Starting phenix.real_space_refine on Thu Mar 5 22:20:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6shj_10199/03_2026/6shj_10199_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/6shj_10199/03_2026/6shj_10199.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6shj_10199/03_2026/6shj_10199_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6shj_10199/03_2026/6shj_10199_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6shj_10199/03_2026/6shj_10199.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6shj_10199/03_2026/6shj_10199.map" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.129 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: 6 Type Number sf(0) Gaussians P 8 5.49 5 S 82 5.16 5 C 8240 2.51 5 N 2310 2.21 5 O 2462 1.98 5 H 12832 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 112 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 25934 Number of models: 1 Model: "" Number of chains: 4 Chain: "D" Number of atoms: 6462 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 416, 6420 Classifications: {'peptide': 416} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 21, 'TRANS': 394} Chain breaks: 1 Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 68 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 3, 'TYR:plan': 1, 'GLU:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 45 Conformer: "B" Number of residues, atoms: 416, 6420 Classifications: {'peptide': 416} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 21, 'TRANS': 394} Chain breaks: 1 Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 68 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 3, 'TYR:plan': 1, 'GLU:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 45 bond proxies already assigned to first conformer: 6443 Chain: "A" Number of atoms: 6465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 416, 6465 Classifications: {'peptide': 416} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 21, 'TRANS': 394} Chain breaks: 1 Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 4, 'GLN:plan1': 1, 'ASP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 28 Chain: "D" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 20 Unusual residues: {'FBP': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 20 Unusual residues: {'FBP': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: B, C Time building chain proxies: 11.45, per 1000 atoms: 0.44 Number of scatterers: 25934 At special positions: 0 Unit cell: (107.841, 107.841, 100.512, 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 82 16.00 P 8 15.00 O 2462 8.00 N 2310 7.00 C 8240 6.00 H 12832 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: 2.07 Conformation dependent library (CDL) restraints added in 1.0 seconds 3304 Ramachandran restraints generated. 1652 Oldfield, 0 Emsley, 1652 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3128 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 0 sheets defined 21.8% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing helix chain 'D' and resid 13 through 18 Proline residue: D 17 - end of helix No H-bonds generated for 'chain 'D' and resid 13 through 18' Processing helix chain 'D' and resid 42 through 44 No H-bonds generated for 'chain 'D' and resid 42 through 44' Processing helix chain 'D' and resid 54 through 63 removed outlier: 3.727A pdb=" N CYS D 61 " --> pdb=" O ALA D 57 " (cutoff:3.500A) Processing helix chain 'D' and resid 79 through 86 Processing helix chain 'D' and resid 93 through 95 No H-bonds generated for 'chain 'D' and resid 93 through 95' Processing helix chain 'D' and resid 125 through 131 removed outlier: 3.569A pdb=" N ARG D 129 " --> pdb=" O LEU D 125 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N ARG D 130 " --> pdb=" O ASP D 126 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N TYR D 131 " --> pdb=" O ILE D 127 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 125 through 131' Processing helix chain 'D' and resid 150 through 159 removed outlier: 3.515A pdb=" N ILE D 154 " --> pdb=" O SER D 150 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ASP D 155 " --> pdb=" O ARG D 151 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LYS D 159 " --> pdb=" O ASP D 155 " (cutoff:3.500A) Processing helix chain 'D' and resid 175 through 177 No H-bonds generated for 'chain 'D' and resid 175 through 177' Processing helix chain 'D' and resid 221 through 231 removed outlier: 3.554A pdb=" N GLU D 225 " --> pdb=" O ASP D 221 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N GLU D 229 " --> pdb=" O GLU D 225 " (cutoff:3.500A) Processing helix chain 'D' and resid 245 through 251 removed outlier: 4.008A pdb=" N GLU D 250 " --> pdb=" O PRO D 246 " (cutoff:3.500A) Processing helix chain 'D' and resid 259 through 261 No H-bonds generated for 'chain 'D' and resid 259 through 261' Processing helix chain 'D' and resid 280 through 288 Processing helix chain 'D' and resid 419 through 425 removed outlier: 3.714A pdb=" N ARG D 423 " --> pdb=" O ARG D 419 " (cutoff:3.500A) Processing helix chain 'A' and resid 15 through 18 No H-bonds generated for 'chain 'A' and resid 15 through 18' Processing helix chain 'A' and resid 42 through 44 No H-bonds generated for 'chain 'A' and resid 42 through 44' Processing helix chain 'A' and resid 53 through 63 removed outlier: 4.158A pdb=" N ALA A 57 " --> pdb=" O ILE A 53 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N CYS A 61 " --> pdb=" O ALA A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 87 Processing helix chain 'A' and resid 117 through 123 removed outlier: 4.094A pdb=" N THR A 122 " --> pdb=" O ASP A 119 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N GLN A 123 " --> pdb=" O ALA A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 131 No H-bonds generated for 'chain 'A' and resid 129 through 131' Processing helix chain 'A' and resid 149 through 158 Processing helix chain 'A' and resid 175 through 177 No H-bonds generated for 'chain 'A' and resid 175 through 177' Processing helix chain 'A' and resid 220 through 231 removed outlier: 3.774A pdb=" N TYR A 224 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N GLU A 225 " --> pdb=" O ASP A 221 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N GLU A 229 " --> pdb=" O GLU A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 251 removed outlier: 3.643A pdb=" N ALA A 251 " --> pdb=" O LYS A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 261 No H-bonds generated for 'chain 'A' and resid 259 through 261' Processing helix chain 'A' and resid 282 through 290 removed outlier: 3.850A pdb=" N ASN A 287 " --> pdb=" O TYR A 283 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N LEU A 290 " --> pdb=" O ALA A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 406 Processing helix chain 'A' and resid 419 through 425 removed outlier: 3.829A pdb=" N LYS A 424 " --> pdb=" O GLU A 420 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N LEU A 425 " --> pdb=" O MET A 421 " (cutoff:3.500A) Processing helix chain 'B' and resid 13 through 18 Proline residue: B 17 - end of helix No H-bonds generated for 'chain 'B' and resid 13 through 18' Processing helix chain 'B' and resid 42 through 44 No H-bonds generated for 'chain 'B' and resid 42 through 44' Processing helix chain 'B' and resid 54 through 63 removed outlier: 3.727A pdb=" N CYS B 61 " --> pdb=" O ALA B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 86 Processing helix chain 'B' and resid 93 through 95 No H-bonds generated for 'chain 'B' and resid 93 through 95' Processing helix chain 'B' and resid 125 through 131 removed outlier: 3.569A pdb=" N ARG B 129 " --> pdb=" O LEU B 125 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N ARG B 130 " --> pdb=" O ASP B 126 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N TYR B 131 " --> pdb=" O ILE B 127 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 125 through 131' Processing helix chain 'B' and resid 150 through 159 removed outlier: 3.514A pdb=" N ILE B 154 " --> pdb=" O SER B 150 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ASP B 155 " --> pdb=" O ARG B 151 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LYS B 159 " --> pdb=" O ASP B 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 177 No H-bonds generated for 'chain 'B' and resid 175 through 177' Processing helix chain 'B' and resid 221 through 231 removed outlier: 3.554A pdb=" N GLU B 225 " --> pdb=" O ASP B 221 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N GLU B 229 " --> pdb=" O GLU B 225 " (cutoff:3.500A) Processing helix chain 'B' and resid 245 through 251 removed outlier: 4.008A pdb=" N GLU B 250 " --> pdb=" O PRO B 246 " (cutoff:3.500A) Processing helix chain 'B' and resid 259 through 261 No H-bonds generated for 'chain 'B' and resid 259 through 261' Processing helix chain 'B' and resid 280 through 288 Processing helix chain 'B' and resid 419 through 425 removed outlier: 3.715A pdb=" N ARG B 423 " --> pdb=" O ARG B 419 " (cutoff:3.500A) Processing helix chain 'C' and resid 15 through 18 No H-bonds generated for 'chain 'C' and resid 15 through 18' Processing helix chain 'C' and resid 42 through 44 No H-bonds generated for 'chain 'C' and resid 42 through 44' Processing helix chain 'C' and resid 53 through 63 removed outlier: 4.158A pdb=" N ALA C 57 " --> pdb=" O ILE C 53 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N CYS C 61 " --> pdb=" O ALA C 57 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 87 Processing helix chain 'C' and resid 117 through 123 removed outlier: 4.094A pdb=" N THR C 122 " --> pdb=" O ASP C 119 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N GLN C 123 " --> pdb=" O ALA C 120 " (cutoff:3.500A) Processing helix chain 'C' and resid 129 through 131 No H-bonds generated for 'chain 'C' and resid 129 through 131' Processing helix chain 'C' and resid 149 through 158 Processing helix chain 'C' and resid 175 through 177 No H-bonds generated for 'chain 'C' and resid 175 through 177' Processing helix chain 'C' and resid 220 through 231 removed outlier: 3.773A pdb=" N TYR C 224 " --> pdb=" O ALA C 220 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N GLU C 225 " --> pdb=" O ASP C 221 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N GLU C 229 " --> pdb=" O GLU C 225 " (cutoff:3.500A) Processing helix chain 'C' and resid 244 through 251 removed outlier: 3.643A pdb=" N ALA C 251 " --> pdb=" O LYS C 247 " (cutoff:3.500A) Processing helix chain 'C' and resid 259 through 261 No H-bonds generated for 'chain 'C' and resid 259 through 261' Processing helix chain 'C' and resid 282 through 290 removed outlier: 3.850A pdb=" N ASN C 287 " --> pdb=" O TYR C 283 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N LEU C 290 " --> pdb=" O ALA C 286 " (cutoff:3.500A) Processing helix chain 'C' and resid 400 through 406 Processing helix chain 'C' and resid 419 through 425 removed outlier: 3.830A pdb=" N LYS C 424 " --> pdb=" O GLU C 420 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N LEU C 425 " --> pdb=" O MET C 421 " (cutoff:3.500A) 114 hydrogen bonds defined for protein. 330 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: 3.98 Time building geometry restraints manager: 2.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.69 - 0.91: 2914 0.91 - 1.14: 9880 1.14 - 1.36: 4496 1.36 - 1.58: 8780 1.58 - 1.81: 136 Bond restraints: 26206 Sorted by residual: bond pdb=" CE1 PHE C 91 " pdb=" HE1 PHE C 91 " ideal model delta sigma weight residual 0.930 1.155 -0.225 2.00e-02 2.50e+03 1.26e+02 bond pdb=" CE1 PHE A 91 " pdb=" HE1 PHE A 91 " ideal model delta sigma weight residual 0.930 1.155 -0.225 2.00e-02 2.50e+03 1.26e+02 bond pdb=" ND2 ASN C 96 " pdb="HD22 ASN C 96 " ideal model delta sigma weight residual 0.860 1.070 -0.210 2.00e-02 2.50e+03 1.10e+02 bond pdb=" ND2 ASN A 96 " pdb="HD22 ASN A 96 " ideal model delta sigma weight residual 0.860 1.069 -0.209 2.00e-02 2.50e+03 1.10e+02 bond pdb=" C5 FBP A 501 " pdb=" O5 FBP A 501 " ideal model delta sigma weight residual 1.608 1.407 0.201 2.00e-02 2.50e+03 1.01e+02 ... (remaining 26201 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.45: 46768 3.45 - 6.90: 486 6.90 - 10.34: 42 10.34 - 13.79: 8 13.79 - 17.24: 6 Bond angle restraints: 47310 Sorted by residual: angle pdb=" N HIS A 78 " pdb=" CA HIS A 78 " pdb=" C HIS A 78 " ideal model delta sigma weight residual 113.97 102.99 10.98 1.28e+00 6.10e-01 7.36e+01 angle pdb=" N HIS C 78 " pdb=" CA HIS C 78 " pdb=" C HIS C 78 " ideal model delta sigma weight residual 113.97 103.00 10.97 1.28e+00 6.10e-01 7.35e+01 angle pdb=" C TYR A 75 " pdb=" N GLN A 76 " pdb=" CA GLN A 76 " ideal model delta sigma weight residual 121.54 136.19 -14.65 1.91e+00 2.74e-01 5.88e+01 angle pdb=" C TYR C 75 " pdb=" N GLN C 76 " pdb=" CA GLN C 76 " ideal model delta sigma weight residual 121.54 136.14 -14.60 1.91e+00 2.74e-01 5.84e+01 angle pdb=" C TYR C 75 " pdb=" CA TYR C 75 " pdb=" CB TYR C 75 " ideal model delta sigma weight residual 110.19 123.90 -13.71 2.18e+00 2.10e-01 3.96e+01 ... (remaining 47305 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.53: 10805 16.53 - 33.06: 1180 33.06 - 49.58: 325 49.58 - 66.11: 110 66.11 - 82.64: 14 Dihedral angle restraints: 12434 sinusoidal: 6834 harmonic: 5600 Sorted by residual: dihedral pdb=" CG PHE A 91 " pdb=" CD1 PHE A 91 " pdb=" CE1 PHE A 91 " pdb=" HE1 PHE A 91 " ideal model delta harmonic sigma weight residual 180.00 133.77 46.23 0 5.00e+00 4.00e-02 8.55e+01 dihedral pdb=" CG PHE C 91 " pdb=" CD1 PHE C 91 " pdb=" CE1 PHE C 91 " pdb=" HE1 PHE C 91 " ideal model delta harmonic sigma weight residual 180.00 133.81 46.19 0 5.00e+00 4.00e-02 8.54e+01 dihedral pdb=" CG HIS D 83 " pdb=" ND1 HIS D 83 " pdb=" CE1 HIS D 83 " pdb=" HE1 HIS D 83 " ideal model delta harmonic sigma weight residual 180.00 139.11 40.89 0 5.00e+00 4.00e-02 6.69e+01 ... (remaining 12431 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.116: 1856 0.116 - 0.232: 126 0.232 - 0.348: 24 0.348 - 0.465: 0 0.465 - 0.581: 6 Chirality restraints: 2012 Sorted by residual: chirality pdb=" CA ARG B 232 " pdb=" N ARG B 232 " pdb=" C ARG B 232 " pdb=" CB ARG B 232 " both_signs ideal model delta sigma weight residual False 2.51 1.93 0.58 2.00e-01 2.50e+01 8.43e+00 chirality pdb=" CA ARG D 232 " pdb=" N ARG D 232 " pdb=" C ARG D 232 " pdb=" CB ARG D 232 " both_signs ideal model delta sigma weight residual False 2.51 1.93 0.58 2.00e-01 2.50e+01 8.41e+00 chirality pdb=" CA TYR A 75 " pdb=" N TYR A 75 " pdb=" C TYR A 75 " pdb=" CB TYR A 75 " both_signs ideal model delta sigma weight residual False 2.51 1.95 0.56 2.00e-01 2.50e+01 7.73e+00 ... (remaining 2009 not shown) Planarity restraints: 3940 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 91 " 0.053 2.00e-02 2.50e+03 1.62e-01 7.85e+02 pdb=" CG PHE A 91 " 0.002 2.00e-02 2.50e+03 pdb=" CD1 PHE A 91 " -0.140 2.00e-02 2.50e+03 pdb=" CD2 PHE A 91 " 0.043 2.00e-02 2.50e+03 pdb=" CE1 PHE A 91 " -0.228 2.00e-02 2.50e+03 pdb=" CE2 PHE A 91 " 0.030 2.00e-02 2.50e+03 pdb=" CZ PHE A 91 " -0.088 2.00e-02 2.50e+03 pdb=" HD1 PHE A 91 " -0.110 2.00e-02 2.50e+03 pdb=" HD2 PHE A 91 " 0.084 2.00e-02 2.50e+03 pdb=" HE1 PHE A 91 " 0.450 2.00e-02 2.50e+03 pdb=" HE2 PHE A 91 " -0.009 2.00e-02 2.50e+03 pdb=" HZ PHE A 91 " -0.087 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 91 " -0.053 2.00e-02 2.50e+03 1.62e-01 7.85e+02 pdb=" CG PHE C 91 " -0.002 2.00e-02 2.50e+03 pdb=" CD1 PHE C 91 " 0.140 2.00e-02 2.50e+03 pdb=" CD2 PHE C 91 " -0.043 2.00e-02 2.50e+03 pdb=" CE1 PHE C 91 " 0.228 2.00e-02 2.50e+03 pdb=" CE2 PHE C 91 " -0.030 2.00e-02 2.50e+03 pdb=" CZ PHE C 91 " 0.088 2.00e-02 2.50e+03 pdb=" HD1 PHE C 91 " 0.110 2.00e-02 2.50e+03 pdb=" HD2 PHE C 91 " -0.084 2.00e-02 2.50e+03 pdb=" HE1 PHE C 91 " -0.450 2.00e-02 2.50e+03 pdb=" HE2 PHE C 91 " 0.009 2.00e-02 2.50e+03 pdb=" HZ PHE C 91 " 0.087 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 96 " -0.122 2.00e-02 2.50e+03 2.04e-01 6.24e+02 pdb=" CG ASN C 96 " 0.055 2.00e-02 2.50e+03 pdb=" OD1 ASN C 96 " 0.146 2.00e-02 2.50e+03 pdb=" ND2 ASN C 96 " -0.304 2.00e-02 2.50e+03 pdb="HD21 ASN C 96 " -0.102 2.00e-02 2.50e+03 pdb="HD22 ASN C 96 " 0.328 2.00e-02 2.50e+03 ... (remaining 3937 not shown) Histogram of nonbonded interaction distances: 1.58 - 2.19: 1650 2.19 - 2.79: 52958 2.79 - 3.39: 70899 3.39 - 4.00: 97597 4.00 - 4.60: 152816 Nonbonded interactions: 375920 Sorted by model distance: nonbonded pdb=" O GLN A 76 " pdb="HE21 GLN A 76 " model vdw 1.585 2.450 nonbonded pdb=" O GLN C 76 " pdb="HE21 GLN C 76 " model vdw 1.585 2.450 nonbonded pdb=" O ASN C 60 " pdb=" HG SER C 64 " model vdw 1.677 2.450 nonbonded pdb=" O ASN A 60 " pdb=" HG SER A 64 " model vdw 1.678 2.450 nonbonded pdb=" HZ2 LYS C 146 " pdb=" O ASP C 298 " model vdw 1.686 2.450 ... (remaining 375915 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' } ncs_group { reference = chain 'A' selection = chain 'C' } 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=0.50 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: 0.460 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: 0.100 Extract box with map and model: 0.350 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 27.860 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5590 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 : 0.010 0.201 13374 Z= 0.487 Angle : 1.036 14.648 18150 Z= 0.602 Chirality : 0.074 0.581 2012 Planarity : 0.011 0.072 2364 Dihedral : 14.699 82.640 5078 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.98 % Favored : 92.90 % Rotamer: Outliers : 3.58 % Allowed : 7.15 % Favored : 89.27 % Cbeta Deviations : 0.38 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.39 (0.16), residues: 1652 helix: -3.63 (0.17), residues: 404 sheet: -3.63 (0.25), residues: 256 loop : -2.43 (0.17), residues: 992 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.082 0.008 ARG D 232 TYR 0.079 0.009 TYR B 224 PHE 0.096 0.011 PHE C 218 TRP 0.070 0.008 TRP A 274 HIS 0.045 0.009 HIS C 238 Details of bonding type rmsd covalent geometry : bond 0.00959 (13374) covalent geometry : angle 1.03576 (18150) hydrogen bonds : bond 0.21013 ( 114) hydrogen bonds : angle 8.65677 ( 330) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3304 Ramachandran restraints generated. 1652 Oldfield, 0 Emsley, 1652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3304 Ramachandran restraints generated. 1652 Oldfield, 0 Emsley, 1652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 10 is missing expected H atoms. Skipping. Residue MET 11 is missing expected H atoms. Skipping. Residue TYR 114 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue MET 11 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue MET 11 is missing expected H atoms. Skipping. Residue TYR 114 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue MET 11 is missing expected H atoms. Skipping. Evaluate side-chains 337 residues out of total 1432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 291 time to evaluate : 0.503 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 93 GLU cc_start: 0.7356 (tm-30) cc_final: 0.7044 (mp0) REVERT: D 134 GLU cc_start: 0.7367 (OUTLIER) cc_final: 0.7011 (mt-10) REVERT: D 375 ARG cc_start: 0.6869 (ttm-80) cc_final: 0.6416 (ttm110) REVERT: D 421 MET cc_start: 0.7609 (mtt) cc_final: 0.7332 (mtt) REVERT: D 430 GLU cc_start: 0.7339 (OUTLIER) cc_final: 0.6874 (mm-30) REVERT: A 18 LEU cc_start: 0.8191 (OUTLIER) cc_final: 0.7889 (mt) REVERT: A 78 HIS cc_start: 0.7760 (OUTLIER) cc_final: 0.7085 (t70) REVERT: A 100 ASP cc_start: 0.6875 (t0) cc_final: 0.6113 (t70) REVERT: A 134 GLU cc_start: 0.6565 (tp30) cc_final: 0.6078 (mm-30) REVERT: A 174 GLU cc_start: 0.9013 (mt-10) cc_final: 0.8772 (pt0) REVERT: A 213 MET cc_start: 0.8206 (mtp) cc_final: 0.7982 (mtp) REVERT: A 408 TYR cc_start: 0.6469 (t80) cc_final: 0.6258 (t80) REVERT: A 430 GLU cc_start: 0.7071 (tt0) cc_final: 0.6518 (tm-30) REVERT: B 100 ASP cc_start: 0.7040 (t70) cc_final: 0.6688 (t70) REVERT: B 298 ASP cc_start: 0.7699 (t0) cc_final: 0.7379 (t0) REVERT: B 328 MET cc_start: 0.6161 (mtm) cc_final: 0.5954 (mtp) REVERT: B 394 MET cc_start: 0.7270 (ttm) cc_final: 0.6630 (ttm) REVERT: B 421 MET cc_start: 0.7418 (mtt) cc_final: 0.7217 (mtt) REVERT: B 430 GLU cc_start: 0.7558 (OUTLIER) cc_final: 0.7089 (mm-30) REVERT: C 18 LEU cc_start: 0.7863 (OUTLIER) cc_final: 0.7660 (mt) REVERT: C 78 HIS cc_start: 0.7773 (OUTLIER) cc_final: 0.7317 (t70) REVERT: C 100 ASP cc_start: 0.6939 (t0) cc_final: 0.5950 (t70) REVERT: C 242 LYS cc_start: 0.8183 (mttt) cc_final: 0.7979 (mtpp) REVERT: C 352 SER cc_start: 0.6391 (OUTLIER) cc_final: 0.6123 (p) REVERT: C 428 LYS cc_start: 0.7811 (tptt) cc_final: 0.7602 (tppt) REVERT: C 430 GLU cc_start: 0.6800 (tt0) cc_final: 0.6394 (tm-30) outliers start: 46 outliers final: 29 residues processed: 329 average time/residue: 0.3152 time to fit residues: 139.2889 Evaluate side-chains 222 residues out of total 1432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 185 time to evaluate : 0.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 134 GLU Chi-restraints excluded: chain D residue 142 ASP Chi-restraints excluded: chain D residue 312 SER Chi-restraints excluded: chain D residue 418 THR Chi-restraints excluded: chain D residue 425 LEU Chi-restraints excluded: chain D residue 430 GLU Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 78 HIS Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 108 MET Chi-restraints excluded: chain A residue 145 TYR Chi-restraints excluded: chain A residue 225 GLU Chi-restraints excluded: chain A residue 358 SER Chi-restraints excluded: chain A residue 386 ARG Chi-restraints excluded: chain A residue 405 ARG Chi-restraints excluded: chain A residue 406 ARG Chi-restraints excluded: chain A residue 424 LYS Chi-restraints excluded: chain B residue 134 GLU Chi-restraints excluded: chain B residue 142 ASP Chi-restraints excluded: chain B residue 312 SER Chi-restraints excluded: chain B residue 418 THR Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 430 GLU Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 78 HIS Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 108 MET Chi-restraints excluded: chain C residue 145 TYR Chi-restraints excluded: chain C residue 225 GLU Chi-restraints excluded: chain C residue 277 VAL Chi-restraints excluded: chain C residue 352 SER Chi-restraints excluded: chain C residue 358 SER Chi-restraints excluded: chain C residue 386 ARG Chi-restraints excluded: chain C residue 401 GLU Chi-restraints excluded: chain C residue 405 ARG Chi-restraints excluded: chain C residue 406 ARG Chi-restraints excluded: chain C residue 424 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 98 optimal weight: 0.9980 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 6.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 0.6980 chunk 91 optimal weight: 0.9980 chunk 149 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 303 ASN A 78 HIS A 429 GLN B 303 ASN B 429 GLN C 265 GLN C 310 ASN C 429 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.175079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.131086 restraints weight = 58161.682| |-----------------------------------------------------------------------------| r_work (start): 0.3761 rms_B_bonded: 3.25 r_work: 0.3583 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3583 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3630 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3630 r_free = 0.3630 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3630 r_free = 0.3630 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3630 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7443 moved from start: 0.1642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 13374 Z= 0.121 Angle : 0.575 6.170 18150 Z= 0.300 Chirality : 0.046 0.149 2012 Planarity : 0.006 0.071 2364 Dihedral : 10.103 86.094 2059 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 3.43 % Allowed : 12.80 % Favored : 83.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -3.65 (0.18), residues: 1652 helix: -2.75 (0.21), residues: 410 sheet: -3.45 (0.28), residues: 226 loop : -2.06 (0.17), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 355 TYR 0.033 0.001 TYR A 75 PHE 0.007 0.001 PHE C 56 TRP 0.009 0.001 TRP D 284 HIS 0.006 0.001 HIS A 238 Details of bonding type rmsd covalent geometry : bond 0.00266 (13374) covalent geometry : angle 0.57540 (18150) hydrogen bonds : bond 0.04447 ( 114) hydrogen bonds : angle 4.90478 ( 330) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3304 Ramachandran restraints generated. 1652 Oldfield, 0 Emsley, 1652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3304 Ramachandran restraints generated. 1652 Oldfield, 0 Emsley, 1652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 10 is missing expected H atoms. Skipping. Residue MET 11 is missing expected H atoms. Skipping. Residue TYR 114 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue MET 11 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue MET 11 is missing expected H atoms. Skipping. Residue TYR 114 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue MET 11 is missing expected H atoms. Skipping. Evaluate side-chains 249 residues out of total 1432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 205 time to evaluate : 0.607 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 134 GLU cc_start: 0.7789 (OUTLIER) cc_final: 0.7547 (mt-10) REVERT: D 250 GLU cc_start: 0.8383 (mm-30) cc_final: 0.8142 (mm-30) REVERT: D 421 MET cc_start: 0.8328 (mtt) cc_final: 0.7949 (mtt) REVERT: D 430 GLU cc_start: 0.7301 (OUTLIER) cc_final: 0.6935 (mm-30) REVERT: A 38 ASN cc_start: 0.8600 (OUTLIER) cc_final: 0.8281 (p0) REVERT: A 39 LYS cc_start: 0.8389 (tppp) cc_final: 0.8178 (tppp) REVERT: A 78 HIS cc_start: 0.8818 (OUTLIER) cc_final: 0.8578 (t70) REVERT: A 399 ASN cc_start: 0.7893 (t0) cc_final: 0.7521 (t0) REVERT: B 134 GLU cc_start: 0.7869 (OUTLIER) cc_final: 0.7568 (mt-10) REVERT: B 298 ASP cc_start: 0.8416 (t0) cc_final: 0.7953 (t0) REVERT: B 394 MET cc_start: 0.7923 (ttm) cc_final: 0.7648 (ttm) REVERT: B 430 GLU cc_start: 0.7474 (OUTLIER) cc_final: 0.7104 (mm-30) REVERT: C 39 LYS cc_start: 0.8294 (tppp) cc_final: 0.8088 (tppp) REVERT: C 100 ASP cc_start: 0.7773 (t0) cc_final: 0.7480 (t70) REVERT: C 378 ARG cc_start: 0.7771 (mtm-85) cc_final: 0.7532 (mtm180) REVERT: C 399 ASN cc_start: 0.7960 (t0) cc_final: 0.7337 (t0) outliers start: 44 outliers final: 29 residues processed: 233 average time/residue: 0.2982 time to fit residues: 96.3940 Evaluate side-chains 221 residues out of total 1432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 186 time to evaluate : 0.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 134 GLU Chi-restraints excluded: chain D residue 142 ASP Chi-restraints excluded: chain D residue 190 ILE Chi-restraints excluded: chain D residue 235 ASN Chi-restraints excluded: chain D residue 418 THR Chi-restraints excluded: chain D residue 430 GLU Chi-restraints excluded: chain A residue 38 ASN Chi-restraints excluded: chain A residue 78 HIS Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 108 MET Chi-restraints excluded: chain A residue 145 TYR Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 225 GLU Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 386 ARG Chi-restraints excluded: chain A residue 401 GLU Chi-restraints excluded: chain A residue 405 ARG Chi-restraints excluded: chain A residue 424 LYS Chi-restraints excluded: chain B residue 134 GLU Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 142 ASP Chi-restraints excluded: chain B residue 235 ASN Chi-restraints excluded: chain B residue 418 THR Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 430 GLU Chi-restraints excluded: chain C residue 24 ILE Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 108 MET Chi-restraints excluded: chain C residue 145 TYR Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 225 GLU Chi-restraints excluded: chain C residue 277 VAL Chi-restraints excluded: chain C residue 386 ARG Chi-restraints excluded: chain C residue 405 ARG Chi-restraints excluded: chain C residue 424 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 124 optimal weight: 3.9990 chunk 71 optimal weight: 2.9990 chunk 84 optimal weight: 6.9990 chunk 132 optimal weight: 5.9990 chunk 73 optimal weight: 1.9990 chunk 106 optimal weight: 3.9990 chunk 79 optimal weight: 7.9990 chunk 23 optimal weight: 6.9990 chunk 48 optimal weight: 1.9990 chunk 141 optimal weight: 0.4980 chunk 118 optimal weight: 2.9990 overall best weight: 2.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 303 ASN A 331 ASN B 265 GLN B 303 ASN C 331 ASN C 399 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.169749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.123954 restraints weight = 66731.472| |-----------------------------------------------------------------------------| r_work (start): 0.3679 rms_B_bonded: 3.53 r_work: 0.3486 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3486 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3526 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3526 r_free = 0.3526 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3526 r_free = 0.3526 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3526 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7533 moved from start: 0.2161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 13374 Z= 0.181 Angle : 0.552 5.355 18150 Z= 0.288 Chirality : 0.047 0.136 2012 Planarity : 0.005 0.052 2364 Dihedral : 8.884 62.863 2035 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.16 % Favored : 92.84 % Rotamer: Outliers : 3.36 % Allowed : 14.38 % Favored : 82.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -3.32 (0.18), residues: 1652 helix: -2.30 (0.22), residues: 408 sheet: -3.38 (0.28), residues: 232 loop : -1.88 (0.18), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 353 TYR 0.025 0.001 TYR C 75 PHE 0.012 0.001 PHE A 259 TRP 0.010 0.001 TRP D 88 HIS 0.004 0.001 HIS B 78 Details of bonding type rmsd covalent geometry : bond 0.00435 (13374) covalent geometry : angle 0.55193 (18150) hydrogen bonds : bond 0.04107 ( 114) hydrogen bonds : angle 4.77445 ( 330) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3304 Ramachandran restraints generated. 1652 Oldfield, 0 Emsley, 1652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3304 Ramachandran restraints generated. 1652 Oldfield, 0 Emsley, 1652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 10 is missing expected H atoms. Skipping. Residue MET 11 is missing expected H atoms. Skipping. Residue TYR 114 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue MET 11 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue MET 11 is missing expected H atoms. Skipping. Residue TYR 114 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue MET 11 is missing expected H atoms. Skipping. Evaluate side-chains 234 residues out of total 1432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 191 time to evaluate : 0.470 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 134 GLU cc_start: 0.8010 (OUTLIER) cc_final: 0.7757 (mt-10) REVERT: D 190 ILE cc_start: 0.8886 (OUTLIER) cc_final: 0.8581 (pt) REVERT: D 250 GLU cc_start: 0.8392 (mm-30) cc_final: 0.8150 (mm-30) REVERT: D 430 GLU cc_start: 0.7337 (OUTLIER) cc_final: 0.7040 (mm-30) REVERT: A 108 MET cc_start: 0.7926 (OUTLIER) cc_final: 0.6977 (mtm) REVERT: A 151 ARG cc_start: 0.7452 (OUTLIER) cc_final: 0.6850 (tpp80) REVERT: A 213 MET cc_start: 0.8980 (mtp) cc_final: 0.8651 (mtp) REVERT: A 328 MET cc_start: 0.7125 (mtt) cc_final: 0.6661 (ttt) REVERT: A 355 ARG cc_start: 0.8275 (OUTLIER) cc_final: 0.7207 (ttt90) REVERT: B 55 ASP cc_start: 0.7892 (m-30) cc_final: 0.7552 (t0) REVERT: B 134 GLU cc_start: 0.7866 (OUTLIER) cc_final: 0.7509 (mt-10) REVERT: B 298 ASP cc_start: 0.8485 (t0) cc_final: 0.8077 (t0) REVERT: B 394 MET cc_start: 0.8010 (ttm) cc_final: 0.7618 (ttm) REVERT: B 421 MET cc_start: 0.8123 (mtt) cc_final: 0.7762 (mtt) REVERT: B 430 GLU cc_start: 0.7505 (OUTLIER) cc_final: 0.7217 (mm-30) REVERT: C 38 ASN cc_start: 0.8540 (OUTLIER) cc_final: 0.8212 (p0) REVERT: C 39 LYS cc_start: 0.8291 (tppp) cc_final: 0.8082 (tppp) REVERT: C 100 ASP cc_start: 0.7720 (t0) cc_final: 0.7446 (t0) REVERT: C 108 MET cc_start: 0.7784 (OUTLIER) cc_final: 0.6855 (mtm) REVERT: C 151 ARG cc_start: 0.7030 (OUTLIER) cc_final: 0.6770 (mmm-85) REVERT: C 328 MET cc_start: 0.7329 (mtt) cc_final: 0.6455 (ttt) REVERT: C 421 MET cc_start: 0.8581 (ttm) cc_final: 0.8069 (mtp) outliers start: 43 outliers final: 28 residues processed: 219 average time/residue: 0.3011 time to fit residues: 90.1305 Evaluate side-chains 219 residues out of total 1432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 180 time to evaluate : 0.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 100 ASP Chi-restraints excluded: chain D residue 134 GLU Chi-restraints excluded: chain D residue 142 ASP Chi-restraints excluded: chain D residue 190 ILE Chi-restraints excluded: chain D residue 235 ASN Chi-restraints excluded: chain D residue 418 THR Chi-restraints excluded: chain D residue 430 GLU Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 108 MET Chi-restraints excluded: chain A residue 134 GLU Chi-restraints excluded: chain A residue 145 TYR Chi-restraints excluded: chain A residue 151 ARG Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 225 GLU Chi-restraints excluded: chain A residue 355 ARG Chi-restraints excluded: chain A residue 386 ARG Chi-restraints excluded: chain A residue 401 GLU Chi-restraints excluded: chain A residue 405 ARG Chi-restraints excluded: chain A residue 424 LYS Chi-restraints excluded: chain B residue 100 ASP Chi-restraints excluded: chain B residue 134 GLU Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 142 ASP Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain B residue 168 MET Chi-restraints excluded: chain B residue 235 ASN Chi-restraints excluded: chain B residue 418 THR Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 430 GLU Chi-restraints excluded: chain C residue 20 SER Chi-restraints excluded: chain C residue 38 ASN Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 108 MET Chi-restraints excluded: chain C residue 145 TYR Chi-restraints excluded: chain C residue 151 ARG Chi-restraints excluded: chain C residue 225 GLU Chi-restraints excluded: chain C residue 386 ARG Chi-restraints excluded: chain C residue 405 ARG Chi-restraints excluded: chain C residue 424 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 87 optimal weight: 0.9990 chunk 53 optimal weight: 2.9990 chunk 32 optimal weight: 4.9990 chunk 111 optimal weight: 2.9990 chunk 66 optimal weight: 4.9990 chunk 68 optimal weight: 0.3980 chunk 39 optimal weight: 5.9990 chunk 80 optimal weight: 5.9990 chunk 147 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 303 ASN D 429 GLN C 235 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.171893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.124639 restraints weight = 63502.591| |-----------------------------------------------------------------------------| r_work (start): 0.3682 rms_B_bonded: 3.66 r_work: 0.3494 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3494 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3531 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3531 r_free = 0.3531 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3531 r_free = 0.3531 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3531 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7528 moved from start: 0.2444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 13374 Z= 0.128 Angle : 0.509 4.624 18150 Z= 0.263 Chirality : 0.045 0.136 2012 Planarity : 0.004 0.040 2364 Dihedral : 8.411 59.303 2032 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 3.22 % Allowed : 15.24 % Favored : 81.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -3.07 (0.19), residues: 1652 helix: -1.95 (0.24), residues: 410 sheet: -3.34 (0.29), residues: 232 loop : -1.76 (0.18), residues: 1010 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 86 TYR 0.022 0.001 TYR C 75 PHE 0.007 0.001 PHE A 259 TRP 0.008 0.001 TRP B 88 HIS 0.003 0.001 HIS A 78 Details of bonding type rmsd covalent geometry : bond 0.00305 (13374) covalent geometry : angle 0.50893 (18150) hydrogen bonds : bond 0.03423 ( 114) hydrogen bonds : angle 4.46098 ( 330) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3304 Ramachandran restraints generated. 1652 Oldfield, 0 Emsley, 1652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3304 Ramachandran restraints generated. 1652 Oldfield, 0 Emsley, 1652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 10 is missing expected H atoms. Skipping. Residue MET 11 is missing expected H atoms. Skipping. Residue TYR 114 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue MET 11 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue MET 11 is missing expected H atoms. Skipping. Residue TYR 114 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue MET 11 is missing expected H atoms. Skipping. Evaluate side-chains 233 residues out of total 1432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 192 time to evaluate : 0.613 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 55 ASP cc_start: 0.7693 (m-30) cc_final: 0.7437 (t0) REVERT: D 134 GLU cc_start: 0.7921 (mm-30) cc_final: 0.7665 (mt-10) REVERT: D 190 ILE cc_start: 0.8913 (tt) cc_final: 0.8611 (pt) REVERT: D 250 GLU cc_start: 0.8399 (mm-30) cc_final: 0.8162 (mm-30) REVERT: D 298 ASP cc_start: 0.8557 (t0) cc_final: 0.8354 (t0) REVERT: D 430 GLU cc_start: 0.7287 (OUTLIER) cc_final: 0.7034 (mm-30) REVERT: A 38 ASN cc_start: 0.8512 (OUTLIER) cc_final: 0.8190 (p0) REVERT: A 69 MET cc_start: 0.8773 (mtm) cc_final: 0.8259 (mtt) REVERT: A 108 MET cc_start: 0.7909 (OUTLIER) cc_final: 0.7178 (mtm) REVERT: A 151 ARG cc_start: 0.7419 (OUTLIER) cc_final: 0.6910 (tpp80) REVERT: A 213 MET cc_start: 0.8988 (mtp) cc_final: 0.8636 (mtp) REVERT: A 355 ARG cc_start: 0.8224 (OUTLIER) cc_final: 0.7056 (ttt90) REVERT: A 363 ASP cc_start: 0.8366 (t0) cc_final: 0.8074 (t0) REVERT: B 55 ASP cc_start: 0.7760 (m-30) cc_final: 0.7520 (t0) REVERT: B 134 GLU cc_start: 0.7843 (mm-30) cc_final: 0.7527 (mt-10) REVERT: B 298 ASP cc_start: 0.8480 (t0) cc_final: 0.8108 (t0) REVERT: B 421 MET cc_start: 0.8077 (mtt) cc_final: 0.7691 (mtt) REVERT: B 430 GLU cc_start: 0.7528 (OUTLIER) cc_final: 0.7268 (mm-30) REVERT: C 38 ASN cc_start: 0.8526 (OUTLIER) cc_final: 0.8197 (p0) REVERT: C 100 ASP cc_start: 0.7647 (t0) cc_final: 0.7318 (t0) REVERT: C 108 MET cc_start: 0.7704 (OUTLIER) cc_final: 0.7026 (mtm) REVERT: C 135 TYR cc_start: 0.8310 (m-80) cc_final: 0.8037 (m-80) REVERT: C 151 ARG cc_start: 0.7089 (OUTLIER) cc_final: 0.6821 (mmm-85) REVERT: C 162 ARG cc_start: 0.8022 (mmm160) cc_final: 0.7607 (mmm-85) REVERT: C 328 MET cc_start: 0.7281 (mtt) cc_final: 0.6423 (ttt) outliers start: 41 outliers final: 25 residues processed: 221 average time/residue: 0.3005 time to fit residues: 92.4017 Evaluate side-chains 222 residues out of total 1432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 188 time to evaluate : 0.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 100 ASP Chi-restraints excluded: chain D residue 142 ASP Chi-restraints excluded: chain D residue 235 ASN Chi-restraints excluded: chain D residue 289 ASP Chi-restraints excluded: chain D residue 418 THR Chi-restraints excluded: chain D residue 430 GLU Chi-restraints excluded: chain A residue 38 ASN Chi-restraints excluded: chain A residue 108 MET Chi-restraints excluded: chain A residue 145 TYR Chi-restraints excluded: chain A residue 151 ARG Chi-restraints excluded: chain A residue 225 GLU Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain A residue 355 ARG Chi-restraints excluded: chain A residue 386 ARG Chi-restraints excluded: chain A residue 401 GLU Chi-restraints excluded: chain A residue 405 ARG Chi-restraints excluded: chain B residue 100 ASP Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 142 ASP Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain B residue 168 MET Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 235 ASN Chi-restraints excluded: chain B residue 289 ASP Chi-restraints excluded: chain B residue 418 THR Chi-restraints excluded: chain B residue 430 GLU Chi-restraints excluded: chain C residue 20 SER Chi-restraints excluded: chain C residue 38 ASN Chi-restraints excluded: chain C residue 108 MET Chi-restraints excluded: chain C residue 145 TYR Chi-restraints excluded: chain C residue 151 ARG Chi-restraints excluded: chain C residue 225 GLU Chi-restraints excluded: chain C residue 386 ARG Chi-restraints excluded: chain C residue 405 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 109 optimal weight: 4.9990 chunk 52 optimal weight: 5.9990 chunk 154 optimal weight: 5.9990 chunk 45 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 44 optimal weight: 0.6980 chunk 152 optimal weight: 2.9990 chunk 18 optimal weight: 0.7980 chunk 80 optimal weight: 4.9990 chunk 157 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 303 ASN B 76 GLN C 82 GLN C 235 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.162428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.121010 restraints weight = 58389.421| |-----------------------------------------------------------------------------| r_work (start): 0.3655 rms_B_bonded: 3.39 r_work: 0.3468 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3468 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3505 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3505 r_free = 0.3505 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3505 r_free = 0.3505 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3505 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7530 moved from start: 0.2720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 13374 Z= 0.179 Angle : 0.524 5.086 18150 Z= 0.272 Chirality : 0.046 0.139 2012 Planarity : 0.004 0.041 2364 Dihedral : 7.687 59.800 2012 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.89 % Favored : 92.11 % Rotamer: Outliers : 3.36 % Allowed : 15.81 % Favored : 80.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.94 (0.19), residues: 1652 helix: -1.77 (0.24), residues: 400 sheet: -3.17 (0.29), residues: 248 loop : -1.70 (0.18), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 232 TYR 0.023 0.001 TYR C 75 PHE 0.010 0.001 PHE A 98 TRP 0.010 0.001 TRP D 88 HIS 0.004 0.001 HIS A 78 Details of bonding type rmsd covalent geometry : bond 0.00429 (13374) covalent geometry : angle 0.52374 (18150) hydrogen bonds : bond 0.03567 ( 114) hydrogen bonds : angle 4.55621 ( 330) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3304 Ramachandran restraints generated. 1652 Oldfield, 0 Emsley, 1652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3304 Ramachandran restraints generated. 1652 Oldfield, 0 Emsley, 1652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 10 is missing expected H atoms. Skipping. Residue MET 11 is missing expected H atoms. Skipping. Residue TYR 114 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue MET 11 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue MET 11 is missing expected H atoms. Skipping. Residue TYR 114 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue MET 11 is missing expected H atoms. Skipping. Evaluate side-chains 235 residues out of total 1432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 192 time to evaluate : 0.794 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 55 ASP cc_start: 0.7731 (m-30) cc_final: 0.7457 (t0) REVERT: D 134 GLU cc_start: 0.7977 (mm-30) cc_final: 0.7701 (mt-10) REVERT: D 190 ILE cc_start: 0.8929 (tt) cc_final: 0.8619 (pt) REVERT: D 250 GLU cc_start: 0.8407 (mm-30) cc_final: 0.8166 (mm-30) REVERT: D 298 ASP cc_start: 0.8532 (t0) cc_final: 0.8328 (t0) REVERT: D 430 GLU cc_start: 0.7412 (OUTLIER) cc_final: 0.7169 (mm-30) REVERT: A 38 ASN cc_start: 0.8511 (OUTLIER) cc_final: 0.8149 (p0) REVERT: A 69 MET cc_start: 0.8820 (mtm) cc_final: 0.8337 (mtt) REVERT: A 108 MET cc_start: 0.7926 (OUTLIER) cc_final: 0.7675 (mtm) REVERT: A 151 ARG cc_start: 0.7414 (OUTLIER) cc_final: 0.6887 (tpp80) REVERT: A 213 MET cc_start: 0.8971 (mtp) cc_final: 0.8637 (mtp) REVERT: A 328 MET cc_start: 0.7250 (mtt) cc_final: 0.6782 (ttt) REVERT: A 355 ARG cc_start: 0.8179 (OUTLIER) cc_final: 0.7151 (ttt90) REVERT: A 424 LYS cc_start: 0.8490 (OUTLIER) cc_final: 0.8142 (mptm) REVERT: B 134 GLU cc_start: 0.7889 (mm-30) cc_final: 0.7566 (mt-10) REVERT: B 298 ASP cc_start: 0.8495 (t0) cc_final: 0.8089 (t0) REVERT: B 430 GLU cc_start: 0.7568 (OUTLIER) cc_final: 0.7275 (mm-30) REVERT: C 151 ARG cc_start: 0.7043 (OUTLIER) cc_final: 0.6713 (mmm-85) REVERT: C 424 LYS cc_start: 0.8386 (OUTLIER) cc_final: 0.7990 (mptm) outliers start: 43 outliers final: 29 residues processed: 224 average time/residue: 0.2903 time to fit residues: 90.0714 Evaluate side-chains 219 residues out of total 1432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 181 time to evaluate : 0.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 100 ASP Chi-restraints excluded: chain D residue 142 ASP Chi-restraints excluded: chain D residue 235 ASN Chi-restraints excluded: chain D residue 289 ASP Chi-restraints excluded: chain D residue 418 THR Chi-restraints excluded: chain D residue 430 GLU Chi-restraints excluded: chain A residue 38 ASN Chi-restraints excluded: chain A residue 108 MET Chi-restraints excluded: chain A residue 145 TYR Chi-restraints excluded: chain A residue 151 ARG Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 225 GLU Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain A residue 355 ARG Chi-restraints excluded: chain A residue 386 ARG Chi-restraints excluded: chain A residue 401 GLU Chi-restraints excluded: chain A residue 405 ARG Chi-restraints excluded: chain A residue 424 LYS Chi-restraints excluded: chain B residue 100 ASP Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 142 ASP Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain B residue 168 MET Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 235 ASN Chi-restraints excluded: chain B residue 289 ASP Chi-restraints excluded: chain B residue 418 THR Chi-restraints excluded: chain B residue 430 GLU Chi-restraints excluded: chain C residue 20 SER Chi-restraints excluded: chain C residue 108 MET Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 145 TYR Chi-restraints excluded: chain C residue 151 ARG Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 225 GLU Chi-restraints excluded: chain C residue 386 ARG Chi-restraints excluded: chain C residue 405 ARG Chi-restraints excluded: chain C residue 424 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 67 optimal weight: 3.9990 chunk 95 optimal weight: 3.9990 chunk 118 optimal weight: 3.9990 chunk 98 optimal weight: 5.9990 chunk 162 optimal weight: 5.9990 chunk 127 optimal weight: 0.9990 chunk 89 optimal weight: 2.9990 chunk 92 optimal weight: 0.9990 chunk 19 optimal weight: 6.9990 chunk 122 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 303 ASN D 357 ASN A 235 ASN B 76 GLN B 357 ASN C 38 ASN C 235 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.169249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.121530 restraints weight = 64386.919| |-----------------------------------------------------------------------------| r_work (start): 0.3628 rms_B_bonded: 3.70 r_work: 0.3447 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3447 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3490 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3490 r_free = 0.3490 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3490 r_free = 0.3490 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3490 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7547 moved from start: 0.2894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 13374 Z= 0.162 Angle : 0.505 4.666 18150 Z= 0.263 Chirality : 0.045 0.139 2012 Planarity : 0.004 0.039 2364 Dihedral : 7.547 59.835 2012 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.16 % Favored : 92.84 % Rotamer: Outliers : 3.22 % Allowed : 16.31 % Favored : 80.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.82 (0.19), residues: 1652 helix: -1.63 (0.25), residues: 400 sheet: -3.11 (0.29), residues: 248 loop : -1.64 (0.18), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 232 TYR 0.019 0.001 TYR C 75 PHE 0.007 0.001 PHE A 91 TRP 0.009 0.001 TRP D 284 HIS 0.004 0.001 HIS A 78 Details of bonding type rmsd covalent geometry : bond 0.00390 (13374) covalent geometry : angle 0.50522 (18150) hydrogen bonds : bond 0.03307 ( 114) hydrogen bonds : angle 4.54859 ( 330) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3304 Ramachandran restraints generated. 1652 Oldfield, 0 Emsley, 1652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3304 Ramachandran restraints generated. 1652 Oldfield, 0 Emsley, 1652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 10 is missing expected H atoms. Skipping. Residue MET 11 is missing expected H atoms. Skipping. Residue TYR 114 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue MET 11 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue MET 11 is missing expected H atoms. Skipping. Residue TYR 114 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue MET 11 is missing expected H atoms. Skipping. Evaluate side-chains 232 residues out of total 1432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 191 time to evaluate : 0.703 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 55 ASP cc_start: 0.7754 (m-30) cc_final: 0.7478 (t0) REVERT: D 123 GLN cc_start: 0.8163 (mm-40) cc_final: 0.7774 (mt0) REVERT: D 134 GLU cc_start: 0.7914 (mm-30) cc_final: 0.7629 (mt-10) REVERT: D 250 GLU cc_start: 0.8382 (mm-30) cc_final: 0.8143 (mm-30) REVERT: D 298 ASP cc_start: 0.8523 (t0) cc_final: 0.8142 (t0) REVERT: D 430 GLU cc_start: 0.7393 (OUTLIER) cc_final: 0.7127 (mm-30) REVERT: A 38 ASN cc_start: 0.8506 (OUTLIER) cc_final: 0.8251 (p0) REVERT: A 69 MET cc_start: 0.8833 (mtm) cc_final: 0.8333 (mtt) REVERT: A 151 ARG cc_start: 0.7424 (OUTLIER) cc_final: 0.6893 (tpp80) REVERT: A 213 MET cc_start: 0.8988 (mtp) cc_final: 0.8669 (mtp) REVERT: A 328 MET cc_start: 0.7278 (mtt) cc_final: 0.6803 (ttt) REVERT: A 355 ARG cc_start: 0.8166 (OUTLIER) cc_final: 0.7108 (ttt90) REVERT: A 424 LYS cc_start: 0.8513 (OUTLIER) cc_final: 0.8121 (mptm) REVERT: B 55 ASP cc_start: 0.7740 (m-30) cc_final: 0.7434 (t0) REVERT: B 123 GLN cc_start: 0.7876 (mm-40) cc_final: 0.7386 (mt0) REVERT: B 134 GLU cc_start: 0.7902 (mm-30) cc_final: 0.7580 (mt-10) REVERT: B 190 ILE cc_start: 0.8797 (OUTLIER) cc_final: 0.8459 (mm) REVERT: B 298 ASP cc_start: 0.8514 (t0) cc_final: 0.8110 (t0) REVERT: B 421 MET cc_start: 0.8084 (mtt) cc_final: 0.7704 (mtt) REVERT: B 430 GLU cc_start: 0.7568 (OUTLIER) cc_final: 0.7286 (mm-30) REVERT: C 108 MET cc_start: 0.7722 (OUTLIER) cc_final: 0.7485 (mtm) REVERT: C 134 GLU cc_start: 0.7411 (tp30) cc_final: 0.6772 (tp30) REVERT: C 424 LYS cc_start: 0.8412 (OUTLIER) cc_final: 0.7971 (mptm) outliers start: 41 outliers final: 30 residues processed: 221 average time/residue: 0.3196 time to fit residues: 97.6011 Evaluate side-chains 223 residues out of total 1432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 184 time to evaluate : 0.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 100 ASP Chi-restraints excluded: chain D residue 142 ASP Chi-restraints excluded: chain D residue 235 ASN Chi-restraints excluded: chain D residue 289 ASP Chi-restraints excluded: chain D residue 418 THR Chi-restraints excluded: chain D residue 430 GLU Chi-restraints excluded: chain A residue 38 ASN Chi-restraints excluded: chain A residue 108 MET Chi-restraints excluded: chain A residue 134 GLU Chi-restraints excluded: chain A residue 145 TYR Chi-restraints excluded: chain A residue 151 ARG Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 190 ILE Chi-restraints excluded: chain A residue 225 GLU Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain A residue 355 ARG Chi-restraints excluded: chain A residue 386 ARG Chi-restraints excluded: chain A residue 401 GLU Chi-restraints excluded: chain A residue 405 ARG Chi-restraints excluded: chain A residue 424 LYS Chi-restraints excluded: chain B residue 100 ASP Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 142 ASP Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain B residue 168 MET Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 235 ASN Chi-restraints excluded: chain B residue 289 ASP Chi-restraints excluded: chain B residue 418 THR Chi-restraints excluded: chain B residue 430 GLU Chi-restraints excluded: chain C residue 20 SER Chi-restraints excluded: chain C residue 108 MET Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 145 TYR Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 225 GLU Chi-restraints excluded: chain C residue 386 ARG Chi-restraints excluded: chain C residue 405 ARG Chi-restraints excluded: chain C residue 424 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 75 optimal weight: 1.9990 chunk 156 optimal weight: 1.9990 chunk 124 optimal weight: 0.9980 chunk 97 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 35 optimal weight: 0.9990 chunk 159 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 chunk 139 optimal weight: 4.9990 chunk 155 optimal weight: 2.9990 chunk 58 optimal weight: 6.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 303 ASN B 76 GLN C 235 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.162633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.121421 restraints weight = 58775.440| |-----------------------------------------------------------------------------| r_work (start): 0.3660 rms_B_bonded: 3.38 r_work: 0.3479 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3479 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3511 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3511 r_free = 0.3511 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3511 r_free = 0.3511 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3511 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7528 moved from start: 0.3000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 13374 Z= 0.138 Angle : 0.494 5.091 18150 Z= 0.255 Chirality : 0.045 0.141 2012 Planarity : 0.004 0.040 2364 Dihedral : 7.371 59.896 2012 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.10 % Favored : 92.90 % Rotamer: Outliers : 3.43 % Allowed : 15.95 % Favored : 80.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.71 (0.19), residues: 1652 helix: -1.54 (0.25), residues: 410 sheet: -3.04 (0.30), residues: 248 loop : -1.56 (0.18), residues: 994 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 232 TYR 0.021 0.001 TYR C 75 PHE 0.006 0.001 PHE A 91 TRP 0.009 0.001 TRP D 284 HIS 0.003 0.001 HIS A 78 Details of bonding type rmsd covalent geometry : bond 0.00335 (13374) covalent geometry : angle 0.49379 (18150) hydrogen bonds : bond 0.03220 ( 114) hydrogen bonds : angle 4.37782 ( 330) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3304 Ramachandran restraints generated. 1652 Oldfield, 0 Emsley, 1652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3304 Ramachandran restraints generated. 1652 Oldfield, 0 Emsley, 1652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 10 is missing expected H atoms. Skipping. Residue MET 11 is missing expected H atoms. Skipping. Residue TYR 114 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue MET 11 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue MET 11 is missing expected H atoms. Skipping. Residue TYR 114 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue MET 11 is missing expected H atoms. Skipping. Evaluate side-chains 236 residues out of total 1432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 192 time to evaluate : 0.666 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: D 55 ASP cc_start: 0.7702 (m-30) cc_final: 0.7432 (t0) REVERT: D 123 GLN cc_start: 0.8213 (mm-40) cc_final: 0.7829 (mt0) REVERT: D 134 GLU cc_start: 0.7916 (mm-30) cc_final: 0.7630 (mt-10) REVERT: D 250 GLU cc_start: 0.8356 (mm-30) cc_final: 0.8124 (mm-30) REVERT: D 298 ASP cc_start: 0.8517 (t0) cc_final: 0.8148 (t0) REVERT: D 430 GLU cc_start: 0.7371 (OUTLIER) cc_final: 0.7093 (mm-30) REVERT: A 38 ASN cc_start: 0.8514 (OUTLIER) cc_final: 0.8124 (p0) REVERT: A 69 MET cc_start: 0.8854 (mtm) cc_final: 0.8348 (mtt) REVERT: A 151 ARG cc_start: 0.7406 (OUTLIER) cc_final: 0.6891 (tpp80) REVERT: A 213 MET cc_start: 0.8952 (mtp) cc_final: 0.8637 (mtp) REVERT: A 328 MET cc_start: 0.7404 (mtt) cc_final: 0.6987 (ttt) REVERT: A 355 ARG cc_start: 0.8166 (OUTLIER) cc_final: 0.7052 (ttt90) REVERT: B 55 ASP cc_start: 0.7688 (m-30) cc_final: 0.7379 (t0) REVERT: B 123 GLN cc_start: 0.7939 (mm-40) cc_final: 0.7492 (mt0) REVERT: B 134 GLU cc_start: 0.7877 (mm-30) cc_final: 0.7564 (mt-10) REVERT: B 190 ILE cc_start: 0.8786 (mm) cc_final: 0.8451 (mm) REVERT: B 298 ASP cc_start: 0.8499 (t0) cc_final: 0.8103 (t0) REVERT: B 421 MET cc_start: 0.8067 (mtt) cc_final: 0.7686 (mtt) REVERT: B 429 GLN cc_start: 0.8107 (OUTLIER) cc_final: 0.7404 (mp-120) REVERT: B 430 GLU cc_start: 0.7535 (OUTLIER) cc_final: 0.7244 (mm-30) REVERT: C 134 GLU cc_start: 0.7390 (tp30) cc_final: 0.6749 (tp30) REVERT: C 151 ARG cc_start: 0.7070 (OUTLIER) cc_final: 0.6720 (mmm-85) REVERT: C 289 ASP cc_start: 0.8246 (t70) cc_final: 0.7854 (t0) REVERT: C 424 LYS cc_start: 0.8398 (OUTLIER) cc_final: 0.7926 (mptm) outliers start: 44 outliers final: 31 residues processed: 224 average time/residue: 0.3062 time to fit residues: 94.4400 Evaluate side-chains 225 residues out of total 1432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 186 time to evaluate : 0.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 100 ASP Chi-restraints excluded: chain D residue 142 ASP Chi-restraints excluded: chain D residue 213 MET Chi-restraints excluded: chain D residue 235 ASN Chi-restraints excluded: chain D residue 289 ASP Chi-restraints excluded: chain D residue 418 THR Chi-restraints excluded: chain D residue 430 GLU Chi-restraints excluded: chain A residue 20 SER Chi-restraints excluded: chain A residue 38 ASN Chi-restraints excluded: chain A residue 108 MET Chi-restraints excluded: chain A residue 134 GLU Chi-restraints excluded: chain A residue 145 TYR Chi-restraints excluded: chain A residue 151 ARG Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 190 ILE Chi-restraints excluded: chain A residue 225 GLU Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain A residue 355 ARG Chi-restraints excluded: chain A residue 386 ARG Chi-restraints excluded: chain A residue 401 GLU Chi-restraints excluded: chain A residue 405 ARG Chi-restraints excluded: chain B residue 100 ASP Chi-restraints excluded: chain B residue 142 ASP Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain B residue 168 MET Chi-restraints excluded: chain B residue 235 ASN Chi-restraints excluded: chain B residue 289 ASP Chi-restraints excluded: chain B residue 418 THR Chi-restraints excluded: chain B residue 429 GLN Chi-restraints excluded: chain B residue 430 GLU Chi-restraints excluded: chain C residue 20 SER Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 145 TYR Chi-restraints excluded: chain C residue 151 ARG Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 225 GLU Chi-restraints excluded: chain C residue 386 ARG Chi-restraints excluded: chain C residue 405 ARG Chi-restraints excluded: chain C residue 424 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 66 optimal weight: 0.0020 chunk 149 optimal weight: 3.9990 chunk 57 optimal weight: 2.9990 chunk 59 optimal weight: 3.9990 chunk 89 optimal weight: 2.9990 chunk 69 optimal weight: 0.9990 chunk 132 optimal weight: 4.9990 chunk 53 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 chunk 125 optimal weight: 0.9990 chunk 157 optimal weight: 3.9990 overall best weight: 1.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 235 ASN B 76 GLN C 235 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.170328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.124755 restraints weight = 53473.951| |-----------------------------------------------------------------------------| r_work (start): 0.3676 rms_B_bonded: 3.26 r_work: 0.3497 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3497 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3528 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3528 r_free = 0.3528 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3528 r_free = 0.3528 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3528 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7510 moved from start: 0.3089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 13374 Z= 0.125 Angle : 0.484 4.610 18150 Z= 0.251 Chirality : 0.045 0.139 2012 Planarity : 0.004 0.059 2364 Dihedral : 7.184 59.915 2009 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.04 % Favored : 92.96 % Rotamer: Outliers : 3.15 % Allowed : 16.24 % Favored : 80.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.61 (0.20), residues: 1652 helix: -1.39 (0.26), residues: 410 sheet: -2.98 (0.30), residues: 248 loop : -1.53 (0.18), residues: 994 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 232 TYR 0.017 0.001 TYR C 75 PHE 0.005 0.001 PHE A 318 TRP 0.009 0.001 TRP D 284 HIS 0.003 0.001 HIS A 78 Details of bonding type rmsd covalent geometry : bond 0.00302 (13374) covalent geometry : angle 0.48446 (18150) hydrogen bonds : bond 0.03124 ( 114) hydrogen bonds : angle 4.27265 ( 330) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3304 Ramachandran restraints generated. 1652 Oldfield, 0 Emsley, 1652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3304 Ramachandran restraints generated. 1652 Oldfield, 0 Emsley, 1652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 10 is missing expected H atoms. Skipping. Residue MET 11 is missing expected H atoms. Skipping. Residue TYR 114 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue MET 11 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue MET 11 is missing expected H atoms. Skipping. Residue TYR 114 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue MET 11 is missing expected H atoms. Skipping. Evaluate side-chains 232 residues out of total 1432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 192 time to evaluate : 0.571 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 55 ASP cc_start: 0.7678 (m-30) cc_final: 0.7436 (t0) REVERT: D 123 GLN cc_start: 0.8190 (mm-40) cc_final: 0.7814 (mt0) REVERT: D 134 GLU cc_start: 0.7891 (mm-30) cc_final: 0.7615 (mt-10) REVERT: D 250 GLU cc_start: 0.8323 (mm-30) cc_final: 0.8097 (mm-30) REVERT: D 298 ASP cc_start: 0.8508 (t0) cc_final: 0.8144 (t0) REVERT: D 308 THR cc_start: 0.8913 (t) cc_final: 0.8673 (t) REVERT: D 430 GLU cc_start: 0.7376 (OUTLIER) cc_final: 0.7141 (mm-30) REVERT: A 38 ASN cc_start: 0.8532 (OUTLIER) cc_final: 0.8137 (p0) REVERT: A 69 MET cc_start: 0.8839 (mtm) cc_final: 0.8334 (mtt) REVERT: A 108 MET cc_start: 0.8236 (OUTLIER) cc_final: 0.7845 (mtm) REVERT: A 151 ARG cc_start: 0.7357 (OUTLIER) cc_final: 0.6899 (mmm-85) REVERT: A 213 MET cc_start: 0.8935 (mtp) cc_final: 0.8620 (mtp) REVERT: A 328 MET cc_start: 0.7382 (mtt) cc_final: 0.6974 (ttt) REVERT: A 355 ARG cc_start: 0.8164 (OUTLIER) cc_final: 0.7033 (ttt90) REVERT: A 424 LYS cc_start: 0.8491 (OUTLIER) cc_final: 0.8116 (mptm) REVERT: B 55 ASP cc_start: 0.7640 (m-30) cc_final: 0.7396 (t0) REVERT: B 123 GLN cc_start: 0.7962 (mm-40) cc_final: 0.7551 (mt0) REVERT: B 134 GLU cc_start: 0.7841 (mm-30) cc_final: 0.7540 (mt-10) REVERT: B 190 ILE cc_start: 0.8782 (mm) cc_final: 0.8436 (mm) REVERT: B 298 ASP cc_start: 0.8490 (t0) cc_final: 0.8096 (t0) REVERT: B 421 MET cc_start: 0.8037 (mtt) cc_final: 0.7664 (mtt) REVERT: B 429 GLN cc_start: 0.8078 (OUTLIER) cc_final: 0.7425 (mp-120) REVERT: B 430 GLU cc_start: 0.7526 (OUTLIER) cc_final: 0.7236 (mm-30) REVERT: C 134 GLU cc_start: 0.7388 (tp30) cc_final: 0.6761 (tp30) REVERT: C 151 ARG cc_start: 0.7069 (OUTLIER) cc_final: 0.6719 (mmm-85) REVERT: C 186 ASN cc_start: 0.8648 (m-40) cc_final: 0.8375 (m-40) REVERT: C 213 MET cc_start: 0.8861 (mtp) cc_final: 0.8595 (mtp) REVERT: C 289 ASP cc_start: 0.8240 (t70) cc_final: 0.7834 (t0) outliers start: 40 outliers final: 29 residues processed: 222 average time/residue: 0.3048 time to fit residues: 92.9837 Evaluate side-chains 223 residues out of total 1432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 185 time to evaluate : 0.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 100 ASP Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 142 ASP Chi-restraints excluded: chain D residue 235 ASN Chi-restraints excluded: chain D residue 289 ASP Chi-restraints excluded: chain D residue 430 GLU Chi-restraints excluded: chain A residue 20 SER Chi-restraints excluded: chain A residue 38 ASN Chi-restraints excluded: chain A residue 108 MET Chi-restraints excluded: chain A residue 134 GLU Chi-restraints excluded: chain A residue 145 TYR Chi-restraints excluded: chain A residue 151 ARG Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 190 ILE Chi-restraints excluded: chain A residue 225 GLU Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain A residue 355 ARG Chi-restraints excluded: chain A residue 386 ARG Chi-restraints excluded: chain A residue 401 GLU Chi-restraints excluded: chain A residue 405 ARG Chi-restraints excluded: chain A residue 424 LYS Chi-restraints excluded: chain B residue 100 ASP Chi-restraints excluded: chain B residue 142 ASP Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain B residue 168 MET Chi-restraints excluded: chain B residue 235 ASN Chi-restraints excluded: chain B residue 289 ASP Chi-restraints excluded: chain B residue 418 THR Chi-restraints excluded: chain B residue 429 GLN Chi-restraints excluded: chain B residue 430 GLU Chi-restraints excluded: chain C residue 20 SER Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 145 TYR Chi-restraints excluded: chain C residue 151 ARG Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 225 GLU Chi-restraints excluded: chain C residue 386 ARG Chi-restraints excluded: chain C residue 405 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 48 optimal weight: 1.9990 chunk 131 optimal weight: 3.9990 chunk 149 optimal weight: 1.9990 chunk 10 optimal weight: 4.9990 chunk 74 optimal weight: 0.8980 chunk 158 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 53 optimal weight: 0.9980 chunk 140 optimal weight: 5.9990 chunk 18 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 76 GLN C 235 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.163120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.122060 restraints weight = 59464.338| |-----------------------------------------------------------------------------| r_work (start): 0.3669 rms_B_bonded: 3.38 r_work: 0.3494 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3494 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3525 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3525 r_free = 0.3525 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3525 r_free = 0.3525 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3525 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7517 moved from start: 0.3186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 13374 Z= 0.122 Angle : 0.481 4.624 18150 Z= 0.248 Chirality : 0.045 0.138 2012 Planarity : 0.004 0.037 2364 Dihedral : 7.023 59.594 2008 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.34 % Favored : 92.66 % Rotamer: Outliers : 2.93 % Allowed : 16.45 % Favored : 80.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.53 (0.20), residues: 1652 helix: -1.28 (0.26), residues: 412 sheet: -2.90 (0.30), residues: 248 loop : -1.50 (0.19), residues: 992 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 232 TYR 0.020 0.001 TYR C 75 PHE 0.005 0.001 PHE A 318 TRP 0.009 0.001 TRP D 284 HIS 0.003 0.001 HIS A 78 Details of bonding type rmsd covalent geometry : bond 0.00296 (13374) covalent geometry : angle 0.48072 (18150) hydrogen bonds : bond 0.03061 ( 114) hydrogen bonds : angle 4.17617 ( 330) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3304 Ramachandran restraints generated. 1652 Oldfield, 0 Emsley, 1652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3304 Ramachandran restraints generated. 1652 Oldfield, 0 Emsley, 1652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 10 is missing expected H atoms. Skipping. Residue MET 11 is missing expected H atoms. Skipping. Residue TYR 114 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue MET 11 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue MET 11 is missing expected H atoms. Skipping. Residue TYR 114 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue MET 11 is missing expected H atoms. Skipping. Evaluate side-chains 230 residues out of total 1432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 193 time to evaluate : 0.678 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 55 ASP cc_start: 0.7698 (m-30) cc_final: 0.7462 (t0) REVERT: D 123 GLN cc_start: 0.8223 (mm-40) cc_final: 0.7828 (mt0) REVERT: D 134 GLU cc_start: 0.7897 (mm-30) cc_final: 0.7638 (mt-10) REVERT: D 190 ILE cc_start: 0.8932 (tt) cc_final: 0.8636 (pt) REVERT: D 250 GLU cc_start: 0.8326 (mm-30) cc_final: 0.8107 (mm-30) REVERT: D 298 ASP cc_start: 0.8506 (t0) cc_final: 0.8153 (t0) REVERT: D 302 ARG cc_start: 0.7769 (mmt-90) cc_final: 0.7219 (mmm160) REVERT: D 308 THR cc_start: 0.8934 (t) cc_final: 0.8728 (t) REVERT: D 421 MET cc_start: 0.8314 (mtt) cc_final: 0.7685 (mtt) REVERT: D 430 GLU cc_start: 0.7451 (OUTLIER) cc_final: 0.7199 (mm-30) REVERT: A 38 ASN cc_start: 0.8531 (OUTLIER) cc_final: 0.8133 (p0) REVERT: A 69 MET cc_start: 0.8837 (mtm) cc_final: 0.8337 (mtt) REVERT: A 108 MET cc_start: 0.8197 (OUTLIER) cc_final: 0.7814 (mtm) REVERT: A 151 ARG cc_start: 0.7323 (OUTLIER) cc_final: 0.6860 (mmm-85) REVERT: A 213 MET cc_start: 0.8930 (mtp) cc_final: 0.8622 (mtp) REVERT: A 328 MET cc_start: 0.7341 (mtt) cc_final: 0.6925 (ttt) REVERT: A 355 ARG cc_start: 0.8183 (OUTLIER) cc_final: 0.7028 (ttt90) REVERT: A 424 LYS cc_start: 0.8486 (OUTLIER) cc_final: 0.8115 (mptm) REVERT: B 55 ASP cc_start: 0.7679 (m-30) cc_final: 0.7444 (t0) REVERT: B 123 GLN cc_start: 0.8046 (mm-40) cc_final: 0.7630 (mt0) REVERT: B 134 GLU cc_start: 0.7860 (mm-30) cc_final: 0.7568 (mt-10) REVERT: B 190 ILE cc_start: 0.8782 (mm) cc_final: 0.8437 (mm) REVERT: B 298 ASP cc_start: 0.8492 (t0) cc_final: 0.8095 (t0) REVERT: B 421 MET cc_start: 0.8037 (mtt) cc_final: 0.7673 (mtt) REVERT: B 429 GLN cc_start: 0.8103 (OUTLIER) cc_final: 0.7436 (mp-120) REVERT: B 430 GLU cc_start: 0.7540 (OUTLIER) cc_final: 0.7241 (mm-30) REVERT: C 134 GLU cc_start: 0.7456 (tp30) cc_final: 0.6784 (tp30) REVERT: C 151 ARG cc_start: 0.7092 (OUTLIER) cc_final: 0.6728 (mmm-85) REVERT: C 186 ASN cc_start: 0.8660 (m-40) cc_final: 0.8383 (m-40) REVERT: C 213 MET cc_start: 0.8863 (mtp) cc_final: 0.8597 (mtp) REVERT: C 289 ASP cc_start: 0.8245 (t70) cc_final: 0.7833 (t0) REVERT: C 424 LYS cc_start: 0.8445 (OUTLIER) cc_final: 0.7967 (mptm) outliers start: 37 outliers final: 27 residues processed: 221 average time/residue: 0.3083 time to fit residues: 95.1861 Evaluate side-chains 224 residues out of total 1432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 187 time to evaluate : 0.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 100 ASP Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 142 ASP Chi-restraints excluded: chain D residue 235 ASN Chi-restraints excluded: chain D residue 289 ASP Chi-restraints excluded: chain D residue 430 GLU Chi-restraints excluded: chain A residue 20 SER Chi-restraints excluded: chain A residue 38 ASN Chi-restraints excluded: chain A residue 108 MET Chi-restraints excluded: chain A residue 134 GLU Chi-restraints excluded: chain A residue 145 TYR Chi-restraints excluded: chain A residue 151 ARG Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 190 ILE Chi-restraints excluded: chain A residue 225 GLU Chi-restraints excluded: chain A residue 355 ARG Chi-restraints excluded: chain A residue 386 ARG Chi-restraints excluded: chain A residue 401 GLU Chi-restraints excluded: chain A residue 405 ARG Chi-restraints excluded: chain A residue 424 LYS Chi-restraints excluded: chain B residue 100 ASP Chi-restraints excluded: chain B residue 142 ASP Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain B residue 168 MET Chi-restraints excluded: chain B residue 235 ASN Chi-restraints excluded: chain B residue 289 ASP Chi-restraints excluded: chain B residue 418 THR Chi-restraints excluded: chain B residue 429 GLN Chi-restraints excluded: chain B residue 430 GLU Chi-restraints excluded: chain C residue 20 SER Chi-restraints excluded: chain C residue 145 TYR Chi-restraints excluded: chain C residue 151 ARG Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 225 GLU Chi-restraints excluded: chain C residue 386 ARG Chi-restraints excluded: chain C residue 405 ARG Chi-restraints excluded: chain C residue 424 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 98 optimal weight: 7.9990 chunk 135 optimal weight: 2.9990 chunk 101 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 1 optimal weight: 0.9990 chunk 142 optimal weight: 0.1980 chunk 121 optimal weight: 4.9990 chunk 116 optimal weight: 0.5980 chunk 27 optimal weight: 3.9990 chunk 56 optimal weight: 0.9990 chunk 49 optimal weight: 4.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 235 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.164068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.123551 restraints weight = 53301.766| |-----------------------------------------------------------------------------| r_work (start): 0.3685 rms_B_bonded: 3.25 r_work: 0.3506 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3506 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3541 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3541 r_free = 0.3541 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3541 r_free = 0.3541 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3541 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7492 moved from start: 0.3239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 13374 Z= 0.109 Angle : 0.474 4.599 18150 Z= 0.244 Chirality : 0.044 0.135 2012 Planarity : 0.004 0.037 2364 Dihedral : 6.906 59.507 2008 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % Rotamer: Outliers : 3.00 % Allowed : 16.38 % Favored : 80.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.43 (0.20), residues: 1652 helix: -1.15 (0.26), residues: 412 sheet: -2.79 (0.32), residues: 238 loop : -1.51 (0.18), residues: 1002 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 232 TYR 0.016 0.001 TYR C 75 PHE 0.004 0.001 PHE A 91 TRP 0.008 0.001 TRP D 284 HIS 0.002 0.001 HIS A 78 Details of bonding type rmsd covalent geometry : bond 0.00265 (13374) covalent geometry : angle 0.47416 (18150) hydrogen bonds : bond 0.02979 ( 114) hydrogen bonds : angle 4.06932 ( 330) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3304 Ramachandran restraints generated. 1652 Oldfield, 0 Emsley, 1652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3304 Ramachandran restraints generated. 1652 Oldfield, 0 Emsley, 1652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 10 is missing expected H atoms. Skipping. Residue MET 11 is missing expected H atoms. Skipping. Residue TYR 114 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue MET 11 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue MET 11 is missing expected H atoms. Skipping. Residue TYR 114 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue MET 11 is missing expected H atoms. Skipping. Evaluate side-chains 229 residues out of total 1432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 191 time to evaluate : 0.732 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 55 ASP cc_start: 0.7671 (m-30) cc_final: 0.7435 (t0) REVERT: D 123 GLN cc_start: 0.8239 (mm-40) cc_final: 0.7866 (mt0) REVERT: D 190 ILE cc_start: 0.8931 (tt) cc_final: 0.8630 (pt) REVERT: D 298 ASP cc_start: 0.8490 (t0) cc_final: 0.8138 (t0) REVERT: D 302 ARG cc_start: 0.7807 (mmt-90) cc_final: 0.7263 (mmm160) REVERT: D 421 MET cc_start: 0.8291 (mtt) cc_final: 0.7675 (mtt) REVERT: D 430 GLU cc_start: 0.7449 (OUTLIER) cc_final: 0.7193 (mm-30) REVERT: A 38 ASN cc_start: 0.8522 (OUTLIER) cc_final: 0.8119 (p0) REVERT: A 69 MET cc_start: 0.8866 (mtm) cc_final: 0.8371 (mtt) REVERT: A 134 GLU cc_start: 0.7277 (OUTLIER) cc_final: 0.6864 (tp30) REVERT: A 151 ARG cc_start: 0.7305 (OUTLIER) cc_final: 0.6843 (mmm-85) REVERT: A 213 MET cc_start: 0.8915 (mtp) cc_final: 0.8607 (mtp) REVERT: A 328 MET cc_start: 0.7344 (mtt) cc_final: 0.6898 (ttt) REVERT: A 355 ARG cc_start: 0.8091 (OUTLIER) cc_final: 0.6921 (ttt90) REVERT: A 424 LYS cc_start: 0.8465 (OUTLIER) cc_final: 0.8069 (mptm) REVERT: B 55 ASP cc_start: 0.7642 (m-30) cc_final: 0.7409 (t0) REVERT: B 134 GLU cc_start: 0.7874 (mm-30) cc_final: 0.7593 (mt-10) REVERT: B 190 ILE cc_start: 0.8774 (mm) cc_final: 0.8418 (mm) REVERT: B 298 ASP cc_start: 0.8485 (t0) cc_final: 0.8088 (t0) REVERT: B 421 MET cc_start: 0.8034 (mtt) cc_final: 0.7639 (mtt) REVERT: B 429 GLN cc_start: 0.8037 (OUTLIER) cc_final: 0.7391 (mp-120) REVERT: B 430 GLU cc_start: 0.7549 (OUTLIER) cc_final: 0.7253 (mm-30) REVERT: C 134 GLU cc_start: 0.7472 (tp30) cc_final: 0.6808 (tp30) REVERT: C 151 ARG cc_start: 0.7037 (OUTLIER) cc_final: 0.6686 (mmm-85) REVERT: C 186 ASN cc_start: 0.8700 (m-40) cc_final: 0.8465 (m-40) REVERT: C 213 MET cc_start: 0.8854 (mtp) cc_final: 0.8619 (mtp) REVERT: C 289 ASP cc_start: 0.8231 (t70) cc_final: 0.7819 (t0) REVERT: C 424 LYS cc_start: 0.8420 (OUTLIER) cc_final: 0.7971 (mptm) outliers start: 38 outliers final: 28 residues processed: 221 average time/residue: 0.3132 time to fit residues: 95.8559 Evaluate side-chains 221 residues out of total 1432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 183 time to evaluate : 0.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 100 ASP Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 142 ASP Chi-restraints excluded: chain D residue 235 ASN Chi-restraints excluded: chain D residue 289 ASP Chi-restraints excluded: chain D residue 430 GLU Chi-restraints excluded: chain A residue 20 SER Chi-restraints excluded: chain A residue 38 ASN Chi-restraints excluded: chain A residue 108 MET Chi-restraints excluded: chain A residue 134 GLU Chi-restraints excluded: chain A residue 145 TYR Chi-restraints excluded: chain A residue 151 ARG Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 190 ILE Chi-restraints excluded: chain A residue 225 GLU Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 355 ARG Chi-restraints excluded: chain A residue 386 ARG Chi-restraints excluded: chain A residue 401 GLU Chi-restraints excluded: chain A residue 405 ARG Chi-restraints excluded: chain A residue 424 LYS Chi-restraints excluded: chain B residue 100 ASP Chi-restraints excluded: chain B residue 142 ASP Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain B residue 168 MET Chi-restraints excluded: chain B residue 235 ASN Chi-restraints excluded: chain B residue 289 ASP Chi-restraints excluded: chain B residue 418 THR Chi-restraints excluded: chain B residue 429 GLN Chi-restraints excluded: chain B residue 430 GLU Chi-restraints excluded: chain C residue 20 SER Chi-restraints excluded: chain C residue 145 TYR Chi-restraints excluded: chain C residue 151 ARG Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 225 GLU Chi-restraints excluded: chain C residue 386 ARG Chi-restraints excluded: chain C residue 405 ARG Chi-restraints excluded: chain C residue 424 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 27 optimal weight: 3.9990 chunk 148 optimal weight: 2.9990 chunk 92 optimal weight: 5.9990 chunk 105 optimal weight: 1.9990 chunk 106 optimal weight: 0.9990 chunk 136 optimal weight: 3.9990 chunk 52 optimal weight: 6.9990 chunk 149 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 117 optimal weight: 0.9980 chunk 140 optimal weight: 0.0370 overall best weight: 1.4064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 235 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.163381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.122740 restraints weight = 54902.626| |-----------------------------------------------------------------------------| r_work (start): 0.3678 rms_B_bonded: 3.27 r_work: 0.3501 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3501 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3537 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3537 r_free = 0.3537 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3537 r_free = 0.3537 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3537 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7512 moved from start: 0.3320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 13374 Z= 0.125 Angle : 0.479 4.700 18150 Z= 0.247 Chirality : 0.045 0.138 2012 Planarity : 0.004 0.036 2364 Dihedral : 6.825 59.548 2008 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.10 % Favored : 92.90 % Rotamer: Outliers : 2.93 % Allowed : 16.24 % Favored : 80.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.39 (0.20), residues: 1652 helix: -1.08 (0.26), residues: 412 sheet: -2.78 (0.31), residues: 252 loop : -1.47 (0.19), residues: 988 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 232 TYR 0.020 0.001 TYR C 75 PHE 0.006 0.001 PHE A 318 TRP 0.009 0.001 TRP D 284 HIS 0.003 0.001 HIS A 78 Details of bonding type rmsd covalent geometry : bond 0.00303 (13374) covalent geometry : angle 0.47928 (18150) hydrogen bonds : bond 0.03011 ( 114) hydrogen bonds : angle 4.05050 ( 330) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5827.73 seconds wall clock time: 99 minutes 22.06 seconds (5962.06 seconds total)