Starting phenix.real_space_refine on Sun Apr 5 03:53:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9x2m_66479/04_2026/9x2m_66479.cif Found real_map, /net/cci-nas-00/data/ceres_data/9x2m_66479/04_2026/9x2m_66479.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.44 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9x2m_66479/04_2026/9x2m_66479.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9x2m_66479/04_2026/9x2m_66479.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9x2m_66479/04_2026/9x2m_66479.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9x2m_66479/04_2026/9x2m_66479.map" } resolution = 3.44 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= 0.004 sd= 0.090 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 52 5.16 5 C 5206 2.51 5 N 1269 2.21 5 O 1353 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7880 Number of models: 1 Model: "" Number of chains: 9 Chain: "1" Number of atoms: 1206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 1206 Classifications: {'peptide': 166} Link IDs: {'PTRANS': 12, 'TRANS': 153} Chain: "2" Number of atoms: 1387 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1387 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 10, 'TRANS': 167} Chain: "A" Number of atoms: 1403 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1403 Classifications: {'peptide': 180} Link IDs: {'PTRANS': 10, 'TRANS': 169} Chain: "B" Number of atoms: 1403 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1403 Classifications: {'peptide': 180} Link IDs: {'PTRANS': 10, 'TRANS': 169} Chain: "E" Number of atoms: 1206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 1206 Classifications: {'peptide': 166} Link IDs: {'PTRANS': 12, 'TRANS': 153} Chain: "F" Number of atoms: 1239 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1239 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 12, 'TRANS': 158} Chain: "2" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 12 Unusual residues: {'SOR': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 12 Unusual residues: {'SOR': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 12 Unusual residues: {'SOR': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.96, per 1000 atoms: 0.25 Number of scatterers: 7880 At special positions: 0 Unit cell: (72.96, 108.48, 109.44, 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 52 16.00 O 1353 8.00 N 1269 7.00 C 5206 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: 0.80 Conformation dependent library (CDL) restraints added in 322.0 milliseconds 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1864 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 0 sheets defined 77.9% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.22 Creating SS restraints... Processing helix chain '1' and resid 155 through 176 Processing helix chain '1' and resid 176 through 195 removed outlier: 3.608A pdb=" N PHE 1 180 " --> pdb=" O THR 1 176 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VAL 1 184 " --> pdb=" O PHE 1 180 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N LEU 1 187 " --> pdb=" O PHE 1 183 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N GLY 1 195 " --> pdb=" O ILE 1 191 " (cutoff:3.500A) Processing helix chain '1' and resid 195 through 203 removed outlier: 3.877A pdb=" N TRP 1 199 " --> pdb=" O GLY 1 195 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ILE 1 200 " --> pdb=" O LEU 1 196 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N ALA 1 201 " --> pdb=" O GLY 1 197 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N GLY 1 203 " --> pdb=" O TRP 1 199 " (cutoff:3.500A) Processing helix chain '1' and resid 204 through 210 removed outlier: 3.600A pdb=" N HIS 1 210 " --> pdb=" O PRO 1 206 " (cutoff:3.500A) Processing helix chain '1' and resid 210 through 222 removed outlier: 3.891A pdb=" N LEU 1 214 " --> pdb=" O HIS 1 210 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N VAL 1 215 " --> pdb=" O PRO 1 211 " (cutoff:3.500A) Processing helix chain '1' and resid 235 through 251 Processing helix chain '1' and resid 261 through 266 removed outlier: 3.808A pdb=" N ILE 1 265 " --> pdb=" O ALA 1 261 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N ASN 1 266 " --> pdb=" O LEU 1 262 " (cutoff:3.500A) No H-bonds generated for 'chain '1' and resid 261 through 266' Processing helix chain '1' and resid 273 through 281 Processing helix chain '1' and resid 287 through 302 removed outlier: 3.740A pdb=" N VAL 1 292 " --> pdb=" O VAL 1 288 " (cutoff:3.500A) Proline residue: 1 293 - end of helix Processing helix chain '1' and resid 304 through 315 removed outlier: 3.653A pdb=" N ALA 1 310 " --> pdb=" O THR 1 306 " (cutoff:3.500A) Processing helix chain '2' and resid 4 through 24 removed outlier: 4.825A pdb=" N GLU 2 10 " --> pdb=" O THR 2 6 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N TRP 2 11 " --> pdb=" O HIS 2 7 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU 2 15 " --> pdb=" O TRP 2 11 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N PHE 2 16 " --> pdb=" O PHE 2 12 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N GLY 2 19 " --> pdb=" O LEU 2 15 " (cutoff:3.500A) Processing helix chain '2' and resid 25 through 30 Processing helix chain '2' and resid 30 through 49 removed outlier: 3.940A pdb=" N GLY 2 49 " --> pdb=" O ILE 2 45 " (cutoff:3.500A) Processing helix chain '2' and resid 50 through 52 No H-bonds generated for 'chain '2' and resid 50 through 52' Processing helix chain '2' and resid 53 through 58 removed outlier: 4.008A pdb=" N GLN 2 58 " --> pdb=" O GLU 2 54 " (cutoff:3.500A) Processing helix chain '2' and resid 63 through 70 removed outlier: 3.590A pdb=" N TYR 2 68 " --> pdb=" O PRO 2 64 " (cutoff:3.500A) Processing helix chain '2' and resid 70 through 79 removed outlier: 4.116A pdb=" N THR 2 76 " --> pdb=" O PRO 2 72 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N PHE 2 77 " --> pdb=" O CYS 2 73 " (cutoff:3.500A) Processing helix chain '2' and resid 82 through 91 removed outlier: 3.966A pdb=" N PHE 2 90 " --> pdb=" O LEU 2 87 " (cutoff:3.500A) Processing helix chain '2' and resid 92 through 94 No H-bonds generated for 'chain '2' and resid 92 through 94' Processing helix chain '2' and resid 95 through 102 removed outlier: 3.826A pdb=" N ALA 2 102 " --> pdb=" O SER 2 98 " (cutoff:3.500A) Processing helix chain '2' and resid 104 through 109 Processing helix chain '2' and resid 122 through 133 removed outlier: 4.160A pdb=" N ILE 2 128 " --> pdb=" O VAL 2 124 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N GLY 2 131 " --> pdb=" O GLY 2 127 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU 2 132 " --> pdb=" O ILE 2 128 " (cutoff:3.500A) Processing helix chain '2' and resid 140 through 173 removed outlier: 3.780A pdb=" N VAL 2 152 " --> pdb=" O LEU 2 148 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N THR 2 161 " --> pdb=" O ARG 2 157 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N ASP 2 162 " --> pdb=" O GLY 2 158 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N LEU 2 163 " --> pdb=" O TRP 2 159 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N THR 2 164 " --> pdb=" O VAL 2 160 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ALA 2 166 " --> pdb=" O ASP 2 162 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LYS 2 170 " --> pdb=" O ALA 2 166 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N LYS 2 171 " --> pdb=" O ILE 2 167 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N MET 2 172 " --> pdb=" O PHE 2 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 2 through 24 removed outlier: 3.593A pdb=" N THR A 6 " --> pdb=" O ILE A 2 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LEU A 15 " --> pdb=" O TRP A 11 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N PHE A 16 " --> pdb=" O PHE A 12 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLY A 19 " --> pdb=" O LEU A 15 " (cutoff:3.500A) Processing helix chain 'A' and resid 26 through 49 Proline residue: A 32 - end of helix removed outlier: 3.862A pdb=" N ILE A 40 " --> pdb=" O SER A 36 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N MET A 41 " --> pdb=" O LEU A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 50 through 55 removed outlier: 3.727A pdb=" N ARG A 55 " --> pdb=" O HIS A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 56 through 60 Processing helix chain 'A' and resid 63 through 69 Processing helix chain 'A' and resid 70 through 74 Processing helix chain 'A' and resid 81 through 91 removed outlier: 3.538A pdb=" N LEU A 87 " --> pdb=" O THR A 84 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLY A 88 " --> pdb=" O LEU A 85 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ARG A 89 " --> pdb=" O SER A 86 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N PHE A 90 " --> pdb=" O LEU A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 105 removed outlier: 4.252A pdb=" N TYR A 105 " --> pdb=" O ALA A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 133 removed outlier: 3.574A pdb=" N LEU A 126 " --> pdb=" O LEU A 122 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ILE A 128 " --> pdb=" O VAL A 124 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLY A 131 " --> pdb=" O GLY A 127 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LEU A 132 " --> pdb=" O ILE A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 166 removed outlier: 3.899A pdb=" N VAL A 152 " --> pdb=" O LEU A 148 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N THR A 161 " --> pdb=" O ARG A 157 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ASP A 162 " --> pdb=" O GLY A 158 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LEU A 163 " --> pdb=" O TRP A 159 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ALA A 166 " --> pdb=" O ASP A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 171 removed outlier: 3.689A pdb=" N LYS A 170 " --> pdb=" O ALA A 166 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LYS A 171 " --> pdb=" O ILE A 167 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 166 through 171' Processing helix chain 'B' and resid 2 through 30 removed outlier: 3.943A pdb=" N GLU B 10 " --> pdb=" O THR B 6 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N TRP B 11 " --> pdb=" O HIS B 7 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N PHE B 16 " --> pdb=" O PHE B 12 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N GLY B 19 " --> pdb=" O LEU B 15 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N GLY B 25 " --> pdb=" O GLU B 21 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N MET B 26 " --> pdb=" O VAL B 22 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N VAL B 27 " --> pdb=" O PHE B 23 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N THR B 28 " --> pdb=" O THR B 24 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 49 removed outlier: 3.535A pdb=" N VAL B 39 " --> pdb=" O ILE B 35 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ILE B 40 " --> pdb=" O SER B 36 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLY B 49 " --> pdb=" O ILE B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 60 removed outlier: 3.632A pdb=" N ILE B 53 " --> pdb=" O GLY B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 63 through 70 removed outlier: 3.742A pdb=" N LEU B 70 " --> pdb=" O SER B 66 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 through 79 removed outlier: 4.080A pdb=" N THR B 76 " --> pdb=" O PRO B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 89 removed outlier: 3.673A pdb=" N LEU B 85 " --> pdb=" O PRO B 82 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ARG B 89 " --> pdb=" O SER B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 102 removed outlier: 3.522A pdb=" N ALA B 102 " --> pdb=" O SER B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 133 removed outlier: 4.355A pdb=" N ILE B 128 " --> pdb=" O VAL B 124 " (cutoff:3.500A) Processing helix chain 'B' and resid 140 through 172 removed outlier: 3.694A pdb=" N VAL B 152 " --> pdb=" O LEU B 148 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ASP B 162 " --> pdb=" O GLY B 158 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N LEU B 163 " --> pdb=" O TRP B 159 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N THR B 164 " --> pdb=" O VAL B 160 " (cutoff:3.500A) Processing helix chain 'E' and resid 155 through 176 removed outlier: 3.879A pdb=" N VAL E 159 " --> pdb=" O MET E 155 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N ALA E 160 " --> pdb=" O GLY E 156 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU E 162 " --> pdb=" O THR E 158 " (cutoff:3.500A) Processing helix chain 'E' and resid 176 through 193 removed outlier: 3.781A pdb=" N PHE E 180 " --> pdb=" O THR E 176 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N ALA E 186 " --> pdb=" O ALA E 182 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LEU E 187 " --> pdb=" O PHE E 183 " (cutoff:3.500A) Processing helix chain 'E' and resid 203 through 209 Processing helix chain 'E' and resid 210 through 222 Processing helix chain 'E' and resid 226 through 230 Processing helix chain 'E' and resid 235 through 251 Processing helix chain 'E' and resid 258 through 267 removed outlier: 3.729A pdb=" N PHE E 263 " --> pdb=" O LEU E 259 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ILE E 265 " --> pdb=" O ALA E 261 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ASN E 266 " --> pdb=" O LEU E 262 " (cutoff:3.500A) Processing helix chain 'E' and resid 273 through 281 removed outlier: 3.880A pdb=" N SER E 279 " --> pdb=" O PRO E 275 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ALA E 281 " --> pdb=" O GLY E 277 " (cutoff:3.500A) Processing helix chain 'E' and resid 287 through 302 Proline residue: E 293 - end of helix Processing helix chain 'E' and resid 303 through 315 removed outlier: 3.657A pdb=" N VAL E 307 " --> pdb=" O GLY E 303 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLY E 315 " --> pdb=" O TRP E 311 " (cutoff:3.500A) Processing helix chain 'F' and resid 154 through 176 removed outlier: 3.643A pdb=" N ALA F 160 " --> pdb=" O GLY F 156 " (cutoff:3.500A) Processing helix chain 'F' and resid 176 through 194 removed outlier: 3.554A pdb=" N ALA F 182 " --> pdb=" O LEU F 178 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N PHE F 183 " --> pdb=" O PRO F 179 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N VAL F 184 " --> pdb=" O PHE F 180 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LEU F 187 " --> pdb=" O PHE F 183 " (cutoff:3.500A) Processing helix chain 'F' and resid 199 through 203 removed outlier: 3.663A pdb=" N GLY F 203 " --> pdb=" O ILE F 200 " (cutoff:3.500A) Processing helix chain 'F' and resid 210 through 222 Processing helix chain 'F' and resid 226 through 230 Processing helix chain 'F' and resid 234 through 251 removed outlier: 4.221A pdb=" N LEU F 243 " --> pdb=" O VAL F 239 " (cutoff:3.500A) Processing helix chain 'F' and resid 258 through 265 removed outlier: 3.901A pdb=" N PHE F 263 " --> pdb=" O LEU F 259 " (cutoff:3.500A) Processing helix chain 'F' and resid 273 through 278 Processing helix chain 'F' and resid 287 through 301 Proline residue: F 293 - end of helix Processing helix chain 'F' and resid 302 through 315 452 hydrogen bonds defined for protein. 1290 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: 1.08 Time building geometry restraints manager: 1.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 1194 1.29 - 1.42: 2046 1.42 - 1.55: 4744 1.55 - 1.68: 5 1.68 - 1.81: 86 Bond restraints: 8075 Sorted by residual: bond pdb=" C PRO A 72 " pdb=" O PRO A 72 " ideal model delta sigma weight residual 1.235 1.156 0.079 1.30e-02 5.92e+03 3.72e+01 bond pdb=" N PRO A 72 " pdb=" CA PRO A 72 " ideal model delta sigma weight residual 1.469 1.404 0.065 1.28e-02 6.10e+03 2.55e+01 bond pdb=" C THR A 76 " pdb=" O THR A 76 " ideal model delta sigma weight residual 1.235 1.178 0.057 1.19e-02 7.06e+03 2.27e+01 bond pdb=" C GLY A 75 " pdb=" O GLY A 75 " ideal model delta sigma weight residual 1.235 1.185 0.049 1.35e-02 5.49e+03 1.34e+01 bond pdb=" C LEU A 71 " pdb=" O LEU A 71 " ideal model delta sigma weight residual 1.238 1.202 0.036 1.28e-02 6.10e+03 7.89e+00 ... (remaining 8070 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.37: 10801 2.37 - 4.73: 165 4.73 - 7.10: 32 7.10 - 9.46: 6 9.46 - 11.83: 1 Bond angle restraints: 11005 Sorted by residual: angle pdb=" N THR A 76 " pdb=" CA THR A 76 " pdb=" C THR A 76 " ideal model delta sigma weight residual 114.64 102.81 11.83 1.52e+00 4.33e-01 6.06e+01 angle pdb=" CA PRO A 138 " pdb=" N PRO A 138 " pdb=" CD PRO A 138 " ideal model delta sigma weight residual 112.00 104.34 7.66 1.40e+00 5.10e-01 2.99e+01 angle pdb=" CA PRO E 275 " pdb=" N PRO E 275 " pdb=" CD PRO E 275 " ideal model delta sigma weight residual 112.00 105.02 6.98 1.40e+00 5.10e-01 2.49e+01 angle pdb=" C THR A 76 " pdb=" N PHE A 77 " pdb=" CA PHE A 77 " ideal model delta sigma weight residual 120.44 114.10 6.34 1.36e+00 5.41e-01 2.17e+01 angle pdb=" CA PRO 2 138 " pdb=" N PRO 2 138 " pdb=" CD PRO 2 138 " ideal model delta sigma weight residual 112.00 106.45 5.55 1.40e+00 5.10e-01 1.57e+01 ... (remaining 11000 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.81: 4451 30.81 - 61.61: 260 61.61 - 92.42: 11 92.42 - 123.22: 1 123.22 - 154.03: 3 Dihedral angle restraints: 4726 sinusoidal: 1803 harmonic: 2923 Sorted by residual: dihedral pdb=" CA ASN A 81 " pdb=" C ASN A 81 " pdb=" N PRO A 82 " pdb=" CA PRO A 82 " ideal model delta harmonic sigma weight residual -180.00 -134.59 -45.41 0 5.00e+00 4.00e-02 8.25e+01 dihedral pdb=" C3 SOR A 201 " pdb=" C1 SOR A 201 " pdb=" C2 SOR A 201 " pdb=" O1 SOR A 201 " ideal model delta sinusoidal sigma weight residual 192.20 38.17 154.03 1 3.00e+01 1.11e-03 2.03e+01 dihedral pdb=" C3 SOR B 201 " pdb=" C1 SOR B 201 " pdb=" C2 SOR B 201 " pdb=" O1 SOR B 201 " ideal model delta sinusoidal sigma weight residual 192.20 40.91 151.29 1 3.00e+01 1.11e-03 2.00e+01 ... (remaining 4723 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 1176 0.066 - 0.132: 139 0.132 - 0.198: 6 0.198 - 0.264: 0 0.264 - 0.330: 1 Chirality restraints: 1322 Sorted by residual: chirality pdb=" CA ILE A 74 " pdb=" N ILE A 74 " pdb=" C ILE A 74 " pdb=" CB ILE A 74 " both_signs ideal model delta sigma weight residual False 2.43 2.76 -0.33 2.00e-01 2.50e+01 2.72e+00 chirality pdb=" CA PRO A 82 " pdb=" N PRO A 82 " pdb=" C PRO A 82 " pdb=" CB PRO A 82 " both_signs ideal model delta sigma weight residual False 2.72 2.53 0.19 2.00e-01 2.50e+01 9.00e-01 chirality pdb=" CB ILE 2 45 " pdb=" CA ILE 2 45 " pdb=" CG1 ILE 2 45 " pdb=" CG2 ILE 2 45 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.18 2.00e-01 2.50e+01 7.69e-01 ... (remaining 1319 not shown) Planarity restraints: 1365 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 137 " 0.082 5.00e-02 4.00e+02 1.19e-01 2.28e+01 pdb=" N PRO A 138 " -0.206 5.00e-02 4.00e+02 pdb=" CA PRO A 138 " 0.060 5.00e-02 4.00e+02 pdb=" CD PRO A 138 " 0.064 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU 2 137 " 0.076 5.00e-02 4.00e+02 1.12e-01 1.99e+01 pdb=" N PRO 2 138 " -0.193 5.00e-02 4.00e+02 pdb=" CA PRO 2 138 " 0.057 5.00e-02 4.00e+02 pdb=" CD PRO 2 138 " 0.060 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A 81 " 0.058 5.00e-02 4.00e+02 8.90e-02 1.27e+01 pdb=" N PRO A 82 " -0.154 5.00e-02 4.00e+02 pdb=" CA PRO A 82 " 0.047 5.00e-02 4.00e+02 pdb=" CD PRO A 82 " 0.049 5.00e-02 4.00e+02 ... (remaining 1362 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 215 2.70 - 3.25: 8045 3.25 - 3.80: 12199 3.80 - 4.35: 15241 4.35 - 4.90: 25972 Nonbonded interactions: 61672 Sorted by model distance: nonbonded pdb=" O MET B 83 " pdb=" OG SER B 86 " model vdw 2.151 3.040 nonbonded pdb=" OD1 ASN 2 63 " pdb=" OG SER 2 66 " model vdw 2.187 3.040 nonbonded pdb=" OG SER A 104 " pdb=" NH2 ARG E 299 " model vdw 2.199 3.120 nonbonded pdb=" OD1 ASN B 63 " pdb=" OG SER B 66 " model vdw 2.201 3.040 nonbonded pdb=" O PRO F 275 " pdb=" OG SER F 279 " model vdw 2.212 3.040 ... (remaining 61667 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 '1' selection = chain 'E' selection = (chain 'F' and resid 154 through 319) } ncs_group { reference = chain '2' selection = (chain 'A' and (resid 1 through 178 or resid 201)) selection = (chain 'B' and (resid 1 through 178 or resid 201)) } 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.180 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: 0.120 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 8.790 Find NCS groups from input model: 0.160 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: 0.000 Load rotamer database and sin/cos tables:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.124 8075 Z= 0.211 Angle : 0.715 11.829 11005 Z= 0.378 Chirality : 0.042 0.330 1322 Planarity : 0.007 0.119 1365 Dihedral : 18.391 154.028 2862 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.29 % Allowed : 8.75 % Favored : 90.96 % Rotamer: Outliers : 0.71 % Allowed : 32.58 % Favored : 66.71 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.52 % 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 (0.28), residues: 1029 helix: 0.63 (0.21), residues: 707 sheet: None (None), residues: 0 loop : -2.66 (0.33), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 89 TYR 0.012 0.001 TYR A 95 PHE 0.021 0.001 PHE 1 163 TRP 0.012 0.001 TRP E 199 HIS 0.001 0.000 HIS 2 51 Details of bonding type rmsd covalent geometry : bond 0.00420 ( 8075) covalent geometry : angle 0.71521 (11005) hydrogen bonds : bond 0.17993 ( 452) hydrogen bonds : angle 6.29925 ( 1290) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 176 time to evaluate : 0.232 Fit side-chains REVERT: E 216 MET cc_start: 0.8348 (tpt) cc_final: 0.8047 (tpp) outliers start: 6 outliers final: 2 residues processed: 179 average time/residue: 0.0746 time to fit residues: 18.9274 Evaluate side-chains 169 residues out of total 841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 167 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 GLU Chi-restraints excluded: chain E residue 266 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 49 optimal weight: 4.9990 chunk 97 optimal weight: 0.0770 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 0.5980 chunk 62 optimal weight: 0.0570 chunk 51 optimal weight: 4.9990 chunk 100 optimal weight: 0.9980 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 overall best weight: 0.5458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 51 HIS B 58 GLN B 154 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.126643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.106202 restraints weight = 14074.199| |-----------------------------------------------------------------------------| r_work (start): 0.3299 rms_B_bonded: 2.38 r_work: 0.3193 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.1017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 8075 Z= 0.132 Angle : 0.619 6.348 11005 Z= 0.307 Chirality : 0.041 0.187 1322 Planarity : 0.006 0.079 1365 Dihedral : 9.614 146.764 1142 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.29 % Allowed : 9.62 % Favored : 90.09 % Rotamer: Outliers : 3.92 % Allowed : 28.18 % Favored : 67.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.52 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.02 (0.28), residues: 1029 helix: 1.05 (0.21), residues: 713 sheet: None (None), residues: 0 loop : -2.58 (0.33), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG 2 67 TYR 0.016 0.001 TYR A 95 PHE 0.009 0.001 PHE 2 56 TRP 0.007 0.001 TRP E 199 HIS 0.002 0.000 HIS F 256 Details of bonding type rmsd covalent geometry : bond 0.00306 ( 8075) covalent geometry : angle 0.61944 (11005) hydrogen bonds : bond 0.04185 ( 452) hydrogen bonds : angle 4.41625 ( 1290) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 174 time to evaluate : 0.297 Fit side-chains REVERT: 2 3 GLU cc_start: 0.8396 (pm20) cc_final: 0.8145 (pm20) REVERT: A 94 LYS cc_start: 0.9255 (OUTLIER) cc_final: 0.9013 (ptpp) REVERT: A 178 GLN cc_start: 0.7234 (mm-40) cc_final: 0.6816 (mm-40) REVERT: E 216 MET cc_start: 0.8349 (tpt) cc_final: 0.8108 (tpp) REVERT: F 180 PHE cc_start: 0.8338 (m-80) cc_final: 0.8094 (m-80) outliers start: 33 outliers final: 15 residues processed: 198 average time/residue: 0.0780 time to fit residues: 21.9937 Evaluate side-chains 172 residues out of total 841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 156 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 183 PHE Chi-restraints excluded: chain 1 residue 192 MET Chi-restraints excluded: chain 1 residue 202 HIS Chi-restraints excluded: chain 1 residue 314 SER Chi-restraints excluded: chain 2 residue 7 HIS Chi-restraints excluded: chain 2 residue 36 SER Chi-restraints excluded: chain 2 residue 130 SER Chi-restraints excluded: chain 2 residue 135 LEU Chi-restraints excluded: chain A residue 94 LYS Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain E residue 184 VAL Chi-restraints excluded: chain E residue 210 HIS Chi-restraints excluded: chain E residue 257 LEU Chi-restraints excluded: chain F residue 183 PHE Chi-restraints excluded: chain F residue 210 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 46 optimal weight: 0.9990 chunk 54 optimal weight: 1.9990 chunk 69 optimal weight: 0.3980 chunk 22 optimal weight: 0.8980 chunk 0 optimal weight: 6.9990 chunk 52 optimal weight: 2.9990 chunk 82 optimal weight: 3.9990 chunk 73 optimal weight: 0.7980 chunk 78 optimal weight: 0.9990 chunk 16 optimal weight: 7.9990 chunk 75 optimal weight: 0.7980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 51 HIS ** F 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.125607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.105322 restraints weight = 13895.791| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 2.33 r_work: 0.3188 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.1339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8075 Z= 0.138 Angle : 0.621 6.337 11005 Z= 0.306 Chirality : 0.042 0.217 1322 Planarity : 0.006 0.084 1365 Dihedral : 9.192 135.042 1137 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.29 % Allowed : 8.65 % Favored : 91.06 % Rotamer: Outliers : 3.92 % Allowed : 28.06 % Favored : 68.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.52 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.02 (0.28), residues: 1029 helix: 1.09 (0.21), residues: 715 sheet: None (None), residues: 0 loop : -2.60 (0.32), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 67 TYR 0.016 0.001 TYR B 125 PHE 0.013 0.001 PHE B 56 TRP 0.008 0.001 TRP E 199 HIS 0.002 0.000 HIS B 116 Details of bonding type rmsd covalent geometry : bond 0.00328 ( 8075) covalent geometry : angle 0.62129 (11005) hydrogen bonds : bond 0.04233 ( 452) hydrogen bonds : angle 4.18513 ( 1290) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 167 time to evaluate : 0.291 Fit side-chains REVERT: 2 3 GLU cc_start: 0.8456 (pm20) cc_final: 0.8227 (pm20) REVERT: A 94 LYS cc_start: 0.9284 (OUTLIER) cc_final: 0.9036 (ptpp) REVERT: A 178 GLN cc_start: 0.7208 (mm-40) cc_final: 0.6749 (mm-40) REVERT: B 177 GLU cc_start: 0.6343 (mp0) cc_final: 0.6100 (mp0) REVERT: E 216 MET cc_start: 0.8418 (tpt) cc_final: 0.8178 (tpp) REVERT: F 180 PHE cc_start: 0.8440 (m-80) cc_final: 0.8216 (m-80) outliers start: 33 outliers final: 19 residues processed: 189 average time/residue: 0.0757 time to fit residues: 20.4687 Evaluate side-chains 177 residues out of total 841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 157 time to evaluate : 0.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 308 LEU Chi-restraints excluded: chain 1 residue 314 SER Chi-restraints excluded: chain 2 residue 7 HIS Chi-restraints excluded: chain 2 residue 36 SER Chi-restraints excluded: chain 2 residue 48 ILE Chi-restraints excluded: chain 2 residue 130 SER Chi-restraints excluded: chain 2 residue 135 LEU Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 94 LYS Chi-restraints excluded: chain A residue 121 GLU Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 172 MET Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain E residue 184 VAL Chi-restraints excluded: chain E residue 225 LEU Chi-restraints excluded: chain E residue 257 LEU Chi-restraints excluded: chain F residue 183 PHE Chi-restraints excluded: chain F residue 210 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 1 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 90 optimal weight: 8.9990 chunk 99 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 chunk 4 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 98 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 73 optimal weight: 4.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 51 HIS 2 108 HIS ** F 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.119696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.098891 restraints weight = 14411.532| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 2.39 r_work: 0.3082 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.1698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 8075 Z= 0.209 Angle : 0.691 6.309 11005 Z= 0.344 Chirality : 0.044 0.169 1322 Planarity : 0.006 0.095 1365 Dihedral : 9.499 133.236 1137 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.29 % Allowed : 8.94 % Favored : 90.77 % Rotamer: Outliers : 5.47 % Allowed : 27.35 % Favored : 67.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.52 % 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: -0.40 (0.28), residues: 1029 helix: 0.76 (0.21), residues: 728 sheet: None (None), residues: 0 loop : -2.87 (0.33), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG 2 89 TYR 0.016 0.002 TYR A 146 PHE 0.014 0.001 PHE E 183 TRP 0.009 0.001 TRP E 199 HIS 0.003 0.001 HIS A 7 Details of bonding type rmsd covalent geometry : bond 0.00509 ( 8075) covalent geometry : angle 0.69131 (11005) hydrogen bonds : bond 0.05262 ( 452) hydrogen bonds : angle 4.31613 ( 1290) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 160 time to evaluate : 0.300 Fit side-chains REVERT: 1 247 GLN cc_start: 0.8405 (mm-40) cc_final: 0.8200 (mm-40) REVERT: A 136 ASN cc_start: 0.7992 (t0) cc_final: 0.7722 (t0) REVERT: A 178 GLN cc_start: 0.7141 (mm-40) cc_final: 0.6726 (mm-40) REVERT: B 58 GLN cc_start: 0.7948 (mm-40) cc_final: 0.7532 (tp40) REVERT: E 216 MET cc_start: 0.8551 (tpt) cc_final: 0.8316 (tpp) REVERT: F 285 GLN cc_start: 0.6829 (tp40) cc_final: 0.6628 (tp40) REVERT: F 286 ASP cc_start: 0.7952 (t0) cc_final: 0.7748 (t0) outliers start: 46 outliers final: 32 residues processed: 195 average time/residue: 0.0875 time to fit residues: 23.4560 Evaluate side-chains 185 residues out of total 841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 153 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 165 SER Chi-restraints excluded: chain 1 residue 183 PHE Chi-restraints excluded: chain 1 residue 299 ARG Chi-restraints excluded: chain 2 residue 36 SER Chi-restraints excluded: chain 2 residue 48 ILE Chi-restraints excluded: chain 2 residue 130 SER Chi-restraints excluded: chain 2 residue 135 LEU Chi-restraints excluded: chain 2 residue 165 THR Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 170 LYS Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain E residue 183 PHE Chi-restraints excluded: chain E residue 184 VAL Chi-restraints excluded: chain E residue 200 ILE Chi-restraints excluded: chain E residue 210 HIS Chi-restraints excluded: chain E residue 225 LEU Chi-restraints excluded: chain E residue 246 VAL Chi-restraints excluded: chain E residue 257 LEU Chi-restraints excluded: chain E residue 287 THR Chi-restraints excluded: chain E residue 294 SER Chi-restraints excluded: chain E residue 298 SER Chi-restraints excluded: chain F residue 183 PHE Chi-restraints excluded: chain F residue 210 HIS Chi-restraints excluded: chain F residue 308 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 33 optimal weight: 0.9980 chunk 94 optimal weight: 3.9990 chunk 3 optimal weight: 0.8980 chunk 38 optimal weight: 4.9990 chunk 86 optimal weight: 3.9990 chunk 82 optimal weight: 4.9990 chunk 67 optimal weight: 0.3980 chunk 95 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 85 optimal weight: 0.4980 chunk 35 optimal weight: 0.0770 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 247 GLN 2 51 HIS A 7 HIS F 238 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.123725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.103127 restraints weight = 14144.712| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 2.37 r_work: 0.3148 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.1701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8075 Z= 0.126 Angle : 0.610 6.353 11005 Z= 0.302 Chirality : 0.041 0.181 1322 Planarity : 0.006 0.087 1365 Dihedral : 9.376 130.758 1137 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.29 % Allowed : 8.26 % Favored : 91.45 % Rotamer: Outliers : 4.04 % Allowed : 29.61 % Favored : 66.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.52 % 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: -0.05 (0.28), residues: 1029 helix: 1.04 (0.21), residues: 711 sheet: None (None), residues: 0 loop : -2.59 (0.32), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 89 TYR 0.015 0.001 TYR B 125 PHE 0.008 0.001 PHE B 90 TRP 0.008 0.001 TRP E 199 HIS 0.007 0.001 HIS A 7 Details of bonding type rmsd covalent geometry : bond 0.00293 ( 8075) covalent geometry : angle 0.61046 (11005) hydrogen bonds : bond 0.03935 ( 452) hydrogen bonds : angle 4.06419 ( 1290) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 168 time to evaluate : 0.194 Fit side-chains revert: symmetry clash REVERT: 1 247 GLN cc_start: 0.8377 (mm110) cc_final: 0.8141 (mm-40) REVERT: A 94 LYS cc_start: 0.9348 (OUTLIER) cc_final: 0.8987 (ptpp) REVERT: A 136 ASN cc_start: 0.7936 (t0) cc_final: 0.7693 (t0) REVERT: A 178 GLN cc_start: 0.7120 (mm-40) cc_final: 0.6451 (mm-40) REVERT: B 165 THR cc_start: 0.7940 (m) cc_final: 0.7716 (m) REVERT: B 177 GLU cc_start: 0.6344 (mp0) cc_final: 0.6023 (mp0) REVERT: E 216 MET cc_start: 0.8486 (tpt) cc_final: 0.8240 (tpp) REVERT: F 286 ASP cc_start: 0.8008 (t0) cc_final: 0.7802 (t0) outliers start: 34 outliers final: 26 residues processed: 192 average time/residue: 0.0764 time to fit residues: 20.7244 Evaluate side-chains 183 residues out of total 841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 156 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 165 SER Chi-restraints excluded: chain 1 residue 183 PHE Chi-restraints excluded: chain 1 residue 299 ARG Chi-restraints excluded: chain 1 residue 308 LEU Chi-restraints excluded: chain 2 residue 3 GLU Chi-restraints excluded: chain 2 residue 7 HIS Chi-restraints excluded: chain 2 residue 34 LEU Chi-restraints excluded: chain 2 residue 36 SER Chi-restraints excluded: chain 2 residue 130 SER Chi-restraints excluded: chain 2 residue 135 LEU Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 94 LYS Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 41 MET Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain E residue 184 VAL Chi-restraints excluded: chain E residue 200 ILE Chi-restraints excluded: chain E residue 210 HIS Chi-restraints excluded: chain E residue 225 LEU Chi-restraints excluded: chain E residue 246 VAL Chi-restraints excluded: chain E residue 257 LEU Chi-restraints excluded: chain F residue 183 PHE Chi-restraints excluded: chain F residue 210 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 1 optimal weight: 0.9990 chunk 76 optimal weight: 0.8980 chunk 101 optimal weight: 2.9990 chunk 80 optimal weight: 0.5980 chunk 7 optimal weight: 3.9990 chunk 71 optimal weight: 0.9990 chunk 83 optimal weight: 2.9990 chunk 90 optimal weight: 6.9990 chunk 30 optimal weight: 0.9990 chunk 31 optimal weight: 0.6980 chunk 41 optimal weight: 0.9980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 51 HIS A 7 HIS E 202 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.122969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.102381 restraints weight = 14154.396| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 2.39 r_work: 0.3134 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.1779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8075 Z= 0.139 Angle : 0.624 6.857 11005 Z= 0.308 Chirality : 0.042 0.174 1322 Planarity : 0.006 0.088 1365 Dihedral : 9.087 128.708 1137 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.29 % Allowed : 8.55 % Favored : 91.16 % Rotamer: Outliers : 4.28 % Allowed : 29.96 % Favored : 65.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.52 % 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: -0.01 (0.28), residues: 1029 helix: 1.02 (0.21), residues: 719 sheet: None (None), residues: 0 loop : -2.51 (0.33), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 89 TYR 0.016 0.001 TYR B 125 PHE 0.008 0.001 PHE E 183 TRP 0.010 0.001 TRP E 199 HIS 0.007 0.001 HIS A 7 Details of bonding type rmsd covalent geometry : bond 0.00337 ( 8075) covalent geometry : angle 0.62384 (11005) hydrogen bonds : bond 0.04092 ( 452) hydrogen bonds : angle 4.03206 ( 1290) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 165 time to evaluate : 0.286 Fit side-chains REVERT: A 94 LYS cc_start: 0.9357 (OUTLIER) cc_final: 0.8947 (ptpp) REVERT: A 136 ASN cc_start: 0.7918 (t0) cc_final: 0.7638 (t0) REVERT: A 178 GLN cc_start: 0.7160 (mm-40) cc_final: 0.6390 (mm-40) REVERT: B 165 THR cc_start: 0.7928 (m) cc_final: 0.7698 (m) REVERT: B 177 GLU cc_start: 0.6403 (mp0) cc_final: 0.6072 (mp0) REVERT: E 216 MET cc_start: 0.8533 (tpt) cc_final: 0.8295 (tpp) REVERT: F 285 GLN cc_start: 0.6805 (tp40) cc_final: 0.6368 (tp40) REVERT: F 286 ASP cc_start: 0.7970 (t0) cc_final: 0.7603 (t0) outliers start: 36 outliers final: 34 residues processed: 192 average time/residue: 0.0817 time to fit residues: 21.8664 Evaluate side-chains 195 residues out of total 841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 160 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 165 SER Chi-restraints excluded: chain 1 residue 183 PHE Chi-restraints excluded: chain 1 residue 192 MET Chi-restraints excluded: chain 1 residue 214 LEU Chi-restraints excluded: chain 1 residue 299 ARG Chi-restraints excluded: chain 1 residue 308 LEU Chi-restraints excluded: chain 2 residue 3 GLU Chi-restraints excluded: chain 2 residue 7 HIS Chi-restraints excluded: chain 2 residue 36 SER Chi-restraints excluded: chain 2 residue 48 ILE Chi-restraints excluded: chain 2 residue 130 SER Chi-restraints excluded: chain 2 residue 135 LEU Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 94 LYS Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 41 MET Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain E residue 184 VAL Chi-restraints excluded: chain E residue 190 ILE Chi-restraints excluded: chain E residue 200 ILE Chi-restraints excluded: chain E residue 210 HIS Chi-restraints excluded: chain E residue 225 LEU Chi-restraints excluded: chain E residue 246 VAL Chi-restraints excluded: chain E residue 257 LEU Chi-restraints excluded: chain F residue 183 PHE Chi-restraints excluded: chain F residue 210 HIS Chi-restraints excluded: chain F residue 257 LEU Chi-restraints excluded: chain F residue 308 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 23 optimal weight: 1.9990 chunk 50 optimal weight: 5.9990 chunk 96 optimal weight: 0.9980 chunk 26 optimal weight: 0.9980 chunk 18 optimal weight: 0.0670 chunk 10 optimal weight: 0.0870 chunk 8 optimal weight: 0.9990 chunk 76 optimal weight: 0.9980 chunk 22 optimal weight: 0.3980 chunk 101 optimal weight: 0.4980 chunk 45 optimal weight: 2.9990 overall best weight: 0.4096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 7 HIS B 50 GLN E 202 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.127056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.106680 restraints weight = 14000.027| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 2.36 r_work: 0.3202 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.1916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8075 Z= 0.118 Angle : 0.612 7.655 11005 Z= 0.300 Chirality : 0.041 0.185 1322 Planarity : 0.005 0.083 1365 Dihedral : 8.424 124.137 1137 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.29 % Allowed : 7.97 % Favored : 91.74 % Rotamer: Outliers : 4.64 % Allowed : 29.85 % Favored : 65.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.52 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.07 (0.28), residues: 1029 helix: 1.15 (0.21), residues: 712 sheet: None (None), residues: 0 loop : -2.61 (0.32), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 67 TYR 0.016 0.001 TYR B 125 PHE 0.009 0.001 PHE B 90 TRP 0.010 0.001 TRP E 199 HIS 0.007 0.001 HIS A 7 Details of bonding type rmsd covalent geometry : bond 0.00273 ( 8075) covalent geometry : angle 0.61214 (11005) hydrogen bonds : bond 0.03397 ( 452) hydrogen bonds : angle 3.93174 ( 1290) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 175 time to evaluate : 0.261 Fit side-chains revert: symmetry clash REVERT: 1 220 ILE cc_start: 0.8836 (OUTLIER) cc_final: 0.8586 (mp) REVERT: 1 247 GLN cc_start: 0.8253 (mm-40) cc_final: 0.7947 (mm-40) REVERT: A 58 GLN cc_start: 0.7908 (mt0) cc_final: 0.7648 (mt0) REVERT: A 94 LYS cc_start: 0.9340 (OUTLIER) cc_final: 0.8952 (ptpp) REVERT: A 136 ASN cc_start: 0.7891 (t0) cc_final: 0.7651 (t0) REVERT: A 151 LEU cc_start: 0.8264 (OUTLIER) cc_final: 0.7876 (mp) REVERT: A 178 GLN cc_start: 0.7157 (mm-40) cc_final: 0.6410 (mm-40) REVERT: B 121 GLU cc_start: 0.7675 (mp0) cc_final: 0.7369 (pm20) REVERT: B 165 THR cc_start: 0.7888 (m) cc_final: 0.7685 (m) REVERT: E 216 MET cc_start: 0.8454 (tpt) cc_final: 0.8220 (tpp) REVERT: E 282 GLU cc_start: 0.7929 (OUTLIER) cc_final: 0.6786 (tm-30) REVERT: F 220 ILE cc_start: 0.8587 (mt) cc_final: 0.8275 (mm) REVERT: F 285 GLN cc_start: 0.6707 (tp40) cc_final: 0.6293 (tp40) REVERT: F 286 ASP cc_start: 0.8034 (t0) cc_final: 0.7662 (t0) outliers start: 39 outliers final: 27 residues processed: 204 average time/residue: 0.0764 time to fit residues: 22.0743 Evaluate side-chains 193 residues out of total 841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 162 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 165 SER Chi-restraints excluded: chain 1 residue 183 PHE Chi-restraints excluded: chain 1 residue 192 MET Chi-restraints excluded: chain 1 residue 202 HIS Chi-restraints excluded: chain 1 residue 220 ILE Chi-restraints excluded: chain 1 residue 308 LEU Chi-restraints excluded: chain 1 residue 314 SER Chi-restraints excluded: chain 2 residue 3 GLU Chi-restraints excluded: chain 2 residue 7 HIS Chi-restraints excluded: chain 2 residue 34 LEU Chi-restraints excluded: chain 2 residue 36 SER Chi-restraints excluded: chain 2 residue 48 ILE Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 94 LYS Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 50 GLN Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain E residue 184 VAL Chi-restraints excluded: chain E residue 190 ILE Chi-restraints excluded: chain E residue 210 HIS Chi-restraints excluded: chain E residue 225 LEU Chi-restraints excluded: chain E residue 246 VAL Chi-restraints excluded: chain E residue 257 LEU Chi-restraints excluded: chain E residue 282 GLU Chi-restraints excluded: chain F residue 183 PHE Chi-restraints excluded: chain F residue 210 HIS Chi-restraints excluded: chain F residue 257 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 76 optimal weight: 0.6980 chunk 66 optimal weight: 0.9990 chunk 27 optimal weight: 0.2980 chunk 92 optimal weight: 0.8980 chunk 72 optimal weight: 0.7980 chunk 96 optimal weight: 0.7980 chunk 69 optimal weight: 1.9990 chunk 98 optimal weight: 0.5980 chunk 0 optimal weight: 6.9990 chunk 87 optimal weight: 2.9990 chunk 78 optimal weight: 3.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 247 GLN A 7 HIS B 50 GLN ** E 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.125678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.105271 restraints weight = 14242.472| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 2.36 r_work: 0.3184 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.1988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8075 Z= 0.127 Angle : 0.627 7.645 11005 Z= 0.307 Chirality : 0.042 0.178 1322 Planarity : 0.005 0.082 1365 Dihedral : 8.084 121.561 1137 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.29 % Allowed : 8.65 % Favored : 91.06 % Rotamer: Outliers : 4.64 % Allowed : 30.92 % Favored : 64.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.52 % 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: 0.05 (0.28), residues: 1029 helix: 1.12 (0.21), residues: 724 sheet: None (None), residues: 0 loop : -2.71 (0.32), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 89 TYR 0.016 0.001 TYR B 125 PHE 0.008 0.001 PHE 1 183 TRP 0.008 0.001 TRP E 199 HIS 0.007 0.001 HIS A 7 Details of bonding type rmsd covalent geometry : bond 0.00304 ( 8075) covalent geometry : angle 0.62721 (11005) hydrogen bonds : bond 0.03599 ( 452) hydrogen bonds : angle 3.92445 ( 1290) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 165 time to evaluate : 0.298 Fit side-chains revert: symmetry clash REVERT: 1 220 ILE cc_start: 0.8844 (OUTLIER) cc_final: 0.8592 (mp) REVERT: 1 247 GLN cc_start: 0.8310 (mm110) cc_final: 0.7940 (mm-40) REVERT: A 58 GLN cc_start: 0.7897 (mt0) cc_final: 0.7645 (mt0) REVERT: A 94 LYS cc_start: 0.9353 (OUTLIER) cc_final: 0.8954 (ptpp) REVERT: A 136 ASN cc_start: 0.7852 (t0) cc_final: 0.7603 (t0) REVERT: A 151 LEU cc_start: 0.8246 (OUTLIER) cc_final: 0.7843 (mp) REVERT: A 178 GLN cc_start: 0.7164 (mm-40) cc_final: 0.6410 (mm-40) REVERT: B 121 GLU cc_start: 0.7691 (mp0) cc_final: 0.7375 (pm20) REVERT: B 165 THR cc_start: 0.7930 (m) cc_final: 0.7700 (m) REVERT: E 216 MET cc_start: 0.8490 (tpt) cc_final: 0.8257 (tpp) REVERT: E 282 GLU cc_start: 0.7897 (OUTLIER) cc_final: 0.6768 (tm-30) REVERT: F 220 ILE cc_start: 0.8591 (mt) cc_final: 0.8290 (mm) REVERT: F 285 GLN cc_start: 0.6747 (tp40) cc_final: 0.6332 (tp40) outliers start: 39 outliers final: 32 residues processed: 192 average time/residue: 0.0730 time to fit residues: 20.1436 Evaluate side-chains 199 residues out of total 841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 163 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 165 SER Chi-restraints excluded: chain 1 residue 183 PHE Chi-restraints excluded: chain 1 residue 192 MET Chi-restraints excluded: chain 1 residue 220 ILE Chi-restraints excluded: chain 1 residue 308 LEU Chi-restraints excluded: chain 1 residue 314 SER Chi-restraints excluded: chain 2 residue 3 GLU Chi-restraints excluded: chain 2 residue 7 HIS Chi-restraints excluded: chain 2 residue 34 LEU Chi-restraints excluded: chain 2 residue 36 SER Chi-restraints excluded: chain 2 residue 48 ILE Chi-restraints excluded: chain 2 residue 83 MET Chi-restraints excluded: chain 2 residue 130 SER Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 94 LYS Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 41 MET Chi-restraints excluded: chain B residue 50 GLN Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain E residue 184 VAL Chi-restraints excluded: chain E residue 190 ILE Chi-restraints excluded: chain E residue 200 ILE Chi-restraints excluded: chain E residue 210 HIS Chi-restraints excluded: chain E residue 225 LEU Chi-restraints excluded: chain E residue 246 VAL Chi-restraints excluded: chain E residue 257 LEU Chi-restraints excluded: chain E residue 282 GLU Chi-restraints excluded: chain F residue 183 PHE Chi-restraints excluded: chain F residue 210 HIS Chi-restraints excluded: chain F residue 257 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 37 optimal weight: 0.7980 chunk 5 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 27 optimal weight: 0.5980 chunk 13 optimal weight: 0.1980 chunk 67 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 chunk 78 optimal weight: 4.9990 chunk 29 optimal weight: 0.9980 chunk 90 optimal weight: 4.9990 chunk 66 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 7 HIS B 50 GLN E 202 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.125667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.105262 restraints weight = 14064.908| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 2.36 r_work: 0.3185 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.1999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8075 Z= 0.129 Angle : 0.638 8.182 11005 Z= 0.311 Chirality : 0.042 0.176 1322 Planarity : 0.005 0.082 1365 Dihedral : 7.770 119.051 1137 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.29 % Allowed : 8.36 % Favored : 91.35 % Rotamer: Outliers : 4.76 % Allowed : 31.03 % Favored : 64.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.52 % 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: 0.05 (0.28), residues: 1029 helix: 1.09 (0.21), residues: 724 sheet: None (None), residues: 0 loop : -2.63 (0.33), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 89 TYR 0.018 0.001 TYR B 125 PHE 0.017 0.001 PHE B 90 TRP 0.009 0.001 TRP E 199 HIS 0.007 0.001 HIS A 7 Details of bonding type rmsd covalent geometry : bond 0.00308 ( 8075) covalent geometry : angle 0.63770 (11005) hydrogen bonds : bond 0.03654 ( 452) hydrogen bonds : angle 3.92669 ( 1290) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 165 time to evaluate : 0.285 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 1 220 ILE cc_start: 0.8863 (OUTLIER) cc_final: 0.8598 (mp) REVERT: A 58 GLN cc_start: 0.7898 (mt0) cc_final: 0.7646 (mt0) REVERT: A 94 LYS cc_start: 0.9354 (OUTLIER) cc_final: 0.8950 (ptpp) REVERT: A 136 ASN cc_start: 0.7846 (t0) cc_final: 0.7591 (t0) REVERT: A 151 LEU cc_start: 0.8258 (OUTLIER) cc_final: 0.7845 (mp) REVERT: A 178 GLN cc_start: 0.7174 (mm-40) cc_final: 0.6413 (mm-40) REVERT: B 121 GLU cc_start: 0.7715 (mp0) cc_final: 0.7433 (pm20) REVERT: B 165 THR cc_start: 0.7920 (m) cc_final: 0.7679 (m) REVERT: E 216 MET cc_start: 0.8503 (tpt) cc_final: 0.8269 (tpp) REVERT: E 282 GLU cc_start: 0.7889 (OUTLIER) cc_final: 0.6755 (tm-30) REVERT: F 220 ILE cc_start: 0.8594 (mt) cc_final: 0.8294 (mm) outliers start: 40 outliers final: 34 residues processed: 192 average time/residue: 0.0680 time to fit residues: 18.9296 Evaluate side-chains 201 residues out of total 841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 163 time to evaluate : 0.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 165 SER Chi-restraints excluded: chain 1 residue 183 PHE Chi-restraints excluded: chain 1 residue 192 MET Chi-restraints excluded: chain 1 residue 214 LEU Chi-restraints excluded: chain 1 residue 220 ILE Chi-restraints excluded: chain 1 residue 308 LEU Chi-restraints excluded: chain 1 residue 314 SER Chi-restraints excluded: chain 2 residue 3 GLU Chi-restraints excluded: chain 2 residue 7 HIS Chi-restraints excluded: chain 2 residue 34 LEU Chi-restraints excluded: chain 2 residue 36 SER Chi-restraints excluded: chain 2 residue 48 ILE Chi-restraints excluded: chain 2 residue 83 MET Chi-restraints excluded: chain 2 residue 130 SER Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 94 LYS Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 41 MET Chi-restraints excluded: chain B residue 50 GLN Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain E residue 184 VAL Chi-restraints excluded: chain E residue 190 ILE Chi-restraints excluded: chain E residue 200 ILE Chi-restraints excluded: chain E residue 210 HIS Chi-restraints excluded: chain E residue 225 LEU Chi-restraints excluded: chain E residue 246 VAL Chi-restraints excluded: chain E residue 257 LEU Chi-restraints excluded: chain E residue 282 GLU Chi-restraints excluded: chain F residue 183 PHE Chi-restraints excluded: chain F residue 210 HIS Chi-restraints excluded: chain F residue 257 LEU Chi-restraints excluded: chain F residue 308 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 93 optimal weight: 0.6980 chunk 101 optimal weight: 0.9980 chunk 78 optimal weight: 1.9990 chunk 45 optimal weight: 0.6980 chunk 29 optimal weight: 0.8980 chunk 9 optimal weight: 1.9990 chunk 92 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 58 optimal weight: 0.0980 chunk 61 optimal weight: 6.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 7 HIS B 50 GLN E 202 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.125854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.105325 restraints weight = 14071.024| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 2.35 r_work: 0.3181 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.2050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8075 Z= 0.130 Angle : 0.634 8.453 11005 Z= 0.311 Chirality : 0.042 0.176 1322 Planarity : 0.005 0.081 1365 Dihedral : 7.553 116.588 1137 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.29 % Allowed : 8.75 % Favored : 90.96 % Rotamer: Outliers : 4.76 % Allowed : 31.03 % Favored : 64.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.52 % 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: 0.04 (0.28), residues: 1029 helix: 1.11 (0.21), residues: 718 sheet: None (None), residues: 0 loop : -2.64 (0.32), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 89 TYR 0.018 0.001 TYR B 125 PHE 0.008 0.001 PHE E 312 TRP 0.010 0.001 TRP E 199 HIS 0.007 0.001 HIS A 7 Details of bonding type rmsd covalent geometry : bond 0.00312 ( 8075) covalent geometry : angle 0.63436 (11005) hydrogen bonds : bond 0.03686 ( 452) hydrogen bonds : angle 3.92948 ( 1290) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 167 time to evaluate : 0.193 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 1 220 ILE cc_start: 0.8869 (OUTLIER) cc_final: 0.8601 (mp) REVERT: 1 247 GLN cc_start: 0.8293 (mm-40) cc_final: 0.8039 (mm-40) REVERT: A 58 GLN cc_start: 0.7892 (mt0) cc_final: 0.7650 (mt0) REVERT: A 94 LYS cc_start: 0.9356 (OUTLIER) cc_final: 0.8967 (ptpp) REVERT: A 136 ASN cc_start: 0.7847 (t0) cc_final: 0.7597 (t0) REVERT: A 151 LEU cc_start: 0.8288 (OUTLIER) cc_final: 0.7877 (mp) REVERT: A 178 GLN cc_start: 0.7168 (mm-40) cc_final: 0.6438 (mm-40) REVERT: B 121 GLU cc_start: 0.7721 (mp0) cc_final: 0.7422 (pm20) REVERT: B 165 THR cc_start: 0.7919 (m) cc_final: 0.7691 (m) REVERT: E 216 MET cc_start: 0.8532 (tpt) cc_final: 0.8295 (tpp) REVERT: E 282 GLU cc_start: 0.7896 (OUTLIER) cc_final: 0.6772 (tm-30) REVERT: F 220 ILE cc_start: 0.8596 (mt) cc_final: 0.8294 (mm) outliers start: 40 outliers final: 32 residues processed: 194 average time/residue: 0.0732 time to fit residues: 20.3203 Evaluate side-chains 198 residues out of total 841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 162 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 165 SER Chi-restraints excluded: chain 1 residue 183 PHE Chi-restraints excluded: chain 1 residue 192 MET Chi-restraints excluded: chain 1 residue 214 LEU Chi-restraints excluded: chain 1 residue 220 ILE Chi-restraints excluded: chain 1 residue 308 LEU Chi-restraints excluded: chain 1 residue 314 SER Chi-restraints excluded: chain 2 residue 3 GLU Chi-restraints excluded: chain 2 residue 7 HIS Chi-restraints excluded: chain 2 residue 34 LEU Chi-restraints excluded: chain 2 residue 36 SER Chi-restraints excluded: chain 2 residue 48 ILE Chi-restraints excluded: chain 2 residue 83 MET Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 94 LYS Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 41 MET Chi-restraints excluded: chain B residue 50 GLN Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain E residue 184 VAL Chi-restraints excluded: chain E residue 190 ILE Chi-restraints excluded: chain E residue 200 ILE Chi-restraints excluded: chain E residue 210 HIS Chi-restraints excluded: chain E residue 225 LEU Chi-restraints excluded: chain E residue 246 VAL Chi-restraints excluded: chain E residue 257 LEU Chi-restraints excluded: chain E residue 282 GLU Chi-restraints excluded: chain F residue 183 PHE Chi-restraints excluded: chain F residue 210 HIS Chi-restraints excluded: chain F residue 308 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 83 optimal weight: 0.6980 chunk 72 optimal weight: 1.9990 chunk 58 optimal weight: 0.6980 chunk 96 optimal weight: 0.9990 chunk 28 optimal weight: 0.4980 chunk 48 optimal weight: 1.9990 chunk 39 optimal weight: 0.4980 chunk 95 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 42 optimal weight: 0.8980 chunk 23 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 7 HIS B 50 GLN E 202 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.125852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.105329 restraints weight = 13924.803| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 2.35 r_work: 0.3183 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.2073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8075 Z= 0.130 Angle : 0.642 8.904 11005 Z= 0.316 Chirality : 0.042 0.177 1322 Planarity : 0.006 0.081 1365 Dihedral : 7.430 113.901 1137 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.29 % Allowed : 8.36 % Favored : 91.35 % Rotamer: Outliers : 4.64 % Allowed : 31.27 % Favored : 64.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.52 % 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: 0.05 (0.28), residues: 1029 helix: 1.11 (0.21), residues: 718 sheet: None (None), residues: 0 loop : -2.63 (0.32), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 67 TYR 0.018 0.001 TYR B 125 PHE 0.033 0.001 PHE 2 56 TRP 0.010 0.001 TRP E 199 HIS 0.007 0.001 HIS A 7 Details of bonding type rmsd covalent geometry : bond 0.00312 ( 8075) covalent geometry : angle 0.64198 (11005) hydrogen bonds : bond 0.03680 ( 452) hydrogen bonds : angle 3.92634 ( 1290) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1585.04 seconds wall clock time: 27 minutes 59.31 seconds (1679.31 seconds total)