 LYS cc_start: 0.6955 (mttt) cc_final: 0.6572 (tppt) REVERT: G 185 PHE cc_start: 0.7438 (m-80) cc_final: 0.7212 (m-80) REVERT: G 209 ILE cc_start: 0.8230 (mt) cc_final: 0.7968 (mp) REVERT: G 224 VAL cc_start: 0.8054 (t) cc_final: 0.7847 (t) outliers start: 3 outliers final: 1 residues processed: 282 average time/residue: 0.5467 time to fit residues: 169.4525 Evaluate side-chains 127 residues out of total 1397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 126 time to evaluate : 0.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 233 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 98 optimal weight: 0.0670 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 7.9990 chunk 77 optimal weight: 0.0770 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 4.9990 chunk 149 optimal weight: 3.9990 overall best weight: 0.5878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 16 ASN B 265 HIS C 16 ASN C 265 HIS E 214 GLN D 16 ASN D 265 HIS A 16 ASN A 214 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.124912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.099718 restraints weight = 29697.738| |-----------------------------------------------------------------------------| r_work (start): 0.3649 rms_B_bonded: 3.21 r_work: 0.3527 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.3527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.1846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 14193 Z= 0.114 Angle : 0.450 5.419 19350 Z= 0.247 Chirality : 0.039 0.133 2231 Planarity : 0.004 0.050 2287 Dihedral : 15.140 172.649 2423 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 17.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.15 % Allowed : 11.52 % Favored : 86.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.61 (0.21), residues: 1612 helix: 1.96 (0.25), residues: 477 sheet: 1.12 (0.27), residues: 349 loop : -0.95 (0.21), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 207 TYR 0.013 0.001 TYR A 40 PHE 0.011 0.001 PHE C 159 TRP 0.008 0.001 TRP G 12 HIS 0.005 0.001 HIS A 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.11 (14193) covalent geometry : angle 0.45014 / 0.25 (19350) hydrogen bonds : bond 0.04166 / 2.96 ( 450) hydrogen bonds : angle 4.56190 / 3.25 ( 1250) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 119 time to evaluate : 0.696 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 63 ASP cc_start: 0.8198 (m-30) cc_final: 0.7556 (t0) REVERT: E 78 GLN cc_start: 0.8547 (mp10) cc_final: 0.8259 (pm20) REVERT: E 112 MET cc_start: 0.7711 (ttm) cc_final: 0.7055 (ttp) REVERT: A 132 ARG cc_start: 0.7012 (ttm170) cc_final: 0.6777 (mtt180) REVERT: G 49 ASP cc_start: 0.7865 (m-30) cc_final: 0.7583 (m-30) REVERT: G 68 MET cc_start: 0.6367 (mmt) cc_final: 0.5611 (pmm) REVERT: G 130 LYS cc_start: 0.7197 (mttt) cc_final: 0.6723 (tppt) REVERT: G 179 VAL cc_start: 0.7144 (t) cc_final: 0.6877 (p) REVERT: G 224 VAL cc_start: 0.8164 (t) cc_final: 0.7853 (m) outliers start: 30 outliers final: 13 residues processed: 140 average time/residue: 0.4906 time to fit residues: 76.7294 Evaluate side-chains 117 residues out of total 1397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 104 time to evaluate : 0.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain C residue 63 ASP Chi-restraints excluded: chain C residue 301 VAL Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain E residue 134 THR Chi-restraints excluded: chain E residue 137 ILE Chi-restraints excluded: chain D residue 185 THR Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain G residue 51 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 90 optimal weight: 6.9990 chunk 63 optimal weight: 6.9990 chunk 72 optimal weight: 0.7980 chunk 74 optimal weight: 5.9990 chunk 95 optimal weight: 2.9990 chunk 41 optimal weight: 5.9990 chunk 7 optimal weight: 4.9990 chunk 16 optimal weight: 5.9990 chunk 100 optimal weight: 0.9980 chunk 115 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 16 ASN B 176 ASN C 11 ASN C 16 ASN D 16 ASN D 160 HIS A 295 ASN A 296 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.118166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.092553 restraints weight = 30583.902| |-----------------------------------------------------------------------------| r_work (start): 0.3529 rms_B_bonded: 3.23 r_work: 0.3404 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.3404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.2778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 14193 Z= 0.229 Angle : 0.576 7.217 19350 Z= 0.310 Chirality : 0.043 0.151 2231 Planarity : 0.005 0.047 2287 Dihedral : 15.388 175.885 2421 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 23.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 3.79 % Allowed : 13.67 % Favored : 82.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.33 (0.20), residues: 1612 helix: 1.19 (0.23), residues: 476 sheet: 0.45 (0.26), residues: 337 loop : -1.44 (0.20), residues: 799 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 213 TYR 0.021 0.002 TYR A 292 PHE 0.029 0.002 PHE A 186 TRP 0.012 0.002 TRP G 138 HIS 0.010 0.002 HIS B 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00514 / 0.23 (14193) covalent geometry : angle 0.57617 / 0.31 (19350) hydrogen bonds : bond 0.05227 / 3.61 ( 450) hydrogen bonds : angle 4.84262 / 3.42 ( 1250) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 101 time to evaluate : 0.485 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 124 MET cc_start: 0.7752 (OUTLIER) cc_final: 0.7227 (ttt) REVERT: E 63 ASP cc_start: 0.8347 (m-30) cc_final: 0.7667 (t0) REVERT: E 78 GLN cc_start: 0.8456 (mp10) cc_final: 0.8176 (pm20) REVERT: E 142 MET cc_start: 0.7500 (mpp) cc_final: 0.7135 (mpp) REVERT: E 184 TYR cc_start: 0.4942 (OUTLIER) cc_final: 0.4489 (m-10) REVERT: E 190 LEU cc_start: 0.7811 (OUTLIER) cc_final: 0.7368 (mt) REVERT: A 124 MET cc_start: 0.8192 (OUTLIER) cc_final: 0.7154 (tmm) REVERT: G 66 ASN cc_start: 0.5592 (m-40) cc_final: 0.4812 (t0) REVERT: G 68 MET cc_start: 0.6397 (mmt) cc_final: 0.5584 (pmm) REVERT: G 143 ILE cc_start: 0.7179 (OUTLIER) cc_final: 0.6352 (pp) REVERT: G 179 VAL cc_start: 0.6650 (t) cc_final: 0.6385 (p) REVERT: G 185 PHE cc_start: 0.7434 (m-80) cc_final: 0.7101 (m-80) REVERT: G 224 VAL cc_start: 0.8136 (t) cc_final: 0.7811 (m) outliers start: 53 outliers final: 28 residues processed: 138 average time/residue: 0.4599 time to fit residues: 71.0250 Evaluate side-chains 125 residues out of total 1397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 92 time to evaluate : 0.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 124 MET Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain C residue 63 ASP Chi-restraints excluded: chain C residue 247 LEU Chi-restraints excluded: chain C residue 301 VAL Chi-restraints excluded: chain C residue 313 ASP Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain E residue 134 THR Chi-restraints excluded: chain E residue 137 ILE Chi-restraints excluded: chain E residue 184 TYR Chi-restraints excluded: chain E residue 190 LEU Chi-restraints excluded: chain D residue 6 VAL Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 185 THR Chi-restraints excluded: chain D residue 221 SER Chi-restraints excluded: chain D residue 224 LYS Chi-restraints excluded: chain D residue 268 ASP Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain D residue 311 VAL Chi-restraints excluded: chain A residue 124 MET Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 121 VAL Chi-restraints excluded: chain G residue 143 ILE Chi-restraints excluded: chain G residue 146 LYS Chi-restraints excluded: chain G residue 157 VAL Chi-restraints excluded: chain G residue 238 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 57 optimal weight: 3.9990 chunk 96 optimal weight: 1.9990 chunk 157 optimal weight: 2.9990 chunk 95 optimal weight: 0.9980 chunk 114 optimal weight: 6.9990 chunk 103 optimal weight: 4.9990 chunk 145 optimal weight: 0.8980 chunk 27 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 93 optimal weight: 0.9980 chunk 56 optimal weight: 0.0270 overall best weight: 0.9840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 16 ASN C 16 ASN D 16 ASN A 16 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.119776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.094132 restraints weight = 30346.256| |-----------------------------------------------------------------------------| r_work (start): 0.3557 rms_B_bonded: 3.23 r_work: 0.3434 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.3434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.2830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14193 Z= 0.123 Angle : 0.426 3.971 19350 Z= 0.233 Chirality : 0.039 0.137 2231 Planarity : 0.003 0.040 2287 Dihedral : 15.305 175.416 2421 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 22.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 2.72 % Allowed : 15.53 % Favored : 81.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.10 (0.20), residues: 1612 helix: 1.64 (0.24), residues: 477 sheet: 0.50 (0.27), residues: 334 loop : -1.44 (0.20), residues: 801 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 207 TYR 0.018 0.001 TYR E 227 PHE 0.014 0.001 PHE A 186 TRP 0.008 0.001 TRP G 12 HIS 0.003 0.001 HIS B 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.12 (14193) covalent geometry : angle 0.42563 / 0.23 (19350) hydrogen bonds : bond 0.03985 / 2.85 ( 450) hydrogen bonds : angle 4.29134 / 3.05 ( 1250) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 101 time to evaluate : 0.513 Fit side-chains revert: symmetry clash REVERT: E 63 ASP cc_start: 0.8292 (m-30) cc_final: 0.7687 (t0) REVERT: E 78 GLN cc_start: 0.8459 (mp10) cc_final: 0.8161 (pm20) REVERT: E 190 LEU cc_start: 0.7749 (OUTLIER) cc_final: 0.7400 (mt) REVERT: A 124 MET cc_start: 0.8136 (OUTLIER) cc_final: 0.7024 (tmm) REVERT: A 260 MET cc_start: 0.6443 (mmm) cc_final: 0.5914 (mmm) REVERT: G 66 ASN cc_start: 0.5579 (m-40) cc_final: 0.4842 (t0) REVERT: G 68 MET cc_start: 0.6350 (mmt) cc_final: 0.5565 (pmm) REVERT: G 224 VAL cc_start: 0.8175 (t) cc_final: 0.7847 (m) outliers start: 38 outliers final: 19 residues processed: 127 average time/residue: 0.4358 time to fit residues: 62.5818 Evaluate side-chains 116 residues out of total 1397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 95 time to evaluate : 0.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 63 ASP Chi-restraints excluded: chain C residue 301 VAL Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 64 ILE Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain E residue 134 THR Chi-restraints excluded: chain E residue 190 LEU Chi-restraints excluded: chain D residue 88 GLU Chi-restraints excluded: chain D residue 142 MET Chi-restraints excluded: chain D residue 185 THR Chi-restraints excluded: chain D residue 224 LYS Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain D residue 311 VAL Chi-restraints excluded: chain A residue 124 MET Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 125 THR Chi-restraints excluded: chain G residue 146 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 90 optimal weight: 8.9990 chunk 97 optimal weight: 2.9990 chunk 83 optimal weight: 0.9990 chunk 23 optimal weight: 3.9990 chunk 155 optimal weight: 5.9990 chunk 85 optimal weight: 2.9990 chunk 139 optimal weight: 1.9990 chunk 157 optimal weight: 10.0000 chunk 9 optimal weight: 0.0040 chunk 150 optimal weight: 6.9990 chunk 138 optimal weight: 0.9980 overall best weight: 1.3998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 16 ASN C 16 ASN C 160 HIS D 16 ASN A 16 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.118342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.092740 restraints weight = 30462.444| |-----------------------------------------------------------------------------| r_work (start): 0.3532 rms_B_bonded: 3.22 r_work: 0.3409 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.3078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 14193 Z= 0.166 Angle : 0.460 5.385 19350 Z= 0.250 Chirality : 0.040 0.135 2231 Planarity : 0.003 0.037 2287 Dihedral : 15.310 175.113 2421 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 24.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 3.44 % Allowed : 15.96 % Favored : 80.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.23 (0.20), residues: 1612 helix: 1.59 (0.23), residues: 477 sheet: 0.38 (0.28), residues: 324 loop : -1.52 (0.20), residues: 811 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 174 TYR 0.017 0.001 TYR G 172 PHE 0.022 0.002 PHE G 185 TRP 0.009 0.001 TRP G 12 HIS 0.003 0.001 HIS B 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00374 / 0.17 (14193) covalent geometry : angle 0.45958 / 0.25 (19350) hydrogen bonds : bond 0.04237 / 2.99 ( 450) hydrogen bonds : angle 4.35346 / 3.09 ( 1250) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 98 time to evaluate : 0.503 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 97 GLU cc_start: 0.9008 (pm20) cc_final: 0.8765 (pm20) REVERT: E 63 ASP cc_start: 0.8311 (m-30) cc_final: 0.7699 (t0) REVERT: E 78 GLN cc_start: 0.8447 (mp10) cc_final: 0.8147 (pm20) REVERT: E 124 MET cc_start: 0.7955 (ptt) cc_final: 0.7436 (ptt) REVERT: E 184 TYR cc_start: 0.4908 (OUTLIER) cc_final: 0.4492 (m-80) REVERT: E 190 LEU cc_start: 0.7756 (OUTLIER) cc_final: 0.7411 (mt) REVERT: A 124 MET cc_start: 0.8160 (OUTLIER) cc_final: 0.7036 (tmm) REVERT: A 260 MET cc_start: 0.6340 (mmm) cc_final: 0.5836 (mmm) REVERT: G 66 ASN cc_start: 0.5402 (m-40) cc_final: 0.5108 (t0) REVERT: G 68 MET cc_start: 0.6363 (mmt) cc_final: 0.5592 (pmm) REVERT: G 143 ILE cc_start: 0.6930 (OUTLIER) cc_final: 0.6702 (tt) REVERT: G 174 ARG cc_start: 0.7812 (mmt180) cc_final: 0.7455 (mmp-170) REVERT: G 185 PHE cc_start: 0.7123 (m-80) cc_final: 0.6775 (m-80) REVERT: G 224 VAL cc_start: 0.8196 (t) cc_final: 0.7886 (m) outliers start: 48 outliers final: 30 residues processed: 133 average time/residue: 0.4340 time to fit residues: 65.0128 Evaluate side-chains 127 residues out of total 1397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 93 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 6 VAL Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain C residue 16 ASN Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 63 ASP Chi-restraints excluded: chain C residue 301 VAL Chi-restraints excluded: chain C residue 313 ASP Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 64 ILE Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain E residue 134 THR Chi-restraints excluded: chain E residue 184 TYR Chi-restraints excluded: chain E residue 190 LEU Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 88 GLU Chi-restraints excluded: chain D residue 142 MET Chi-restraints excluded: chain D residue 185 THR Chi-restraints excluded: chain D residue 221 SER Chi-restraints excluded: chain D residue 253 THR Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain D residue 311 VAL Chi-restraints excluded: chain A residue 124 MET Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 121 VAL Chi-restraints excluded: chain G residue 143 ILE Chi-restraints excluded: chain G residue 146 LYS Chi-restraints excluded: chain G residue 157 VAL Chi-restraints excluded: chain G residue 210 LEU Chi-restraints excluded: chain G residue 238 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 76 optimal weight: 0.0270 chunk 116 optimal weight: 0.7980 chunk 137 optimal weight: 0.0970 chunk 23 optimal weight: 1.9990 chunk 127 optimal weight: 6.9990 chunk 124 optimal weight: 0.9980 chunk 66 optimal weight: 9.9990 chunk 68 optimal weight: 5.9990 chunk 78 optimal weight: 7.9990 chunk 5 optimal weight: 0.9980 chunk 110 optimal weight: 5.9990 overall best weight: 0.5836 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 16 ASN C 16 ASN D 16 ASN A 16 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.119606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.093989 restraints weight = 30251.197| |-----------------------------------------------------------------------------| r_work (start): 0.3553 rms_B_bonded: 3.22 r_work: 0.3431 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.3431 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.3091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 14193 Z= 0.094 Angle : 0.411 6.280 19350 Z= 0.222 Chirality : 0.039 0.135 2231 Planarity : 0.003 0.065 2287 Dihedral : 15.239 175.151 2421 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 24.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.79 % Allowed : 17.11 % Favored : 80.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.02 (0.21), residues: 1612 helix: 1.90 (0.24), residues: 479 sheet: 0.39 (0.28), residues: 334 loop : -1.46 (0.20), residues: 799 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 207 TYR 0.010 0.001 TYR G 172 PHE 0.018 0.001 PHE G 185 TRP 0.009 0.001 TRP G 12 HIS 0.003 0.001 HIS B 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00206 / 0.09 (14193) covalent geometry : angle 0.41088 / 0.22 (19350) hydrogen bonds : bond 0.03721 / 2.69 ( 450) hydrogen bonds : angle 4.06413 / 2.89 ( 1250) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 100 time to evaluate : 0.507 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 97 GLU cc_start: 0.8953 (pm20) cc_final: 0.8708 (pm20) REVERT: E 63 ASP cc_start: 0.8299 (m-30) cc_final: 0.7697 (t0) REVERT: E 78 GLN cc_start: 0.8444 (mp10) cc_final: 0.8136 (pm20) REVERT: E 124 MET cc_start: 0.8158 (ptt) cc_final: 0.7678 (ptt) REVERT: A 124 MET cc_start: 0.8076 (OUTLIER) cc_final: 0.6860 (tmm) REVERT: A 260 MET cc_start: 0.6351 (mmm) cc_final: 0.5812 (mmm) REVERT: G 66 ASN cc_start: 0.5376 (m-40) cc_final: 0.5098 (t0) REVERT: G 68 MET cc_start: 0.6334 (mmt) cc_final: 0.5596 (pmm) REVERT: G 174 ARG cc_start: 0.7803 (mmt180) cc_final: 0.7453 (mmp-170) REVERT: G 185 PHE cc_start: 0.7041 (m-80) cc_final: 0.6677 (m-80) REVERT: G 224 VAL cc_start: 0.8190 (t) cc_final: 0.7873 (m) outliers start: 39 outliers final: 25 residues processed: 129 average time/residue: 0.4362 time to fit residues: 63.1176 Evaluate side-chains 120 residues out of total 1397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 94 time to evaluate : 0.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 6 VAL Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain C residue 63 ASP Chi-restraints excluded: chain C residue 301 VAL Chi-restraints excluded: chain C residue 313 ASP Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 64 ILE Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain E residue 134 THR Chi-restraints excluded: chain E residue 190 LEU Chi-restraints excluded: chain D residue 88 GLU Chi-restraints excluded: chain D residue 142 MET Chi-restraints excluded: chain D residue 185 THR Chi-restraints excluded: chain D residue 221 SER Chi-restraints excluded: chain D residue 268 ASP Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain D residue 311 VAL Chi-restraints excluded: chain A residue 124 MET Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 146 LYS Chi-restraints excluded: chain G residue 210 LEU Chi-restraints excluded: chain G residue 238 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 109 optimal weight: 10.0000 chunk 156 optimal weight: 7.9990 chunk 94 optimal weight: 4.9990 chunk 114 optimal weight: 0.0170 chunk 79 optimal weight: 2.9990 chunk 64 optimal weight: 0.9990 chunk 97 optimal weight: 0.8980 chunk 150 optimal weight: 6.9990 chunk 135 optimal weight: 2.9990 chunk 122 optimal weight: 4.9990 chunk 92 optimal weight: 4.9990 overall best weight: 1.5824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 160 HIS C 16 ASN D 16 ASN A 16 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.117601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.092040 restraints weight = 30285.005| |-----------------------------------------------------------------------------| r_work (start): 0.3518 rms_B_bonded: 3.19 r_work: 0.3396 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.3396 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.3314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 14193 Z= 0.176 Angle : 0.475 5.306 19350 Z= 0.257 Chirality : 0.040 0.139 2231 Planarity : 0.004 0.037 2287 Dihedral : 15.307 174.804 2421 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 27.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 3.58 % Allowed : 17.18 % Favored : 79.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.32 (0.20), residues: 1612 helix: 1.66 (0.23), residues: 477 sheet: 0.14 (0.28), residues: 326 loop : -1.58 (0.20), residues: 809 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG E 213 TYR 0.014 0.001 TYR G 172 PHE 0.015 0.002 PHE C 175 TRP 0.009 0.002 TRP G 12 HIS 0.003 0.001 HIS C 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00397 / 0.18 (14193) covalent geometry : angle 0.47510 / 0.26 (19350) hydrogen bonds : bond 0.04254 / 3.00 ( 450) hydrogen bonds : angle 4.33312 / 3.07 ( 1250) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 94 time to evaluate : 0.514 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 97 GLU cc_start: 0.9015 (pm20) cc_final: 0.8763 (pm20) REVERT: B 275 MET cc_start: 0.7619 (mpm) cc_final: 0.7415 (mpm) REVERT: E 63 ASP cc_start: 0.8309 (m-30) cc_final: 0.7692 (t0) REVERT: E 78 GLN cc_start: 0.8607 (mp10) cc_final: 0.8213 (pm20) REVERT: E 124 MET cc_start: 0.8018 (ptt) cc_final: 0.7434 (ptt) REVERT: D 1 MET cc_start: 0.8434 (mmm) cc_final: 0.8115 (mmm) REVERT: A 124 MET cc_start: 0.8134 (OUTLIER) cc_final: 0.6990 (tmm) REVERT: G 66 ASN cc_start: 0.5400 (m-40) cc_final: 0.5127 (t0) REVERT: G 68 MET cc_start: 0.6372 (mmt) cc_final: 0.5613 (pmm) REVERT: G 143 ILE cc_start: 0.6927 (OUTLIER) cc_final: 0.6717 (tt) REVERT: G 185 PHE cc_start: 0.7051 (m-80) cc_final: 0.6654 (m-80) REVERT: G 207 ARG cc_start: 0.8532 (ttm110) cc_final: 0.8305 (ttm110) REVERT: G 224 VAL cc_start: 0.8024 (t) cc_final: 0.7700 (m) outliers start: 50 outliers final: 34 residues processed: 128 average time/residue: 0.4247 time to fit residues: 61.4350 Evaluate side-chains 128 residues out of total 1397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 92 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 6 VAL Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 112 MET Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain C residue 16 ASN Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 63 ASP Chi-restraints excluded: chain C residue 301 VAL Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 64 ILE Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain E residue 134 THR Chi-restraints excluded: chain E residue 190 LEU Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 88 GLU Chi-restraints excluded: chain D residue 142 MET Chi-restraints excluded: chain D residue 185 THR Chi-restraints excluded: chain D residue 221 SER Chi-restraints excluded: chain D residue 253 THR Chi-restraints excluded: chain D residue 268 ASP Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain D residue 311 VAL Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 124 MET Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 80 THR Chi-restraints excluded: chain G residue 121 VAL Chi-restraints excluded: chain G residue 143 ILE Chi-restraints excluded: chain G residue 146 LYS Chi-restraints excluded: chain G residue 157 VAL Chi-restraints excluded: chain G residue 210 LEU Chi-restraints excluded: chain G residue 238 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 16 optimal weight: 5.9990 chunk 25 optimal weight: 0.5980 chunk 92 optimal weight: 4.9990 chunk 132 optimal weight: 0.7980 chunk 86 optimal weight: 3.9990 chunk 125 optimal weight: 0.0670 chunk 15 optimal weight: 0.9990 chunk 59 optimal weight: 0.0570 chunk 32 optimal weight: 0.0970 chunk 137 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 overall best weight: 0.3234 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 16 ASN D 16 ASN A 16 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.119624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.094110 restraints weight = 30181.079| |-----------------------------------------------------------------------------| r_work (start): 0.3557 rms_B_bonded: 3.22 r_work: 0.3435 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.3435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.3280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 14193 Z= 0.081 Angle : 0.402 4.882 19350 Z= 0.217 Chirality : 0.039 0.134 2231 Planarity : 0.003 0.061 2287 Dihedral : 15.211 175.101 2421 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 25.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 1.79 % Allowed : 19.11 % Favored : 79.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.07 (0.21), residues: 1612 helix: 2.08 (0.24), residues: 479 sheet: 0.40 (0.28), residues: 328 loop : -1.44 (0.20), residues: 805 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 207 TYR 0.018 0.001 TYR E 227 PHE 0.015 0.001 PHE G 185 TRP 0.010 0.002 TRP G 199 HIS 0.001 0.000 HIS A 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00177 / 0.08 (14193) covalent geometry : angle 0.40227 / 0.22 (19350) hydrogen bonds : bond 0.03538 / 2.58 ( 450) hydrogen bonds : angle 3.91090 / 2.80 ( 1250) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 96 time to evaluate : 0.532 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 97 GLU cc_start: 0.9043 (pm20) cc_final: 0.8786 (pm20) REVERT: E 63 ASP cc_start: 0.8298 (m-30) cc_final: 0.7704 (t0) REVERT: E 78 GLN cc_start: 0.8608 (mp10) cc_final: 0.8203 (pm20) REVERT: D 1 MET cc_start: 0.8289 (mmm) cc_final: 0.7949 (mmm) REVERT: G 66 ASN cc_start: 0.5382 (m-40) cc_final: 0.4893 (t0) REVERT: G 68 MET cc_start: 0.6324 (mmt) cc_final: 0.5593 (pmm) REVERT: G 174 ARG cc_start: 0.7889 (mmt180) cc_final: 0.7443 (mmp-170) REVERT: G 185 PHE cc_start: 0.6980 (m-80) cc_final: 0.6386 (m-80) REVERT: G 207 ARG cc_start: 0.8530 (ttm110) cc_final: 0.8324 (ttm110) REVERT: G 224 VAL cc_start: 0.8200 (t) cc_final: 0.7896 (m) outliers start: 25 outliers final: 17 residues processed: 114 average time/residue: 0.4258 time to fit residues: 54.8862 Evaluate side-chains 111 residues out of total 1397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 94 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 6 VAL Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain C residue 63 ASP Chi-restraints excluded: chain C residue 301 VAL Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 64 ILE Chi-restraints excluded: chain E residue 134 THR Chi-restraints excluded: chain D residue 88 GLU Chi-restraints excluded: chain D residue 142 MET Chi-restraints excluded: chain D residue 221 SER Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain G residue 238 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 30 optimal weight: 4.9990 chunk 77 optimal weight: 6.9990 chunk 112 optimal weight: 3.9990 chunk 117 optimal weight: 0.9990 chunk 132 optimal weight: 2.9990 chunk 159 optimal weight: 10.0000 chunk 55 optimal weight: 3.9990 chunk 43 optimal weight: 4.9990 chunk 129 optimal weight: 0.3980 chunk 123 optimal weight: 4.9990 chunk 58 optimal weight: 0.7980 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 16 ASN A 16 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.116627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.091196 restraints weight = 30587.144| |-----------------------------------------------------------------------------| r_work (start): 0.3507 rms_B_bonded: 3.20 r_work: 0.3385 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.3496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 14193 Z= 0.206 Angle : 0.515 6.452 19350 Z= 0.275 Chirality : 0.041 0.154 2231 Planarity : 0.004 0.050 2287 Dihedral : 15.338 174.664 2421 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 29.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 2.15 % Allowed : 19.11 % Favored : 78.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.44 (0.20), residues: 1612 helix: 1.57 (0.23), residues: 478 sheet: -0.04 (0.28), residues: 326 loop : -1.61 (0.20), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG G 207 TYR 0.015 0.002 TYR G 172 PHE 0.018 0.002 PHE C 175 TRP 0.010 0.002 TRP G 199 HIS 0.004 0.001 HIS C 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00467 / 0.21 (14193) covalent geometry : angle 0.51472 / 0.28 (19350) hydrogen bonds : bond 0.04535 / 3.17 ( 450) hydrogen bonds : angle 4.43355 / 3.14 ( 1250) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 94 time to evaluate : 0.496 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 97 GLU cc_start: 0.9101 (pm20) cc_final: 0.8848 (pm20) REVERT: E 63 ASP cc_start: 0.8314 (m-30) cc_final: 0.7697 (t0) REVERT: E 78 GLN cc_start: 0.8576 (mp10) cc_final: 0.8167 (pm20) REVERT: D 1 MET cc_start: 0.8391 (mmm) cc_final: 0.8061 (mmm) REVERT: G 66 ASN cc_start: 0.5407 (m-40) cc_final: 0.5144 (t0) REVERT: G 68 MET cc_start: 0.6386 (mmt) cc_final: 0.5643 (pmm) REVERT: G 143 ILE cc_start: 0.6946 (OUTLIER) cc_final: 0.6745 (tt) REVERT: G 174 ARG cc_start: 0.7944 (mmt180) cc_final: 0.7479 (mmp-170) REVERT: G 185 PHE cc_start: 0.7046 (m-80) cc_final: 0.6667 (m-80) REVERT: G 224 VAL cc_start: 0.8044 (t) cc_final: 0.7723 (m) outliers start: 30 outliers final: 23 residues processed: 116 average time/residue: 0.4431 time to fit residues: 58.2034 Evaluate side-chains 117 residues out of total 1397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 93 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 6 VAL Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 112 MET Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain C residue 16 ASN Chi-restraints excluded: chain C residue 63 ASP Chi-restraints excluded: chain C residue 301 VAL Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 64 ILE Chi-restraints excluded: chain E residue 134 THR Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 88 GLU Chi-restraints excluded: chain D residue 221 SER Chi-restraints excluded: chain D residue 268 ASP Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 142 MET Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 121 VAL Chi-restraints excluded: chain G residue 143 ILE Chi-restraints excluded: chain G residue 238 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 5 optimal weight: 0.9990 chunk 32 optimal weight: 2.9990 chunk 110 optimal weight: 4.9990 chunk 36 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 72 optimal weight: 0.6980 chunk 22 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 149 optimal weight: 8.9990 chunk 54 optimal weight: 0.6980 chunk 31 optimal weight: 2.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 16 ASN A 11 ASN A 16 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.117299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.091926 restraints weight = 30563.130| |-----------------------------------------------------------------------------| r_work (start): 0.3518 rms_B_bonded: 3.20 r_work: 0.3397 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.3531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14193 Z= 0.148 Angle : 0.462 8.626 19350 Z= 0.247 Chirality : 0.040 0.151 2231 Planarity : 0.003 0.063 2287 Dihedral : 15.325 175.085 2421 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 28.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 1.86 % Allowed : 19.40 % Favored : 78.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.37 (0.20), residues: 1612 helix: 1.69 (0.23), residues: 478 sheet: -0.01 (0.29), residues: 314 loop : -1.58 (0.20), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG G 207 TYR 0.015 0.001 TYR E 227 PHE 0.014 0.001 PHE G 185 TRP 0.011 0.002 TRP G 199 HIS 0.003 0.001 HIS C 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.15 (14193) covalent geometry : angle 0.46199 / 0.25 (19350) hydrogen bonds : bond 0.04067 / 2.89 ( 450) hydrogen bonds : angle 4.23393 / 3.01 ( 1250) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 93 time to evaluate : 0.523 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 97 GLU cc_start: 0.9121 (pm20) cc_final: 0.8865 (pm20) REVERT: E 63 ASP cc_start: 0.8316 (m-30) cc_final: 0.7707 (t0) REVERT: E 78 GLN cc_start: 0.8590 (mp10) cc_final: 0.8178 (pm20) REVERT: E 213 ARG cc_start: 0.8697 (mmt90) cc_final: 0.8317 (tpm170) REVERT: D 1 MET cc_start: 0.8408 (mmm) cc_final: 0.8066 (mmm) REVERT: A 124 MET cc_start: 0.8057 (OUTLIER) cc_final: 0.6881 (tmm) REVERT: G 66 ASN cc_start: 0.5406 (m-40) cc_final: 0.5149 (t0) REVERT: G 68 MET cc_start: 0.6393 (mmt) cc_final: 0.5645 (pmm) REVERT: G 174 ARG cc_start: 0.7914 (mmt180) cc_final: 0.7458 (mmp-170) REVERT: G 185 PHE cc_start: 0.7095 (m-80) cc_final: 0.6696 (m-80) REVERT: G 207 ARG cc_start: 0.8320 (ttm110) cc_final: 0.7602 (mtp-110) REVERT: G 224 VAL cc_start: 0.8024 (t) cc_final: 0.7776 (m) outliers start: 26 outliers final: 19 residues processed: 113 average time/residue: 0.4489 time to fit residues: 57.0983 Evaluate side-chains 113 residues out of total 1397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 93 time to evaluate : 0.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 6 VAL Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain C residue 63 ASP Chi-restraints excluded: chain C residue 301 VAL Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 64 ILE Chi-restraints excluded: chain E residue 134 THR Chi-restraints excluded: chain D residue 88 GLU Chi-restraints excluded: chain D residue 221 SER Chi-restraints excluded: chain D residue 268 ASP Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 124 MET Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 210 LEU Chi-restraints excluded: chain G residue 238 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 72 optimal weight: 2.9990 chunk 62 optimal weight: 20.0000 chunk 160 optimal weight: 6.9990 chunk 41 optimal weight: 3.9990 chunk 90 optimal weight: 4.9990 chunk 139 optimal weight: 6.9990 chunk 123 optimal weight: 7.9990 chunk 163 optimal weight: 1.9990 chunk 101 optimal weight: 3.9990 chunk 109 optimal weight: 0.2980 chunk 6 optimal weight: 3.9990 overall best weight: 2.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 23 ASN D 16 ASN A 16 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.115311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.090058 restraints weight = 30625.176| |-----------------------------------------------------------------------------| r_work (start): 0.3482 rms_B_bonded: 3.17 r_work: 0.3360 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.3837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 14193 Z= 0.284 Angle : 0.621 8.064 19350 Z= 0.332 Chirality : 0.044 0.173 2231 Planarity : 0.005 0.069 2287 Dihedral : 15.527 175.014 2421 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 33.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.81 % Favored : 91.19 % Rotamer: Outliers : 2.15 % Allowed : 19.33 % Favored : 78.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % 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: -1.17 (0.20), residues: 1612 helix: 0.83 (0.22), residues: 477 sheet: -0.54 (0.29), residues: 314 loop : -1.91 (0.19), residues: 821 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG G 207 TYR 0.017 0.002 TYR G 172 PHE 0.022 0.002 PHE A 186 TRP 0.010 0.002 TRP G 199 HIS 0.006 0.001 HIS B 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00643 / 0.28 (14193) covalent geometry : angle 0.62072 / 0.33 (19350) hydrogen bonds : bond 0.05414 / 3.75 ( 450) hydrogen bonds : angle 4.94649 / 3.47 ( 1250) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3505.65 seconds wall clock time: 61 minutes 7.18 seconds (3667.18 seconds total)