Starting phenix.real_space_refine on Wed Feb 4 13:22:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jek_61419/02_2026/9jek_61419.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jek_61419/02_2026/9jek_61419.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9jek_61419/02_2026/9jek_61419.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jek_61419/02_2026/9jek_61419.map" model { file = "/net/cci-nas-00/data/ceres_data/9jek_61419/02_2026/9jek_61419.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jek_61419/02_2026/9jek_61419.cif" } resolution = 3.1 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= 0.022 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: 4 Type Number sf(0) Gaussians S 48 5.16 5 C 6943 2.51 5 N 1823 2.21 5 O 2038 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10852 Number of models: 1 Model: "" Number of chains: 4 Chain: "C" Number of atoms: 2717 Number of conformers: 1 Conformer: "" Number of residues, atoms: 342, 2717 Classifications: {'peptide': 342} Link IDs: {'PTRANS': 14, 'TRANS': 327} Chain: "D" Number of atoms: 2701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2701 Classifications: {'peptide': 341} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 14, 'TRANS': 326} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "A" Number of atoms: 2717 Number of conformers: 1 Conformer: "" Number of residues, atoms: 342, 2717 Classifications: {'peptide': 342} Link IDs: {'PTRANS': 14, 'TRANS': 327} Chain: "B" Number of atoms: 2717 Number of conformers: 1 Conformer: "" Number of residues, atoms: 342, 2717 Classifications: {'peptide': 342} Link IDs: {'PTRANS': 14, 'TRANS': 327} Time building chain proxies: 2.40, per 1000 atoms: 0.22 Number of scatterers: 10852 At special positions: 0 Unit cell: (76.65, 88.33, 124.1, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 48 16.00 O 2038 8.00 N 1823 7.00 C 6943 6.00 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: 0.68 Conformation dependent library (CDL) restraints added in 575.4 milliseconds 2718 Ramachandran restraints generated. 1359 Oldfield, 0 Emsley, 1359 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2558 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 9 sheets defined 55.8% alpha, 10.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.37 Creating SS restraints... Processing helix chain 'C' and resid 18 through 20 No H-bonds generated for 'chain 'C' and resid 18 through 20' Processing helix chain 'C' and resid 21 through 41 removed outlier: 4.049A pdb=" N THR C 25 " --> pdb=" O ARG C 21 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 51 removed outlier: 4.021A pdb=" N TYR C 50 " --> pdb=" O ILE C 47 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N PHE C 51 " --> pdb=" O GLY C 48 " (cutoff:3.500A) Processing helix chain 'C' and resid 58 through 69 Processing helix chain 'C' and resid 72 through 88 removed outlier: 3.783A pdb=" N PHE C 88 " --> pdb=" O ALA C 84 " (cutoff:3.500A) Processing helix chain 'C' and resid 89 through 95 Processing helix chain 'C' and resid 108 through 120 removed outlier: 4.360A pdb=" N LEU C 112 " --> pdb=" O GLU C 108 " (cutoff:3.500A) Processing helix chain 'C' and resid 163 through 172 Processing helix chain 'C' and resid 194 through 196 No H-bonds generated for 'chain 'C' and resid 194 through 196' Processing helix chain 'C' and resid 200 through 212 removed outlier: 3.852A pdb=" N MET C 212 " --> pdb=" O VAL C 208 " (cutoff:3.500A) Processing helix chain 'C' and resid 239 through 246 Processing helix chain 'C' and resid 258 through 285 Processing helix chain 'C' and resid 286 through 288 No H-bonds generated for 'chain 'C' and resid 286 through 288' Processing helix chain 'C' and resid 298 through 303 removed outlier: 3.732A pdb=" N ALA C 303 " --> pdb=" O ASN C 299 " (cutoff:3.500A) Processing helix chain 'C' and resid 311 through 333 Processing helix chain 'C' and resid 333 through 341 removed outlier: 3.893A pdb=" N ARG C 337 " --> pdb=" O ASN C 333 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N PHE C 340 " --> pdb=" O LEU C 336 " (cutoff:3.500A) Processing helix chain 'D' and resid 18 through 20 No H-bonds generated for 'chain 'D' and resid 18 through 20' Processing helix chain 'D' and resid 21 through 40 removed outlier: 3.825A pdb=" N THR D 25 " --> pdb=" O ARG D 21 " (cutoff:3.500A) Processing helix chain 'D' and resid 46 through 51 removed outlier: 3.714A pdb=" N TYR D 50 " --> pdb=" O ILE D 47 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N PHE D 51 " --> pdb=" O GLY D 48 " (cutoff:3.500A) Processing helix chain 'D' and resid 58 through 69 Processing helix chain 'D' and resid 72 through 88 removed outlier: 4.739A pdb=" N THR D 85 " --> pdb=" O GLU D 81 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N LYS D 86 " --> pdb=" O ILE D 82 " (cutoff:3.500A) Processing helix chain 'D' and resid 89 through 94 Processing helix chain 'D' and resid 97 through 104 removed outlier: 3.661A pdb=" N LEU D 101 " --> pdb=" O GLN D 97 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ARG D 103 " --> pdb=" O TRP D 99 " (cutoff:3.500A) Processing helix chain 'D' and resid 108 through 120 removed outlier: 4.619A pdb=" N LEU D 112 " --> pdb=" O GLU D 108 " (cutoff:3.500A) Processing helix chain 'D' and resid 125 through 129 removed outlier: 3.527A pdb=" N LEU D 129 " --> pdb=" O PHE D 126 " (cutoff:3.500A) Processing helix chain 'D' and resid 163 through 172 Processing helix chain 'D' and resid 192 through 196 removed outlier: 3.603A pdb=" N LEU D 195 " --> pdb=" O ASP D 192 " (cutoff:3.500A) Processing helix chain 'D' and resid 200 through 211 Processing helix chain 'D' and resid 220 through 222 No H-bonds generated for 'chain 'D' and resid 220 through 222' Processing helix chain 'D' and resid 239 through 244 Processing helix chain 'D' and resid 248 through 253 Processing helix chain 'D' and resid 258 through 284 Processing helix chain 'D' and resid 311 through 333 Processing helix chain 'D' and resid 334 through 340 Processing helix chain 'A' and resid 18 through 20 No H-bonds generated for 'chain 'A' and resid 18 through 20' Processing helix chain 'A' and resid 21 through 40 removed outlier: 4.227A pdb=" N THR A 25 " --> pdb=" O ARG A 21 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 51 removed outlier: 3.570A pdb=" N TYR A 50 " --> pdb=" O ILE A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 69 Processing helix chain 'A' and resid 72 through 88 removed outlier: 4.414A pdb=" N THR A 85 " --> pdb=" O GLU A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 95 Processing helix chain 'A' and resid 98 through 104 Processing helix chain 'A' and resid 109 through 120 Processing helix chain 'A' and resid 125 through 129 Processing helix chain 'A' and resid 163 through 172 Processing helix chain 'A' and resid 192 through 196 removed outlier: 3.628A pdb=" N LEU A 195 " --> pdb=" O ASP A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 211 Processing helix chain 'A' and resid 220 through 222 No H-bonds generated for 'chain 'A' and resid 220 through 222' Processing helix chain 'A' and resid 239 through 245 Processing helix chain 'A' and resid 248 through 253 Processing helix chain 'A' and resid 258 through 284 Processing helix chain 'A' and resid 286 through 288 No H-bonds generated for 'chain 'A' and resid 286 through 288' Processing helix chain 'A' and resid 301 through 305 removed outlier: 3.817A pdb=" N ILE A 305 " --> pdb=" O ALA A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 333 Processing helix chain 'A' and resid 333 through 340 removed outlier: 3.923A pdb=" N ARG A 337 " --> pdb=" O ASN A 333 " (cutoff:3.500A) Processing helix chain 'B' and resid 20 through 40 Processing helix chain 'B' and resid 46 through 51 removed outlier: 3.954A pdb=" N TYR B 50 " --> pdb=" O ILE B 47 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N PHE B 51 " --> pdb=" O GLY B 48 " (cutoff:3.500A) Processing helix chain 'B' and resid 58 through 69 Processing helix chain 'B' and resid 72 through 88 removed outlier: 4.001A pdb=" N ILE B 82 " --> pdb=" O GLU B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 89 through 95 Processing helix chain 'B' and resid 98 through 104 Processing helix chain 'B' and resid 108 through 120 removed outlier: 4.629A pdb=" N LEU B 112 " --> pdb=" O GLU B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 125 through 129 removed outlier: 3.629A pdb=" N LEU B 129 " --> pdb=" O PHE B 126 " (cutoff:3.500A) Processing helix chain 'B' and resid 157 through 162 removed outlier: 4.429A pdb=" N GLU B 161 " --> pdb=" O MET B 158 " (cutoff:3.500A) Processing helix chain 'B' and resid 163 through 172 Processing helix chain 'B' and resid 192 through 196 removed outlier: 3.504A pdb=" N LEU B 195 " --> pdb=" O ASP B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 201 through 212 Processing helix chain 'B' and resid 220 through 222 No H-bonds generated for 'chain 'B' and resid 220 through 222' Processing helix chain 'B' and resid 239 through 246 Processing helix chain 'B' and resid 256 through 284 Processing helix chain 'B' and resid 286 through 288 No H-bonds generated for 'chain 'B' and resid 286 through 288' Processing helix chain 'B' and resid 311 through 333 Processing helix chain 'B' and resid 333 through 340 removed outlier: 3.844A pdb=" N ARG B 337 " --> pdb=" O ASN B 333 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N PHE B 340 " --> pdb=" O LEU B 336 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 145 through 149 Processing sheet with id=AA2, first strand: chain 'C' and resid 145 through 149 removed outlier: 6.763A pdb=" N ILE C 54 " --> pdb=" O MET C 134 " (cutoff:3.500A) removed outlier: 8.117A pdb=" N THR C 136 " --> pdb=" O ILE C 54 " (cutoff:3.500A) removed outlier: 7.822A pdb=" N GLY C 56 " --> pdb=" O THR C 136 " (cutoff:3.500A) removed outlier: 9.967A pdb=" N VAL C 138 " --> pdb=" O GLY C 56 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N ILE C 10 " --> pdb=" O LYS C 225 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N LEU C 227 " --> pdb=" O ILE C 10 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N ILE C 12 " --> pdb=" O LEU C 227 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N ILE C 229 " --> pdb=" O ILE C 12 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N SER C 14 " --> pdb=" O ILE C 229 " (cutoff:3.500A) removed outlier: 7.711A pdb=" N VAL C 291 " --> pdb=" O ILE C 224 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N VAL C 226 " --> pdb=" O VAL C 291 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N ILE C 293 " --> pdb=" O VAL C 226 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N ASN C 228 " --> pdb=" O ILE C 293 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 133 through 135 removed outlier: 3.623A pdb=" N MET D 134 " --> pdb=" O ILE D 54 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLY D 56 " --> pdb=" O MET D 134 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEU D 15 " --> pdb=" O THR D 55 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N ILE D 10 " --> pdb=" O LYS D 225 " (cutoff:3.500A) removed outlier: 7.501A pdb=" N LEU D 227 " --> pdb=" O ILE D 10 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N ILE D 12 " --> pdb=" O LEU D 227 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N ILE D 229 " --> pdb=" O ILE D 12 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N SER D 14 " --> pdb=" O ILE D 229 " (cutoff:3.500A) removed outlier: 7.755A pdb=" N VAL D 291 " --> pdb=" O ILE D 224 " (cutoff:3.500A) removed outlier: 5.982A pdb=" N VAL D 226 " --> pdb=" O VAL D 291 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N ILE D 293 " --> pdb=" O VAL D 226 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N ASN D 228 " --> pdb=" O ILE D 293 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 145 through 146 removed outlier: 3.550A pdb=" N VAL D 138 " --> pdb=" O ALA D 191 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ASN D 188 " --> pdb=" O ILE D 183 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 10 through 15 removed outlier: 6.162A pdb=" N ILE A 10 " --> pdb=" O LYS A 225 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N LEU A 227 " --> pdb=" O ILE A 10 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ILE A 12 " --> pdb=" O LEU A 227 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N ILE A 229 " --> pdb=" O ILE A 12 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N SER A 14 " --> pdb=" O ILE A 229 " (cutoff:3.500A) removed outlier: 8.144A pdb=" N VAL A 291 " --> pdb=" O ILE A 224 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N VAL A 226 " --> pdb=" O VAL A 291 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N ILE A 293 " --> pdb=" O VAL A 226 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N ASN A 228 " --> pdb=" O ILE A 293 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 56 through 57 removed outlier: 7.616A pdb=" N GLY A 56 " --> pdb=" O THR A 136 " (cutoff:3.500A) removed outlier: 9.908A pdb=" N VAL A 138 " --> pdb=" O GLY A 56 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 56 through 57 removed outlier: 7.616A pdb=" N GLY A 56 " --> pdb=" O THR A 136 " (cutoff:3.500A) removed outlier: 9.908A pdb=" N VAL A 138 " --> pdb=" O GLY A 56 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 145 through 149 removed outlier: 3.616A pdb=" N VAL B 138 " --> pdb=" O ALA B 191 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 145 through 149 removed outlier: 6.211A pdb=" N ILE B 54 " --> pdb=" O MET B 134 " (cutoff:3.500A) removed outlier: 8.095A pdb=" N THR B 136 " --> pdb=" O ILE B 54 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N GLY B 56 " --> pdb=" O THR B 136 " (cutoff:3.500A) removed outlier: 9.812A pdb=" N VAL B 138 " --> pdb=" O GLY B 56 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N LYS B 11 " --> pdb=" O LEU B 53 " (cutoff:3.500A) removed outlier: 7.761A pdb=" N THR B 55 " --> pdb=" O LYS B 11 " (cutoff:3.500A) removed outlier: 5.902A pdb=" N LEU B 13 " --> pdb=" O THR B 55 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N ILE B 10 " --> pdb=" O LYS B 225 " (cutoff:3.500A) removed outlier: 7.870A pdb=" N LEU B 227 " --> pdb=" O ILE B 10 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N ILE B 12 " --> pdb=" O LEU B 227 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N ILE B 229 " --> pdb=" O ILE B 12 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N SER B 14 " --> pdb=" O ILE B 229 " (cutoff:3.500A) removed outlier: 7.927A pdb=" N VAL B 291 " --> pdb=" O ILE B 224 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N VAL B 226 " --> pdb=" O VAL B 291 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N ILE B 293 " --> pdb=" O VAL B 226 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N ASN B 228 " --> pdb=" O ILE B 293 " (cutoff:3.500A) 516 hydrogen bonds defined for protein. 1464 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: 1.83 Time building geometry restraints manager: 0.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3377 1.34 - 1.45: 1396 1.45 - 1.57: 6195 1.57 - 1.69: 0 1.69 - 1.81: 84 Bond restraints: 11052 Sorted by residual: bond pdb=" C LEU D 341 " pdb=" O LEU D 341 " ideal model delta sigma weight residual 1.234 1.247 -0.012 1.17e-02 7.31e+03 1.08e+00 bond pdb=" CB ASP D 235 " pdb=" CG ASP D 235 " ideal model delta sigma weight residual 1.516 1.542 -0.026 2.50e-02 1.60e+03 1.08e+00 bond pdb=" CB ILE A 238 " pdb=" CG2 ILE A 238 " ideal model delta sigma weight residual 1.521 1.491 0.030 3.30e-02 9.18e+02 8.27e-01 bond pdb=" CA ILE A 293 " pdb=" CB ILE A 293 " ideal model delta sigma weight residual 1.528 1.540 -0.012 1.34e-02 5.57e+03 7.57e-01 bond pdb=" CB ASP A 211 " pdb=" CG ASP A 211 " ideal model delta sigma weight residual 1.516 1.537 -0.021 2.50e-02 1.60e+03 7.38e-01 ... (remaining 11047 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.88: 14672 1.88 - 3.77: 191 3.77 - 5.65: 20 5.65 - 7.53: 3 7.53 - 9.41: 3 Bond angle restraints: 14889 Sorted by residual: angle pdb=" C GLN A 97 " pdb=" N TRP A 98 " pdb=" CA TRP A 98 " ideal model delta sigma weight residual 122.15 113.56 8.59 2.83e+00 1.25e-01 9.21e+00 angle pdb=" CA LEU D 90 " pdb=" CB LEU D 90 " pdb=" CG LEU D 90 " ideal model delta sigma weight residual 116.30 125.71 -9.41 3.50e+00 8.16e-02 7.23e+00 angle pdb=" N ASN C 299 " pdb=" CA ASN C 299 " pdb=" C ASN C 299 " ideal model delta sigma weight residual 111.02 114.11 -3.09 1.22e+00 6.72e-01 6.40e+00 angle pdb=" N LEU D 341 " pdb=" CA LEU D 341 " pdb=" C LEU D 341 " ideal model delta sigma weight residual 111.96 108.46 3.50 1.41e+00 5.03e-01 6.15e+00 angle pdb=" CB MET C 257 " pdb=" CG MET C 257 " pdb=" SD MET C 257 " ideal model delta sigma weight residual 112.70 120.05 -7.35 3.00e+00 1.11e-01 6.00e+00 ... (remaining 14884 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.89: 5794 17.89 - 35.78: 754 35.78 - 53.68: 178 53.68 - 71.57: 46 71.57 - 89.46: 7 Dihedral angle restraints: 6779 sinusoidal: 2814 harmonic: 3965 Sorted by residual: dihedral pdb=" CA ASP C 308 " pdb=" C ASP C 308 " pdb=" N ASN C 309 " pdb=" CA ASN C 309 " ideal model delta harmonic sigma weight residual 180.00 -162.81 -17.19 0 5.00e+00 4.00e-02 1.18e+01 dihedral pdb=" CB GLU A 345 " pdb=" CG GLU A 345 " pdb=" CD GLU A 345 " pdb=" OE1 GLU A 345 " ideal model delta sinusoidal sigma weight residual 0.00 -89.46 89.46 1 3.00e+01 1.11e-03 1.06e+01 dihedral pdb=" CB GLU D 282 " pdb=" CG GLU D 282 " pdb=" CD GLU D 282 " pdb=" OE1 GLU D 282 " ideal model delta sinusoidal sigma weight residual 0.00 89.44 -89.44 1 3.00e+01 1.11e-03 1.06e+01 ... (remaining 6776 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 1037 0.032 - 0.064: 437 0.064 - 0.096: 101 0.096 - 0.127: 84 0.127 - 0.159: 4 Chirality restraints: 1663 Sorted by residual: chirality pdb=" CG LEU A 243 " pdb=" CB LEU A 243 " pdb=" CD1 LEU A 243 " pdb=" CD2 LEU A 243 " both_signs ideal model delta sigma weight residual False -2.59 -2.43 -0.16 2.00e-01 2.50e+01 6.34e-01 chirality pdb=" CB ILE C 286 " pdb=" CA ILE C 286 " pdb=" CG1 ILE C 286 " pdb=" CG2 ILE C 286 " both_signs ideal model delta sigma weight residual False 2.64 2.50 0.14 2.00e-01 2.50e+01 5.17e-01 chirality pdb=" CA ASP D 235 " pdb=" N ASP D 235 " pdb=" C ASP D 235 " pdb=" CB ASP D 235 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.14 2.00e-01 2.50e+01 4.58e-01 ... (remaining 1660 not shown) Planarity restraints: 1906 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL D 348 " -0.010 2.00e-02 2.50e+03 1.90e-02 3.60e+00 pdb=" C VAL D 348 " 0.033 2.00e-02 2.50e+03 pdb=" O VAL D 348 " -0.012 2.00e-02 2.50e+03 pdb=" N PRO D 349 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 275 " 0.012 2.00e-02 2.50e+03 1.39e-02 3.36e+00 pdb=" CG PHE B 275 " -0.032 2.00e-02 2.50e+03 pdb=" CD1 PHE B 275 " 0.007 2.00e-02 2.50e+03 pdb=" CD2 PHE B 275 " 0.011 2.00e-02 2.50e+03 pdb=" CE1 PHE B 275 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE B 275 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE B 275 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP D 235 " -0.009 2.00e-02 2.50e+03 1.80e-02 3.23e+00 pdb=" C ASP D 235 " 0.031 2.00e-02 2.50e+03 pdb=" O ASP D 235 " -0.012 2.00e-02 2.50e+03 pdb=" N TYR D 236 " -0.010 2.00e-02 2.50e+03 ... (remaining 1903 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 227 2.67 - 3.23: 10330 3.23 - 3.78: 17597 3.78 - 4.34: 24479 4.34 - 4.90: 40598 Nonbonded interactions: 93231 Sorted by model distance: nonbonded pdb=" O THR B 265 " pdb=" ND2 ASN B 269 " model vdw 2.109 3.120 nonbonded pdb=" OD1 ASN C 199 " pdb=" OG SER C 201 " model vdw 2.165 3.040 nonbonded pdb=" OE1 GLU C 304 " pdb=" OG SER B 239 " model vdw 2.168 3.040 nonbonded pdb=" O ALA A 327 " pdb=" OG1 THR A 331 " model vdw 2.200 3.040 nonbonded pdb=" O THR B 150 " pdb=" ND1 HIS B 152 " model vdw 2.230 3.120 ... (remaining 93226 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 9 through 219 or (resid 220 and (name N or name CA or name \ C or name O or name CB )) or resid 221 through 259 or (resid 260 and (name N or \ name CA or name C or name O or name CB )) or resid 261 through 349)) selection = (chain 'B' and (resid 9 through 219 or (resid 220 and (name N or name CA or name \ C or name O or name CB )) or resid 221 through 259 or (resid 260 and (name N or \ name CA or name C or name O or name CB )) or resid 261 through 349)) selection = (chain 'C' and (resid 9 through 219 or (resid 220 and (name N or name CA or name \ C or name O or name CB )) or resid 221 through 259 or (resid 260 and (name N or \ name CA or name C or name O or name CB )) or resid 261 through 349)) selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.420 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: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 10.710 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.020 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:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 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 : 0.002 0.030 11052 Z= 0.117 Angle : 0.541 9.414 14889 Z= 0.293 Chirality : 0.041 0.159 1663 Planarity : 0.004 0.044 1906 Dihedral : 16.970 89.460 4221 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.64 % Favored : 95.29 % Rotamer: Outliers : 2.38 % Allowed : 24.13 % Favored : 73.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.03 (0.23), residues: 1359 helix: 1.25 (0.21), residues: 624 sheet: -0.77 (0.39), residues: 198 loop : -1.10 (0.26), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 279 TYR 0.011 0.001 TYR D 182 PHE 0.032 0.001 PHE B 275 TRP 0.019 0.002 TRP A 98 HIS 0.002 0.001 HIS C 152 Details of bonding type rmsd covalent geometry : bond 0.00233 (11052) covalent geometry : angle 0.54094 (14889) hydrogen bonds : bond 0.15637 ( 508) hydrogen bonds : angle 6.37869 ( 1464) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2718 Ramachandran restraints generated. 1359 Oldfield, 0 Emsley, 1359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2718 Ramachandran restraints generated. 1359 Oldfield, 0 Emsley, 1359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 193 time to evaluate : 0.390 Fit side-chains revert: symmetry clash REVERT: C 158 MET cc_start: 0.7861 (mpp) cc_final: 0.7658 (ptp) REVERT: C 282 GLU cc_start: 0.8517 (tt0) cc_final: 0.8059 (tm-30) REVERT: D 93 PHE cc_start: 0.8312 (t80) cc_final: 0.8005 (t80) REVERT: D 97 GLN cc_start: 0.7514 (mp10) cc_final: 0.7203 (mp10) REVERT: D 282 GLU cc_start: 0.7858 (mt-10) cc_final: 0.7535 (mt-10) REVERT: A 103 ARG cc_start: 0.7540 (ttp80) cc_final: 0.7147 (ttp-110) REVERT: A 155 MET cc_start: 0.8875 (mmm) cc_final: 0.8433 (mmt) REVERT: B 16 ASN cc_start: 0.8993 (OUTLIER) cc_final: 0.8686 (m-40) REVERT: B 31 GLU cc_start: 0.8335 (mm-30) cc_final: 0.7941 (mm-30) REVERT: B 128 ASP cc_start: 0.7933 (m-30) cc_final: 0.6695 (t0) REVERT: B 134 MET cc_start: 0.8352 (tmm) cc_final: 0.7931 (ttp) REVERT: B 338 ASN cc_start: 0.7608 (t0) cc_final: 0.7237 (t0) outliers start: 28 outliers final: 26 residues processed: 213 average time/residue: 0.0840 time to fit residues: 26.4053 Evaluate side-chains 212 residues out of total 1179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 185 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 128 ASP Chi-restraints excluded: chain C residue 142 THR Chi-restraints excluded: chain C residue 207 GLU Chi-restraints excluded: chain C residue 307 LEU Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain C residue 347 PHE Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 120 ILE Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 218 ASP Chi-restraints excluded: chain D residue 249 LYS Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain A residue 75 GLU Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 187 GLU Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain B residue 16 ASN Chi-restraints excluded: chain B residue 32 LEU Chi-restraints excluded: chain B residue 52 ASP Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 159 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 7.9990 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 10.0000 chunk 55 optimal weight: 3.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 188 ASN D 100 ASN D 271 HIS B 269 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.141566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.117111 restraints weight = 14284.376| |-----------------------------------------------------------------------------| r_work (start): 0.3529 rms_B_bonded: 2.50 r_work: 0.3394 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.1383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 11052 Z= 0.250 Angle : 0.621 7.063 14889 Z= 0.333 Chirality : 0.047 0.164 1663 Planarity : 0.005 0.048 1906 Dihedral : 6.664 59.716 1525 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.62 % Favored : 93.30 % Rotamer: Outliers : 5.61 % Allowed : 20.39 % Favored : 74.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.55 (0.23), residues: 1359 helix: 0.51 (0.20), residues: 646 sheet: -1.03 (0.41), residues: 171 loop : -1.11 (0.27), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D 279 TYR 0.011 0.002 TYR D 251 PHE 0.025 0.002 PHE D 275 TRP 0.021 0.002 TRP A 99 HIS 0.007 0.002 HIS B 152 Details of bonding type rmsd covalent geometry : bond 0.00580 (11052) covalent geometry : angle 0.62148 (14889) hydrogen bonds : bond 0.05592 ( 508) hydrogen bonds : angle 5.43032 ( 1464) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2718 Ramachandran restraints generated. 1359 Oldfield, 0 Emsley, 1359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2718 Ramachandran restraints generated. 1359 Oldfield, 0 Emsley, 1359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 199 time to evaluate : 0.368 Fit side-chains revert: symmetry clash REVERT: C 158 MET cc_start: 0.7831 (mpp) cc_final: 0.7367 (ptp) REVERT: C 161 GLU cc_start: 0.7981 (OUTLIER) cc_final: 0.7653 (mp0) REVERT: C 210 ILE cc_start: 0.8830 (pt) cc_final: 0.8544 (pt) REVERT: C 275 PHE cc_start: 0.8682 (t80) cc_final: 0.8443 (t80) REVERT: C 282 GLU cc_start: 0.8526 (tt0) cc_final: 0.8088 (tm-30) REVERT: D 97 GLN cc_start: 0.7623 (mp10) cc_final: 0.7322 (mp10) REVERT: D 282 GLU cc_start: 0.7901 (mt-10) cc_final: 0.7555 (mt-10) REVERT: A 103 ARG cc_start: 0.7772 (ttp80) cc_final: 0.7387 (ttp-110) REVERT: B 28 LEU cc_start: 0.8760 (OUTLIER) cc_final: 0.8506 (tt) REVERT: B 160 ARG cc_start: 0.7697 (ttm-80) cc_final: 0.7368 (ttp80) REVERT: B 220 LYS cc_start: 0.8144 (OUTLIER) cc_final: 0.7809 (mppt) REVERT: B 338 ASN cc_start: 0.8132 (t0) cc_final: 0.7836 (t0) outliers start: 66 outliers final: 44 residues processed: 247 average time/residue: 0.0878 time to fit residues: 31.8952 Evaluate side-chains 230 residues out of total 1179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 183 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain C residue 142 THR Chi-restraints excluded: chain C residue 161 GLU Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain C residue 296 THR Chi-restraints excluded: chain C residue 307 LEU Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 347 PHE Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 120 ILE Chi-restraints excluded: chain D residue 172 SER Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain D residue 249 LYS Chi-restraints excluded: chain D residue 284 LEU Chi-restraints excluded: chain D residue 314 CYS Chi-restraints excluded: chain D residue 328 GLU Chi-restraints excluded: chain A residue 72 SER Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 211 ASP Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 82 ILE Chi-restraints excluded: chain B residue 95 ASN Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 159 ASP Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain B residue 220 LYS Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain B residue 314 CYS Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 335 GLU Chi-restraints excluded: chain B residue 336 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 38 optimal weight: 0.9990 chunk 135 optimal weight: 6.9990 chunk 107 optimal weight: 2.9990 chunk 4 optimal weight: 0.9980 chunk 81 optimal weight: 1.9990 chunk 46 optimal weight: 5.9990 chunk 102 optimal weight: 5.9990 chunk 134 optimal weight: 3.9990 chunk 76 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 82 optimal weight: 3.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 269 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.145496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.121012 restraints weight = 14189.975| |-----------------------------------------------------------------------------| r_work (start): 0.3578 rms_B_bonded: 2.53 r_work: 0.3441 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.1375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11052 Z= 0.142 Angle : 0.528 7.243 14889 Z= 0.282 Chirality : 0.043 0.149 1663 Planarity : 0.004 0.044 1906 Dihedral : 5.732 58.498 1499 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.37 % Favored : 94.55 % Rotamer: Outliers : 4.16 % Allowed : 21.07 % Favored : 74.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.32 (0.23), residues: 1359 helix: 0.68 (0.20), residues: 647 sheet: -0.60 (0.44), residues: 149 loop : -1.08 (0.26), residues: 563 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 279 TYR 0.011 0.001 TYR D 251 PHE 0.027 0.001 PHE D 275 TRP 0.015 0.002 TRP A 98 HIS 0.004 0.001 HIS B 152 Details of bonding type rmsd covalent geometry : bond 0.00317 (11052) covalent geometry : angle 0.52800 (14889) hydrogen bonds : bond 0.04619 ( 508) hydrogen bonds : angle 5.17467 ( 1464) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2718 Ramachandran restraints generated. 1359 Oldfield, 0 Emsley, 1359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2718 Ramachandran restraints generated. 1359 Oldfield, 0 Emsley, 1359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 201 time to evaluate : 0.388 Fit side-chains revert: symmetry clash REVERT: C 158 MET cc_start: 0.7799 (mpp) cc_final: 0.7454 (ptp) REVERT: C 161 GLU cc_start: 0.7953 (OUTLIER) cc_final: 0.7629 (mp0) REVERT: C 251 TYR cc_start: 0.7658 (OUTLIER) cc_final: 0.7294 (t80) REVERT: C 282 GLU cc_start: 0.8505 (tt0) cc_final: 0.8056 (tm-30) REVERT: D 97 GLN cc_start: 0.7638 (mp10) cc_final: 0.7281 (mp10) REVERT: D 158 MET cc_start: 0.8789 (pmm) cc_final: 0.8584 (pmm) REVERT: D 282 GLU cc_start: 0.7825 (mt-10) cc_final: 0.7441 (mt-10) REVERT: A 103 ARG cc_start: 0.7762 (ttp80) cc_final: 0.7323 (ttp-110) REVERT: A 155 MET cc_start: 0.8972 (mmm) cc_final: 0.8462 (mmt) REVERT: B 31 GLU cc_start: 0.8358 (mm-30) cc_final: 0.7999 (mt-10) REVERT: B 160 ARG cc_start: 0.7611 (ttm-80) cc_final: 0.7293 (ttp80) REVERT: B 338 ASN cc_start: 0.8014 (t0) cc_final: 0.7597 (t0) outliers start: 49 outliers final: 33 residues processed: 240 average time/residue: 0.0877 time to fit residues: 31.5373 Evaluate side-chains 216 residues out of total 1179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 181 time to evaluate : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain C residue 142 THR Chi-restraints excluded: chain C residue 161 GLU Chi-restraints excluded: chain C residue 234 GLU Chi-restraints excluded: chain C residue 251 TYR Chi-restraints excluded: chain C residue 307 LEU Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 347 PHE Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 90 LEU Chi-restraints excluded: chain D residue 120 ILE Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain D residue 218 ASP Chi-restraints excluded: chain D residue 249 LYS Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 328 GLU Chi-restraints excluded: chain A residue 72 SER Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 95 ASN Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain B residue 296 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 79 optimal weight: 4.9990 chunk 18 optimal weight: 0.9980 chunk 114 optimal weight: 3.9990 chunk 7 optimal weight: 0.9990 chunk 57 optimal weight: 0.9990 chunk 119 optimal weight: 10.0000 chunk 39 optimal weight: 0.8980 chunk 40 optimal weight: 0.9990 chunk 95 optimal weight: 3.9990 chunk 118 optimal weight: 0.9990 chunk 46 optimal weight: 6.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 97 GLN B 309 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.146427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.123127 restraints weight = 14005.693| |-----------------------------------------------------------------------------| r_work (start): 0.3606 rms_B_bonded: 2.43 r_work: 0.3469 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.1433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 11052 Z= 0.117 Angle : 0.500 6.576 14889 Z= 0.267 Chirality : 0.042 0.139 1663 Planarity : 0.004 0.045 1906 Dihedral : 5.511 58.286 1496 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.30 % Favored : 94.55 % Rotamer: Outliers : 3.48 % Allowed : 22.26 % Favored : 74.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.18 (0.23), residues: 1359 helix: 0.83 (0.21), residues: 647 sheet: -0.48 (0.45), residues: 139 loop : -1.09 (0.26), residues: 573 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 279 TYR 0.009 0.001 TYR D 251 PHE 0.030 0.001 PHE D 24 TRP 0.020 0.002 TRP A 99 HIS 0.002 0.001 HIS B 152 Details of bonding type rmsd covalent geometry : bond 0.00250 (11052) covalent geometry : angle 0.50012 (14889) hydrogen bonds : bond 0.04254 ( 508) hydrogen bonds : angle 5.02233 ( 1464) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2718 Ramachandran restraints generated. 1359 Oldfield, 0 Emsley, 1359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2718 Ramachandran restraints generated. 1359 Oldfield, 0 Emsley, 1359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 212 time to evaluate : 0.503 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 251 TYR cc_start: 0.7605 (OUTLIER) cc_final: 0.7133 (t80) REVERT: C 282 GLU cc_start: 0.8448 (tt0) cc_final: 0.8012 (tm-30) REVERT: D 93 PHE cc_start: 0.8387 (t80) cc_final: 0.8101 (t80) REVERT: D 97 GLN cc_start: 0.7657 (mp10) cc_final: 0.7306 (mp10) REVERT: D 282 GLU cc_start: 0.7805 (mt-10) cc_final: 0.7413 (mt-10) REVERT: A 103 ARG cc_start: 0.7715 (ttp80) cc_final: 0.7410 (ttp-110) REVERT: A 155 MET cc_start: 0.8939 (mmm) cc_final: 0.8472 (mmt) REVERT: B 31 GLU cc_start: 0.8362 (mm-30) cc_final: 0.8020 (mm-30) REVERT: B 128 ASP cc_start: 0.8338 (m-30) cc_final: 0.7266 (t0) REVERT: B 160 ARG cc_start: 0.7623 (ttm-80) cc_final: 0.7323 (ttp80) REVERT: B 338 ASN cc_start: 0.7901 (t0) cc_final: 0.7471 (t0) outliers start: 41 outliers final: 30 residues processed: 245 average time/residue: 0.0839 time to fit residues: 30.5565 Evaluate side-chains 224 residues out of total 1179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 193 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain C residue 142 THR Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 251 TYR Chi-restraints excluded: chain C residue 307 LEU Chi-restraints excluded: chain C residue 347 PHE Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 26 ILE Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 120 ILE Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain D residue 218 ASP Chi-restraints excluded: chain D residue 249 LYS Chi-restraints excluded: chain D residue 284 LEU Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain A residue 72 SER Chi-restraints excluded: chain A residue 75 GLU Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 82 ILE Chi-restraints excluded: chain B residue 95 ASN Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 296 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 89 optimal weight: 0.9980 chunk 93 optimal weight: 0.6980 chunk 118 optimal weight: 3.9990 chunk 126 optimal weight: 0.0470 chunk 107 optimal weight: 1.9990 chunk 81 optimal weight: 0.9980 chunk 21 optimal weight: 8.9990 chunk 113 optimal weight: 0.4980 chunk 28 optimal weight: 2.9990 chunk 103 optimal weight: 4.9990 chunk 60 optimal weight: 8.9990 overall best weight: 0.6478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 338 ASN ** A 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 269 ASN B 130 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.149412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.125033 restraints weight = 13919.966| |-----------------------------------------------------------------------------| r_work (start): 0.3629 rms_B_bonded: 2.50 r_work: 0.3495 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.1532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 11052 Z= 0.105 Angle : 0.494 5.990 14889 Z= 0.263 Chirality : 0.042 0.139 1663 Planarity : 0.004 0.048 1906 Dihedral : 5.205 57.688 1492 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.93 % Favored : 95.00 % Rotamer: Outliers : 3.40 % Allowed : 21.92 % Favored : 74.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.11 (0.23), residues: 1359 helix: 0.92 (0.21), residues: 652 sheet: -0.38 (0.44), residues: 139 loop : -1.13 (0.26), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 279 TYR 0.009 0.001 TYR C 50 PHE 0.030 0.001 PHE D 24 TRP 0.026 0.002 TRP A 99 HIS 0.002 0.001 HIS A 181 Details of bonding type rmsd covalent geometry : bond 0.00217 (11052) covalent geometry : angle 0.49354 (14889) hydrogen bonds : bond 0.03978 ( 508) hydrogen bonds : angle 4.91918 ( 1464) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2718 Ramachandran restraints generated. 1359 Oldfield, 0 Emsley, 1359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2718 Ramachandran restraints generated. 1359 Oldfield, 0 Emsley, 1359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 212 time to evaluate : 0.397 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 158 MET cc_start: 0.7812 (ptp) cc_final: 0.7487 (ptp) REVERT: C 161 GLU cc_start: 0.7928 (OUTLIER) cc_final: 0.7600 (mp0) REVERT: C 251 TYR cc_start: 0.7540 (OUTLIER) cc_final: 0.7060 (t80) REVERT: C 282 GLU cc_start: 0.8432 (tt0) cc_final: 0.7977 (tm-30) REVERT: D 93 PHE cc_start: 0.8358 (t80) cc_final: 0.8106 (t80) REVERT: D 97 GLN cc_start: 0.7655 (mp10) cc_final: 0.7315 (mp10) REVERT: D 182 TYR cc_start: 0.8579 (t80) cc_final: 0.8367 (t80) REVERT: D 282 GLU cc_start: 0.7764 (mt-10) cc_final: 0.7350 (mt-10) REVERT: A 103 ARG cc_start: 0.7728 (ttp80) cc_final: 0.7298 (ttp-110) REVERT: A 155 MET cc_start: 0.8895 (mmm) cc_final: 0.8478 (mmt) REVERT: B 31 GLU cc_start: 0.8384 (mm-30) cc_final: 0.8005 (mm-30) REVERT: B 128 ASP cc_start: 0.8245 (m-30) cc_final: 0.7206 (t0) REVERT: B 160 ARG cc_start: 0.7601 (ttm-80) cc_final: 0.7323 (ttp80) REVERT: B 338 ASN cc_start: 0.7760 (t0) cc_final: 0.7352 (t0) outliers start: 40 outliers final: 26 residues processed: 242 average time/residue: 0.0861 time to fit residues: 30.4315 Evaluate side-chains 224 residues out of total 1179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 196 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain C residue 161 GLU Chi-restraints excluded: chain C residue 234 GLU Chi-restraints excluded: chain C residue 251 TYR Chi-restraints excluded: chain C residue 307 LEU Chi-restraints excluded: chain C residue 347 PHE Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 26 ILE Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 90 LEU Chi-restraints excluded: chain D residue 120 ILE Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain D residue 218 ASP Chi-restraints excluded: chain D residue 249 LYS Chi-restraints excluded: chain D residue 275 PHE Chi-restraints excluded: chain D residue 284 LEU Chi-restraints excluded: chain A residue 72 SER Chi-restraints excluded: chain A residue 75 GLU Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 82 ILE Chi-restraints excluded: chain B residue 296 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 79 optimal weight: 0.0040 chunk 47 optimal weight: 6.9990 chunk 113 optimal weight: 6.9990 chunk 123 optimal weight: 0.7980 chunk 78 optimal weight: 2.9990 chunk 117 optimal weight: 0.7980 chunk 73 optimal weight: 3.9990 chunk 101 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 81 optimal weight: 7.9990 chunk 63 optimal weight: 7.9990 overall best weight: 1.5196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 271 HIS ** A 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 269 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.147125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.122678 restraints weight = 14097.093| |-----------------------------------------------------------------------------| r_work (start): 0.3594 rms_B_bonded: 2.51 r_work: 0.3459 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.1661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 11052 Z= 0.135 Angle : 0.516 7.511 14889 Z= 0.275 Chirality : 0.043 0.136 1663 Planarity : 0.004 0.049 1906 Dihedral : 5.160 59.292 1490 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.45 % Favored : 94.48 % Rotamer: Outliers : 3.82 % Allowed : 22.68 % Favored : 73.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.17 (0.23), residues: 1359 helix: 0.81 (0.20), residues: 658 sheet: -0.37 (0.44), residues: 139 loop : -1.12 (0.26), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 131 TYR 0.009 0.001 TYR D 182 PHE 0.025 0.001 PHE A 275 TRP 0.020 0.002 TRP A 99 HIS 0.002 0.001 HIS D 152 Details of bonding type rmsd covalent geometry : bond 0.00300 (11052) covalent geometry : angle 0.51575 (14889) hydrogen bonds : bond 0.04280 ( 508) hydrogen bonds : angle 4.98042 ( 1464) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2718 Ramachandran restraints generated. 1359 Oldfield, 0 Emsley, 1359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2718 Ramachandran restraints generated. 1359 Oldfield, 0 Emsley, 1359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 202 time to evaluate : 0.411 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 158 MET cc_start: 0.7830 (ptp) cc_final: 0.7529 (ptp) REVERT: C 251 TYR cc_start: 0.7608 (OUTLIER) cc_final: 0.7174 (t80) REVERT: C 282 GLU cc_start: 0.8476 (tt0) cc_final: 0.8006 (tm-30) REVERT: D 93 PHE cc_start: 0.8385 (t80) cc_final: 0.8147 (t80) REVERT: D 97 GLN cc_start: 0.7709 (mp10) cc_final: 0.7351 (mp10) REVERT: D 282 GLU cc_start: 0.7787 (mt-10) cc_final: 0.7364 (mt-10) REVERT: A 103 ARG cc_start: 0.7743 (ttp80) cc_final: 0.7409 (ttp-110) REVERT: A 155 MET cc_start: 0.8888 (mmm) cc_final: 0.8488 (mmt) REVERT: B 31 GLU cc_start: 0.8404 (mm-30) cc_final: 0.8021 (mm-30) REVERT: B 128 ASP cc_start: 0.8260 (m-30) cc_final: 0.7235 (t0) REVERT: B 160 ARG cc_start: 0.7594 (ttm-80) cc_final: 0.7319 (ttp80) REVERT: B 220 LYS cc_start: 0.8052 (OUTLIER) cc_final: 0.7628 (mppt) REVERT: B 276 MET cc_start: 0.8983 (mtt) cc_final: 0.8764 (mtt) REVERT: B 338 ASN cc_start: 0.7876 (t0) cc_final: 0.7457 (t0) outliers start: 45 outliers final: 33 residues processed: 236 average time/residue: 0.0806 time to fit residues: 27.9353 Evaluate side-chains 224 residues out of total 1179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 189 time to evaluate : 0.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain C residue 234 GLU Chi-restraints excluded: chain C residue 251 TYR Chi-restraints excluded: chain C residue 307 LEU Chi-restraints excluded: chain C residue 347 PHE Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 90 LEU Chi-restraints excluded: chain D residue 120 ILE Chi-restraints excluded: chain D residue 128 ASP Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain D residue 218 ASP Chi-restraints excluded: chain D residue 249 LYS Chi-restraints excluded: chain D residue 284 LEU Chi-restraints excluded: chain D residue 314 CYS Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain A residue 72 SER Chi-restraints excluded: chain A residue 75 GLU Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain A residue 187 GLU Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 82 ILE Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 207 GLU Chi-restraints excluded: chain B residue 220 LYS Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain B residue 336 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 30 optimal weight: 8.9990 chunk 9 optimal weight: 4.9990 chunk 97 optimal weight: 7.9990 chunk 10 optimal weight: 3.9990 chunk 61 optimal weight: 8.9990 chunk 107 optimal weight: 5.9990 chunk 41 optimal weight: 0.9990 chunk 127 optimal weight: 2.9990 chunk 82 optimal weight: 4.9990 chunk 110 optimal weight: 0.7980 chunk 102 optimal weight: 8.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.143231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.118956 restraints weight = 14336.642| |-----------------------------------------------------------------------------| r_work (start): 0.3549 rms_B_bonded: 2.51 r_work: 0.3411 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.1860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 11052 Z= 0.202 Angle : 0.577 9.065 14889 Z= 0.308 Chirality : 0.045 0.153 1663 Planarity : 0.004 0.049 1906 Dihedral : 5.306 59.365 1490 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.89 % Favored : 93.97 % Rotamer: Outliers : 3.82 % Allowed : 22.68 % Favored : 73.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.35 (0.23), residues: 1359 helix: 0.64 (0.21), residues: 654 sheet: -0.53 (0.44), residues: 139 loop : -1.12 (0.26), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 279 TYR 0.012 0.001 TYR D 202 PHE 0.033 0.002 PHE D 24 TRP 0.015 0.002 TRP A 98 HIS 0.006 0.001 HIS A 271 Details of bonding type rmsd covalent geometry : bond 0.00466 (11052) covalent geometry : angle 0.57667 (14889) hydrogen bonds : bond 0.04920 ( 508) hydrogen bonds : angle 5.17143 ( 1464) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2718 Ramachandran restraints generated. 1359 Oldfield, 0 Emsley, 1359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2718 Ramachandran restraints generated. 1359 Oldfield, 0 Emsley, 1359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 189 time to evaluate : 0.455 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 158 MET cc_start: 0.7908 (ptp) cc_final: 0.7637 (ptp) REVERT: C 161 GLU cc_start: 0.8022 (OUTLIER) cc_final: 0.7683 (mp0) REVERT: C 251 TYR cc_start: 0.7727 (OUTLIER) cc_final: 0.7331 (t80) REVERT: C 282 GLU cc_start: 0.8513 (tt0) cc_final: 0.8038 (tm-30) REVERT: C 307 LEU cc_start: 0.8802 (OUTLIER) cc_final: 0.8493 (pt) REVERT: D 97 GLN cc_start: 0.7750 (mp10) cc_final: 0.7371 (mp10) REVERT: D 211 ASP cc_start: 0.8332 (m-30) cc_final: 0.8024 (m-30) REVERT: D 282 GLU cc_start: 0.7880 (mt-10) cc_final: 0.7485 (mt-10) REVERT: A 103 ARG cc_start: 0.7769 (ttp80) cc_final: 0.7315 (ttp80) REVERT: A 155 MET cc_start: 0.8928 (mmm) cc_final: 0.8473 (mmt) REVERT: B 31 GLU cc_start: 0.8402 (mm-30) cc_final: 0.7989 (mm-30) REVERT: B 160 ARG cc_start: 0.7596 (ttm-80) cc_final: 0.7287 (ttp80) REVERT: B 220 LYS cc_start: 0.8112 (OUTLIER) cc_final: 0.7800 (mppt) REVERT: B 276 MET cc_start: 0.8939 (mtt) cc_final: 0.8736 (mtt) REVERT: B 279 ARG cc_start: 0.8453 (mtm180) cc_final: 0.8058 (mtm-85) REVERT: B 338 ASN cc_start: 0.8072 (t0) cc_final: 0.7760 (t0) outliers start: 45 outliers final: 37 residues processed: 220 average time/residue: 0.0869 time to fit residues: 27.7594 Evaluate side-chains 219 residues out of total 1179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 178 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain C residue 161 GLU Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 234 GLU Chi-restraints excluded: chain C residue 251 TYR Chi-restraints excluded: chain C residue 307 LEU Chi-restraints excluded: chain C residue 347 PHE Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 90 LEU Chi-restraints excluded: chain D residue 120 ILE Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain D residue 218 ASP Chi-restraints excluded: chain D residue 249 LYS Chi-restraints excluded: chain D residue 284 LEU Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 314 CYS Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain A residue 72 SER Chi-restraints excluded: chain A residue 75 GLU Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 187 GLU Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 270 GLN Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 82 ILE Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 207 GLU Chi-restraints excluded: chain B residue 220 LYS Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain B residue 336 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 96 optimal weight: 0.0770 chunk 74 optimal weight: 1.9990 chunk 15 optimal weight: 6.9990 chunk 1 optimal weight: 2.9990 chunk 16 optimal weight: 0.5980 chunk 131 optimal weight: 6.9990 chunk 103 optimal weight: 2.9990 chunk 90 optimal weight: 0.5980 chunk 31 optimal weight: 0.8980 chunk 85 optimal weight: 0.0970 chunk 93 optimal weight: 0.9990 overall best weight: 0.4536 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 100 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.149718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.125447 restraints weight = 14033.845| |-----------------------------------------------------------------------------| r_work (start): 0.3628 rms_B_bonded: 2.51 r_work: 0.3499 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3499 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.1837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 11052 Z= 0.105 Angle : 0.512 9.553 14889 Z= 0.270 Chirality : 0.042 0.149 1663 Planarity : 0.004 0.048 1906 Dihedral : 5.059 55.811 1490 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.78 % Favored : 95.14 % Rotamer: Outliers : 2.80 % Allowed : 23.62 % Favored : 73.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.08 (0.23), residues: 1359 helix: 0.96 (0.21), residues: 647 sheet: -0.57 (0.43), residues: 145 loop : -1.05 (0.26), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 279 TYR 0.010 0.001 TYR D 182 PHE 0.033 0.001 PHE D 24 TRP 0.016 0.002 TRP A 99 HIS 0.002 0.001 HIS D 152 Details of bonding type rmsd covalent geometry : bond 0.00216 (11052) covalent geometry : angle 0.51246 (14889) hydrogen bonds : bond 0.03920 ( 508) hydrogen bonds : angle 4.91521 ( 1464) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2718 Ramachandran restraints generated. 1359 Oldfield, 0 Emsley, 1359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2718 Ramachandran restraints generated. 1359 Oldfield, 0 Emsley, 1359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 214 time to evaluate : 0.301 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 39 ARG cc_start: 0.7865 (mmm-85) cc_final: 0.7202 (mtp180) REVERT: C 158 MET cc_start: 0.7876 (ptp) cc_final: 0.7667 (ptp) REVERT: C 161 GLU cc_start: 0.7956 (OUTLIER) cc_final: 0.7613 (mp0) REVERT: C 251 TYR cc_start: 0.7597 (OUTLIER) cc_final: 0.6986 (t80) REVERT: C 282 GLU cc_start: 0.8426 (tt0) cc_final: 0.7979 (tm-30) REVERT: C 307 LEU cc_start: 0.8798 (OUTLIER) cc_final: 0.8549 (pt) REVERT: D 97 GLN cc_start: 0.7636 (mp10) cc_final: 0.7288 (mp10) REVERT: D 211 ASP cc_start: 0.8299 (m-30) cc_final: 0.8021 (m-30) REVERT: D 282 GLU cc_start: 0.7752 (mt-10) cc_final: 0.7375 (mt-10) REVERT: A 103 ARG cc_start: 0.7704 (ttp80) cc_final: 0.7263 (ttp80) REVERT: A 155 MET cc_start: 0.8886 (mmm) cc_final: 0.8505 (mmm) REVERT: B 31 GLU cc_start: 0.8368 (mm-30) cc_final: 0.7957 (mm-30) REVERT: B 128 ASP cc_start: 0.8284 (m-30) cc_final: 0.7248 (t0) REVERT: B 160 ARG cc_start: 0.7584 (ttm-80) cc_final: 0.7306 (ttp80) REVERT: B 338 ASN cc_start: 0.7751 (t0) cc_final: 0.7324 (t0) outliers start: 33 outliers final: 27 residues processed: 239 average time/residue: 0.0781 time to fit residues: 27.3750 Evaluate side-chains 230 residues out of total 1179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 200 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain C residue 161 GLU Chi-restraints excluded: chain C residue 234 GLU Chi-restraints excluded: chain C residue 251 TYR Chi-restraints excluded: chain C residue 307 LEU Chi-restraints excluded: chain C residue 347 PHE Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 26 ILE Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 90 LEU Chi-restraints excluded: chain D residue 120 ILE Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain D residue 218 ASP Chi-restraints excluded: chain D residue 249 LYS Chi-restraints excluded: chain D residue 284 LEU Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain A residue 75 GLU Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 82 ILE Chi-restraints excluded: chain B residue 207 GLU Chi-restraints excluded: chain B residue 296 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 98 optimal weight: 0.2980 chunk 23 optimal weight: 7.9990 chunk 13 optimal weight: 0.8980 chunk 79 optimal weight: 0.9990 chunk 130 optimal weight: 0.9980 chunk 21 optimal weight: 2.9990 chunk 27 optimal weight: 0.5980 chunk 91 optimal weight: 10.0000 chunk 122 optimal weight: 2.9990 chunk 126 optimal weight: 10.0000 chunk 109 optimal weight: 0.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.149124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.124864 restraints weight = 13956.506| |-----------------------------------------------------------------------------| r_work (start): 0.3626 rms_B_bonded: 2.49 r_work: 0.3493 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.1868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 11052 Z= 0.112 Angle : 0.540 10.543 14889 Z= 0.286 Chirality : 0.042 0.172 1663 Planarity : 0.004 0.046 1906 Dihedral : 4.979 56.465 1490 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.08 % Favored : 94.78 % Rotamer: Outliers : 2.72 % Allowed : 24.55 % Favored : 72.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.06 (0.23), residues: 1359 helix: 0.99 (0.21), residues: 641 sheet: -0.50 (0.43), residues: 145 loop : -1.06 (0.26), residues: 573 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 274 TYR 0.010 0.001 TYR A 113 PHE 0.018 0.001 PHE B 275 TRP 0.045 0.002 TRP A 99 HIS 0.004 0.001 HIS B 152 Details of bonding type rmsd covalent geometry : bond 0.00236 (11052) covalent geometry : angle 0.54021 (14889) hydrogen bonds : bond 0.03991 ( 508) hydrogen bonds : angle 4.92582 ( 1464) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2718 Ramachandran restraints generated. 1359 Oldfield, 0 Emsley, 1359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2718 Ramachandran restraints generated. 1359 Oldfield, 0 Emsley, 1359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 200 time to evaluate : 0.426 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 39 ARG cc_start: 0.7877 (mmm-85) cc_final: 0.7190 (mtp180) REVERT: C 161 GLU cc_start: 0.7930 (OUTLIER) cc_final: 0.7592 (mp0) REVERT: C 251 TYR cc_start: 0.7595 (OUTLIER) cc_final: 0.6931 (t80) REVERT: C 282 GLU cc_start: 0.8431 (tt0) cc_final: 0.7967 (tm-30) REVERT: C 307 LEU cc_start: 0.8811 (OUTLIER) cc_final: 0.8606 (pt) REVERT: D 97 GLN cc_start: 0.7669 (mp10) cc_final: 0.7327 (mp10) REVERT: D 211 ASP cc_start: 0.8268 (m-30) cc_final: 0.8003 (m-30) REVERT: D 282 GLU cc_start: 0.7764 (mt-10) cc_final: 0.7360 (mt-10) REVERT: A 80 PHE cc_start: 0.8158 (t80) cc_final: 0.7955 (t80) REVERT: A 97 GLN cc_start: 0.6832 (tm-30) cc_final: 0.6579 (tt0) REVERT: A 103 ARG cc_start: 0.7720 (ttp80) cc_final: 0.7399 (ttp-110) REVERT: A 155 MET cc_start: 0.8848 (mmm) cc_final: 0.8472 (mmm) REVERT: B 31 GLU cc_start: 0.8377 (mm-30) cc_final: 0.7960 (mm-30) REVERT: B 160 ARG cc_start: 0.7591 (ttm-80) cc_final: 0.7317 (ttp80) REVERT: B 338 ASN cc_start: 0.7715 (t0) cc_final: 0.7289 (t0) outliers start: 32 outliers final: 24 residues processed: 224 average time/residue: 0.0916 time to fit residues: 29.8927 Evaluate side-chains 222 residues out of total 1179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 195 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain C residue 161 GLU Chi-restraints excluded: chain C residue 251 TYR Chi-restraints excluded: chain C residue 307 LEU Chi-restraints excluded: chain C residue 347 PHE Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 26 ILE Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 90 LEU Chi-restraints excluded: chain D residue 120 ILE Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain D residue 218 ASP Chi-restraints excluded: chain D residue 249 LYS Chi-restraints excluded: chain D residue 284 LEU Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain A residue 75 GLU Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 82 ILE Chi-restraints excluded: chain B residue 296 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 88 optimal weight: 6.9990 chunk 134 optimal weight: 0.9990 chunk 10 optimal weight: 3.9990 chunk 5 optimal weight: 5.9990 chunk 38 optimal weight: 7.9990 chunk 6 optimal weight: 0.6980 chunk 41 optimal weight: 6.9990 chunk 102 optimal weight: 10.0000 chunk 62 optimal weight: 2.9990 chunk 84 optimal weight: 5.9990 chunk 54 optimal weight: 7.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.142082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.118465 restraints weight = 14157.420| |-----------------------------------------------------------------------------| r_work (start): 0.3549 rms_B_bonded: 2.43 r_work: 0.3411 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.2041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 11052 Z= 0.213 Angle : 0.613 11.397 14889 Z= 0.326 Chirality : 0.046 0.159 1663 Planarity : 0.004 0.049 1906 Dihedral : 5.232 58.566 1490 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.89 % Favored : 93.97 % Rotamer: Outliers : 2.72 % Allowed : 24.55 % Favored : 72.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.32 (0.23), residues: 1359 helix: 0.74 (0.21), residues: 638 sheet: -0.76 (0.42), residues: 157 loop : -1.09 (0.26), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 274 TYR 0.016 0.001 TYR D 182 PHE 0.035 0.002 PHE A 275 TRP 0.038 0.002 TRP A 99 HIS 0.003 0.001 HIS D 181 Details of bonding type rmsd covalent geometry : bond 0.00491 (11052) covalent geometry : angle 0.61326 (14889) hydrogen bonds : bond 0.04979 ( 508) hydrogen bonds : angle 5.19729 ( 1464) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2718 Ramachandran restraints generated. 1359 Oldfield, 0 Emsley, 1359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2718 Ramachandran restraints generated. 1359 Oldfield, 0 Emsley, 1359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 193 time to evaluate : 0.438 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 161 GLU cc_start: 0.8033 (OUTLIER) cc_final: 0.7684 (mp0) REVERT: C 282 GLU cc_start: 0.8442 (tt0) cc_final: 0.8019 (tm-30) REVERT: D 211 ASP cc_start: 0.8301 (m-30) cc_final: 0.8009 (m-30) REVERT: D 282 GLU cc_start: 0.7900 (mt-10) cc_final: 0.7504 (mt-10) REVERT: A 103 ARG cc_start: 0.7760 (ttp80) cc_final: 0.7339 (ttp80) REVERT: A 155 MET cc_start: 0.8903 (mmm) cc_final: 0.8499 (mmm) REVERT: B 160 ARG cc_start: 0.7630 (ttm-80) cc_final: 0.7329 (ttp80) REVERT: B 338 ASN cc_start: 0.8087 (t0) cc_final: 0.7776 (t0) outliers start: 32 outliers final: 25 residues processed: 217 average time/residue: 0.0899 time to fit residues: 28.2951 Evaluate side-chains 209 residues out of total 1179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 183 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain C residue 161 GLU Chi-restraints excluded: chain C residue 234 GLU Chi-restraints excluded: chain C residue 347 PHE Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 90 LEU Chi-restraints excluded: chain D residue 120 ILE Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain D residue 218 ASP Chi-restraints excluded: chain D residue 249 LYS Chi-restraints excluded: chain D residue 284 LEU Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain A residue 75 GLU Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 82 ILE Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 207 GLU Chi-restraints excluded: chain B residue 296 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 98 optimal weight: 5.9990 chunk 64 optimal weight: 8.9990 chunk 26 optimal weight: 0.8980 chunk 92 optimal weight: 7.9990 chunk 117 optimal weight: 0.9980 chunk 37 optimal weight: 9.9990 chunk 42 optimal weight: 0.9980 chunk 119 optimal weight: 1.9990 chunk 4 optimal weight: 3.9990 chunk 58 optimal weight: 0.5980 chunk 88 optimal weight: 0.6980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.148196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.123970 restraints weight = 14052.385| |-----------------------------------------------------------------------------| r_work (start): 0.3616 rms_B_bonded: 2.50 r_work: 0.3483 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3483 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.2008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 11052 Z= 0.119 Angle : 0.575 11.899 14889 Z= 0.301 Chirality : 0.043 0.154 1663 Planarity : 0.004 0.052 1906 Dihedral : 4.974 57.234 1488 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.00 % Favored : 94.85 % Rotamer: Outliers : 2.12 % Allowed : 24.47 % Favored : 73.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.19 (0.23), residues: 1359 helix: 0.86 (0.21), residues: 642 sheet: -0.70 (0.43), residues: 155 loop : -1.06 (0.26), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 274 TYR 0.014 0.001 TYR D 182 PHE 0.013 0.001 PHE C 275 TRP 0.043 0.002 TRP A 99 HIS 0.002 0.001 HIS A 181 Details of bonding type rmsd covalent geometry : bond 0.00250 (11052) covalent geometry : angle 0.57479 (14889) hydrogen bonds : bond 0.04136 ( 508) hydrogen bonds : angle 5.00529 ( 1464) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1936.72 seconds wall clock time: 34 minutes 12.54 seconds (2052.54 seconds total)