Starting phenix.real_space_refine on Sat Aug 23 01:06:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8e3z_27874/08_2025/8e3z_27874.cif Found real_map, /net/cci-nas-00/data/ceres_data/8e3z_27874/08_2025/8e3z_27874.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8e3z_27874/08_2025/8e3z_27874.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8e3z_27874/08_2025/8e3z_27874.map" model { file = "/net/cci-nas-00/data/ceres_data/8e3z_27874/08_2025/8e3z_27874.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8e3z_27874/08_2025/8e3z_27874.cif" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 59 5.16 5 C 5650 2.51 5 N 1550 2.21 5 O 1639 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8898 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 1819 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 217, 1807 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 6, 'TRANS': 210} Chain breaks: 3 Conformer: "B" Number of residues, atoms: 217, 1807 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 6, 'TRANS': 210} Chain breaks: 3 bond proxies already assigned to first conformer: 1827 Chain: "B" Number of atoms: 2572 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2572 Classifications: {'peptide': 334} Link IDs: {'PTRANS': 5, 'TRANS': 328} Chain breaks: 1 Chain: "G" Number of atoms: 424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 424 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 4, 'TRANS': 50} Chain: "N" Number of atoms: 961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 961 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 5, 'TRANS': 120} Chain: "P" Number of atoms: 234 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 234 Classifications: {'peptide': 28} Modifications used: {'COO': 1} Link IDs: {'TRANS': 27} Chain: "R" Number of atoms: 2883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2883 Classifications: {'peptide': 372} Incomplete info: {'truncation_to_alanine': 37} Link IDs: {'PTRANS': 14, 'TRANS': 357} Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 136 Unresolved non-hydrogen angles: 178 Unresolved non-hydrogen dihedrals: 114 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLU:plan': 6, 'GLN:plan1': 3, 'ASN:plan1': 2, 'TRP:plan': 2, 'ARG:plan': 2, 'ASP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 78 Chain: "P" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "R" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N ATYR A 358 " occ=0.50 ... (22 atoms not shown) pdb=" OH BTYR A 358 " occ=0.50 Time building chain proxies: 2.11, per 1000 atoms: 0.24 Number of scatterers: 8898 At special positions: 0 Unit cell: (87.15, 101.26, 166.83, 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 59 16.00 O 1639 8.00 N 1550 7.00 C 5650 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.03 Simple disulfide: pdb=" SG CYS R 37 " - pdb=" SG CYS R 208 " distance=2.03 Simple disulfide: pdb=" SG CYS R 50 " - pdb=" SG CYS R 72 " distance=2.03 Simple disulfide: pdb=" SG CYS R 63 " - pdb=" SG CYS R 105 " distance=2.03 Simple disulfide: pdb=" SG CYS R 86 " - pdb=" SG CYS R 122 " distance=2.03 Simple disulfide: pdb=" SG CYS R 215 " - pdb=" SG CYS R 285 " distance=2.03 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: 0.59 Conformation dependent library (CDL) restraints added in 307.2 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2124 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 11 sheets defined 41.5% alpha, 17.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.17 Creating SS restraints... Processing helix chain 'A' and resid 16 through 38 removed outlier: 3.929A pdb=" N ALA A 22 " --> pdb=" O ALA A 18 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 61 Processing helix chain 'A' and resid 233 through 239 removed outlier: 3.625A pdb=" N ASN A 239 " --> pdb=" O GLN A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 278 Processing helix chain 'A' and resid 295 through 300 Processing helix chain 'A' and resid 312 through 316 Processing helix chain 'A' and resid 331 through 350 removed outlier: 3.932A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 Processing helix chain 'B' and resid 4 through 25 Processing helix chain 'B' and resid 29 through 35 Processing helix chain 'G' and resid 9 through 24 removed outlier: 3.514A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 removed outlier: 3.504A pdb=" N ALA G 33 " --> pdb=" O LYS G 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 45 through 48 Processing helix chain 'G' and resid 55 through 59 Processing helix chain 'N' and resid 28 through 32 removed outlier: 3.585A pdb=" N ASN N 31 " --> pdb=" O THR N 28 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N TYR N 32 " --> pdb=" O PHE N 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 28 through 32' Processing helix chain 'N' and resid 62 through 65 removed outlier: 3.631A pdb=" N LYS N 65 " --> pdb=" O GLY N 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 62 through 65' Processing helix chain 'N' and resid 87 through 91 Processing helix chain 'P' and resid 2 through 26 removed outlier: 3.631A pdb=" N ILE P 26 " --> pdb=" O TYR P 22 " (cutoff:3.500A) Processing helix chain 'R' and resid 39 through 50 removed outlier: 4.127A pdb=" N ILE R 43 " --> pdb=" O TYR R 39 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N GLU R 44 " --> pdb=" O VAL R 40 " (cutoff:3.500A) Processing helix chain 'R' and resid 87 through 92 removed outlier: 3.659A pdb=" N PHE R 90 " --> pdb=" O PRO R 87 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N LEU R 92 " --> pdb=" O ILE R 89 " (cutoff:3.500A) Processing helix chain 'R' and resid 128 through 167 removed outlier: 3.523A pdb=" N ASP R 132 " --> pdb=" O ALA R 128 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLU R 133 " --> pdb=" O ALA R 129 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N VAL R 159 " --> pdb=" O ALA R 155 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N PHE R 167 " --> pdb=" O ILE R 163 " (cutoff:3.500A) Processing helix chain 'R' and resid 172 through 200 Processing helix chain 'R' and resid 203 through 210 Processing helix chain 'R' and resid 212 through 246 removed outlier: 3.593A pdb=" N LYS R 216 " --> pdb=" O SER R 212 " (cutoff:3.500A) Processing helix chain 'R' and resid 251 through 253 No H-bonds generated for 'chain 'R' and resid 251 through 253' Processing helix chain 'R' and resid 254 through 280 removed outlier: 4.561A pdb=" N VAL R 265 " --> pdb=" O ILE R 261 " (cutoff:3.500A) Proline residue: R 266 - end of helix Processing helix chain 'R' and resid 293 through 324 removed outlier: 3.950A pdb=" N ILE R 297 " --> pdb=" O LEU R 293 " (cutoff:3.500A) Proline residue: R 300 - end of helix removed outlier: 3.945A pdb=" N ASN R 308 " --> pdb=" O SER R 304 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLN R 321 " --> pdb=" O ARG R 317 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N LYS R 322 " --> pdb=" O ILE R 318 " (cutoff:3.500A) Processing helix chain 'R' and resid 334 through 351 Proline residue: R 348 - end of helix Processing helix chain 'R' and resid 352 through 357 removed outlier: 3.522A pdb=" N PHE R 357 " --> pdb=" O TYR R 354 " (cutoff:3.500A) Processing helix chain 'R' and resid 368 through 389 removed outlier: 4.390A pdb=" N GLY R 381 " --> pdb=" O GLY R 377 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N PHE R 382 " --> pdb=" O SER R 378 " (cutoff:3.500A) Processing helix chain 'R' and resid 392 through 407 removed outlier: 3.518A pdb=" N ARG R 401 " --> pdb=" O ALA R 397 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 209 through 214 removed outlier: 3.754A pdb=" N HIS A 41 " --> pdb=" O ASN A 218 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.865A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.981A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.588A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.782A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 7.072A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.678A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 7.455A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 189 through 192 removed outlier: 3.535A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL B 200 " --> pdb=" O SER B 191 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.549A pdb=" N SER B 245 " --> pdb=" O THR B 249 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N THR B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ASP B 254 " --> pdb=" O GLN B 259 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 276 removed outlier: 3.756A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'N' and resid 10 through 11 removed outlier: 6.052A pdb=" N GLY N 10 " --> pdb=" O THR N 125 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'R' and resid 83 through 85 426 hydrogen bonds defined for protein. 1206 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: 1.07 Time building geometry restraints manager: 0.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1798 1.33 - 1.45: 2254 1.45 - 1.57: 4949 1.57 - 1.70: 0 1.70 - 1.82: 82 Bond restraints: 9083 Sorted by residual: bond pdb=" N LYS R 365 " pdb=" CA LYS R 365 " ideal model delta sigma weight residual 1.461 1.490 -0.028 9.20e-03 1.18e+04 9.59e+00 bond pdb=" N VAL R 235 " pdb=" CA VAL R 235 " ideal model delta sigma weight residual 1.461 1.495 -0.034 1.19e-02 7.06e+03 8.38e+00 bond pdb=" N ILE R 177 " pdb=" CA ILE R 177 " ideal model delta sigma weight residual 1.461 1.494 -0.034 1.19e-02 7.06e+03 8.08e+00 bond pdb=" N VAL R 368 " pdb=" CA VAL R 368 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.25e-02 6.40e+03 7.32e+00 bond pdb=" N ASN G 59 " pdb=" CA ASN G 59 " ideal model delta sigma weight residual 1.456 1.497 -0.042 1.58e-02 4.01e+03 6.93e+00 ... (remaining 9078 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.49: 11924 1.49 - 2.99: 302 2.99 - 4.48: 56 4.48 - 5.97: 9 5.97 - 7.47: 3 Bond angle restraints: 12294 Sorted by residual: angle pdb=" N ALA R 358 " pdb=" CA ALA R 358 " pdb=" C ALA R 358 " ideal model delta sigma weight residual 113.41 105.94 7.47 1.22e+00 6.72e-01 3.75e+01 angle pdb=" N LEU R 233 " pdb=" CA LEU R 233 " pdb=" C LEU R 233 " ideal model delta sigma weight residual 111.36 106.85 4.51 1.09e+00 8.42e-01 1.71e+01 angle pdb=" C GLU R 373 " pdb=" N LEU R 374 " pdb=" CA LEU R 374 " ideal model delta sigma weight residual 120.58 113.54 7.04 1.71e+00 3.42e-01 1.70e+01 angle pdb=" C ASN G 59 " pdb=" N PRO G 60 " pdb=" CA PRO G 60 " ideal model delta sigma weight residual 119.05 123.11 -4.06 1.11e+00 8.12e-01 1.34e+01 angle pdb=" CA PHE R 360 " pdb=" C PHE R 360 " pdb=" N PRO R 361 " ideal model delta sigma weight residual 119.27 123.25 -3.98 1.13e+00 7.83e-01 1.24e+01 ... (remaining 12289 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.96: 4918 16.96 - 33.91: 398 33.91 - 50.87: 55 50.87 - 67.83: 10 67.83 - 84.78: 15 Dihedral angle restraints: 5396 sinusoidal: 2107 harmonic: 3289 Sorted by residual: dihedral pdb=" CB CYS N 99 " pdb=" SG CYS N 99 " pdb=" SG CYS N 107 " pdb=" CB CYS N 107 " ideal model delta sinusoidal sigma weight residual -86.00 -18.29 -67.71 1 1.00e+01 1.00e-02 5.96e+01 dihedral pdb=" CB CYS R 215 " pdb=" SG CYS R 215 " pdb=" SG CYS R 285 " pdb=" CB CYS R 285 " ideal model delta sinusoidal sigma weight residual 93.00 148.73 -55.73 1 1.00e+01 1.00e-02 4.19e+01 dihedral pdb=" CB CYS R 37 " pdb=" SG CYS R 37 " pdb=" SG CYS R 208 " pdb=" CB CYS R 208 " ideal model delta sinusoidal sigma weight residual -86.00 -138.17 52.17 1 1.00e+01 1.00e-02 3.71e+01 ... (remaining 5393 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 1150 0.058 - 0.115: 183 0.115 - 0.173: 24 0.173 - 0.231: 4 0.231 - 0.288: 1 Chirality restraints: 1362 Sorted by residual: chirality pdb=" CA GLU R 373 " pdb=" N GLU R 373 " pdb=" C GLU R 373 " pdb=" CB GLU R 373 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.08e+00 chirality pdb=" CA PHE R 360 " pdb=" N PHE R 360 " pdb=" C PHE R 360 " pdb=" CB PHE R 360 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 1.02e+00 chirality pdb=" CA ILE R 177 " pdb=" N ILE R 177 " pdb=" C ILE R 177 " pdb=" CB ILE R 177 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.19 2.00e-01 2.50e+01 8.88e-01 ... (remaining 1359 not shown) Planarity restraints: 1572 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE R 231 " 0.017 2.00e-02 2.50e+03 3.36e-02 1.13e+01 pdb=" C PHE R 231 " -0.058 2.00e-02 2.50e+03 pdb=" O PHE R 231 " 0.021 2.00e-02 2.50e+03 pdb=" N TRP R 232 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE R 372 " -0.011 2.00e-02 2.50e+03 2.20e-02 4.85e+00 pdb=" C PHE R 372 " 0.038 2.00e-02 2.50e+03 pdb=" O PHE R 372 " -0.014 2.00e-02 2.50e+03 pdb=" N GLU R 373 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU B 10 " 0.008 2.00e-02 2.50e+03 1.64e-02 2.70e+00 pdb=" CD GLU B 10 " -0.028 2.00e-02 2.50e+03 pdb=" OE1 GLU B 10 " 0.010 2.00e-02 2.50e+03 pdb=" OE2 GLU B 10 " 0.010 2.00e-02 2.50e+03 ... (remaining 1569 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1052 2.76 - 3.29: 8654 3.29 - 3.83: 15204 3.83 - 4.36: 17461 4.36 - 4.90: 30499 Nonbonded interactions: 72870 Sorted by model distance: nonbonded pdb=" OH TYR A 318 " pdb=" OD2 ASP A 343 " model vdw 2.219 3.040 nonbonded pdb=" OG1 THR A 364 " pdb=" OD1 ASN A 371 " model vdw 2.250 3.040 nonbonded pdb=" OD1 ASN A 278 " pdb=" NH1 ARG N 105 " model vdw 2.292 3.120 nonbonded pdb=" OD1 ASP B 228 " pdb=" OH TYR N 117 " model vdw 2.296 3.040 nonbonded pdb=" OD2 ASP A 33 " pdb=" NZ LYS B 78 " model vdw 2.301 3.120 ... (remaining 72865 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.560 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: 0.110 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 7.670 Find NCS groups from input model: 0.030 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:8.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7400 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9090 Z= 0.199 Angle : 0.588 7.466 12308 Z= 0.388 Chirality : 0.044 0.288 1362 Planarity : 0.003 0.040 1572 Dihedral : 12.804 84.782 3251 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 0.11 % Allowed : 0.32 % Favored : 99.57 % 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 aren not related in a simple way. whole: 0.87 (0.25), residues: 1115 helix: 1.80 (0.25), residues: 419 sheet: 0.85 (0.36), residues: 192 loop : -0.57 (0.27), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 38 TYR 0.012 0.001 TYR B 59 PHE 0.015 0.001 PHE B 335 TRP 0.013 0.001 TRP B 82 HIS 0.003 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00290 ( 9083) covalent geometry : angle 0.58767 (12294) SS BOND : bond 0.00146 ( 7) SS BOND : angle 0.66106 ( 14) hydrogen bonds : bond 0.12557 ( 426) hydrogen bonds : angle 5.34864 ( 1206) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 224 time to evaluate : 0.213 Fit side-chains revert: symmetry clash REVERT: A 343 ASP cc_start: 0.7673 (m-30) cc_final: 0.7270 (m-30) REVERT: B 267 ASP cc_start: 0.8619 (m-30) cc_final: 0.8385 (m-30) REVERT: P 3 ASP cc_start: 0.8032 (m-30) cc_final: 0.7581 (m-30) REVERT: P 11 THR cc_start: 0.8235 (t) cc_final: 0.7965 (p) REVERT: R 38 ASP cc_start: 0.6912 (p0) cc_final: 0.6358 (OUTLIER) REVERT: R 42 MET cc_start: 0.8096 (mpp) cc_final: 0.6788 (ppp) REVERT: R 44 GLU cc_start: 0.6976 (pm20) cc_final: 0.6617 (pm20) REVERT: R 134 GLN cc_start: 0.8222 (pt0) cc_final: 0.7960 (pt0) REVERT: R 251 GLU cc_start: 0.7172 (mm-30) cc_final: 0.6961 (mm-30) REVERT: R 252 ARG cc_start: 0.7326 (tpt170) cc_final: 0.6302 (tpm170) REVERT: R 261 ILE cc_start: 0.8141 (tt) cc_final: 0.7842 (tp) REVERT: R 398 GLU cc_start: 0.6917 (tm-30) cc_final: 0.6713 (tm-30) REVERT: R 406 TRP cc_start: 0.6473 (t-100) cc_final: 0.6036 (t60) outliers start: 1 outliers final: 1 residues processed: 224 average time/residue: 0.6043 time to fit residues: 143.4503 Evaluate side-chains 139 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 139 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 108 optimal weight: 3.9990 chunk 49 optimal weight: 3.9990 chunk 97 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 0.0370 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 0.3980 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 100 optimal weight: 0.6980 chunk 106 optimal weight: 2.9990 overall best weight: 0.8260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 GLN B 16 ASN B 125 ASN B 156 GLN B 295 ASN N 53 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.160290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.114451 restraints weight = 23335.329| |-----------------------------------------------------------------------------| r_work (start): 0.3459 rms_B_bonded: 3.22 r_work: 0.3322 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3328 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3328 r_free = 0.3328 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3328 r_free = 0.3328 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3328 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.2148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9090 Z= 0.143 Angle : 0.547 6.266 12308 Z= 0.291 Chirality : 0.042 0.170 1362 Planarity : 0.004 0.046 1572 Dihedral : 4.554 81.752 1235 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 2.13 % Allowed : 12.15 % Favored : 85.71 % 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 aren not related in a simple way. whole: 1.12 (0.25), residues: 1115 helix: 2.32 (0.25), residues: 425 sheet: 0.84 (0.35), residues: 198 loop : -0.74 (0.27), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 283 TYR 0.022 0.001 TYR R 146 PHE 0.013 0.001 PHE N 108 TRP 0.014 0.001 TRP R 232 HIS 0.011 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00327 ( 9083) covalent geometry : angle 0.54591 (12294) SS BOND : bond 0.00595 ( 7) SS BOND : angle 1.27343 ( 14) hydrogen bonds : bond 0.03648 ( 426) hydrogen bonds : angle 4.18544 ( 1206) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 150 time to evaluate : 0.362 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 232 ARG cc_start: 0.8777 (ttp-110) cc_final: 0.8456 (ptp-170) REVERT: A 343 ASP cc_start: 0.8119 (m-30) cc_final: 0.7758 (m-30) REVERT: B 44 GLN cc_start: 0.8249 (mm110) cc_final: 0.7790 (mp10) REVERT: B 285 LEU cc_start: 0.9240 (OUTLIER) cc_final: 0.8906 (tt) REVERT: N 76 LYS cc_start: 0.8568 (mtpp) cc_final: 0.8325 (mtmm) REVERT: N 77 ASN cc_start: 0.8750 (m-40) cc_final: 0.8507 (m-40) REVERT: P 3 ASP cc_start: 0.8553 (m-30) cc_final: 0.8158 (m-30) REVERT: P 11 THR cc_start: 0.8678 (t) cc_final: 0.8344 (p) REVERT: R 42 MET cc_start: 0.8229 (mpp) cc_final: 0.6895 (ppp) REVERT: R 44 GLU cc_start: 0.6978 (pm20) cc_final: 0.6611 (pm20) REVERT: R 252 ARG cc_start: 0.7548 (tpt170) cc_final: 0.6554 (tpm170) REVERT: R 261 ILE cc_start: 0.8435 (tt) cc_final: 0.8184 (tp) outliers start: 20 outliers final: 8 residues processed: 167 average time/residue: 0.7017 time to fit residues: 123.8192 Evaluate side-chains 143 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 134 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 GLU Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain R residue 158 LEU Chi-restraints excluded: chain R residue 159 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 16 optimal weight: 0.9990 chunk 102 optimal weight: 0.0570 chunk 36 optimal weight: 0.0770 chunk 17 optimal weight: 0.3980 chunk 35 optimal weight: 0.5980 chunk 6 optimal weight: 4.9990 chunk 1 optimal weight: 0.5980 chunk 30 optimal weight: 0.9990 chunk 46 optimal weight: 4.9990 chunk 42 optimal weight: 5.9990 chunk 84 optimal weight: 2.9990 overall best weight: 0.3456 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 44 GLN B 268 ASN N 53 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.161258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.118178 restraints weight = 24062.125| |-----------------------------------------------------------------------------| r_work (start): 0.3514 rms_B_bonded: 3.13 r_work: 0.3397 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3395 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3395 r_free = 0.3395 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3395 r_free = 0.3395 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3395 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.2332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 9090 Z= 0.098 Angle : 0.481 6.223 12308 Z= 0.256 Chirality : 0.040 0.159 1362 Planarity : 0.003 0.046 1572 Dihedral : 4.371 81.195 1235 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 1.92 % Allowed : 15.46 % Favored : 82.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.26 (0.25), residues: 1115 helix: 2.55 (0.25), residues: 416 sheet: 0.98 (0.33), residues: 196 loop : -0.73 (0.27), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 283 TYR 0.018 0.001 TYR P 22 PHE 0.014 0.001 PHE A 212 TRP 0.015 0.001 TRP R 232 HIS 0.005 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00216 ( 9083) covalent geometry : angle 0.47824 (12294) SS BOND : bond 0.00228 ( 7) SS BOND : angle 1.52505 ( 14) hydrogen bonds : bond 0.03258 ( 426) hydrogen bonds : angle 4.01001 ( 1206) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 142 time to evaluate : 0.312 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 343 ASP cc_start: 0.8096 (m-30) cc_final: 0.7743 (m-30) REVERT: B 217 MET cc_start: 0.7943 (ppp) cc_final: 0.7663 (ppp) REVERT: B 285 LEU cc_start: 0.9215 (OUTLIER) cc_final: 0.8890 (tt) REVERT: G 17 GLU cc_start: 0.7800 (tt0) cc_final: 0.7523 (tm-30) REVERT: N 77 ASN cc_start: 0.8706 (m-40) cc_final: 0.8495 (m-40) REVERT: P 3 ASP cc_start: 0.8539 (m-30) cc_final: 0.8174 (m-30) REVERT: P 11 THR cc_start: 0.8688 (t) cc_final: 0.8399 (p) REVERT: R 42 MET cc_start: 0.8129 (mpp) cc_final: 0.6790 (ppp) REVERT: R 44 GLU cc_start: 0.6902 (pm20) cc_final: 0.6496 (pm20) REVERT: R 252 ARG cc_start: 0.7476 (tpt170) cc_final: 0.6518 (tpm170) REVERT: R 261 ILE cc_start: 0.8483 (tt) cc_final: 0.8241 (tp) outliers start: 18 outliers final: 7 residues processed: 155 average time/residue: 0.6442 time to fit residues: 105.7928 Evaluate side-chains 141 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 133 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 GLU Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain R residue 158 LEU Chi-restraints excluded: chain R residue 159 VAL Chi-restraints excluded: chain R residue 341 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 68 optimal weight: 5.9990 chunk 69 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 64 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 chunk 37 optimal weight: 0.5980 chunk 96 optimal weight: 0.9980 chunk 90 optimal weight: 20.0000 chunk 2 optimal weight: 3.9990 chunk 9 optimal weight: 0.8980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 156 GLN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 53 GLN N 84 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.154622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.109537 restraints weight = 28318.833| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 3.35 r_work: 0.3261 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3271 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3271 r_free = 0.3271 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3271 r_free = 0.3271 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3271 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.2978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 9090 Z= 0.158 Angle : 0.538 6.039 12308 Z= 0.287 Chirality : 0.043 0.156 1362 Planarity : 0.004 0.043 1572 Dihedral : 4.763 81.381 1235 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 2.77 % Allowed : 16.52 % Favored : 80.70 % 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 aren not related in a simple way. whole: 1.17 (0.25), residues: 1115 helix: 2.48 (0.25), residues: 416 sheet: 0.55 (0.33), residues: 216 loop : -0.66 (0.27), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 283 TYR 0.019 0.002 TYR R 146 PHE 0.015 0.002 PHE A 212 TRP 0.015 0.001 TRP R 232 HIS 0.010 0.001 HIS B 62 Details of bonding type rmsd covalent geometry : bond 0.00370 ( 9083) covalent geometry : angle 0.53649 (12294) SS BOND : bond 0.00199 ( 7) SS BOND : angle 1.47223 ( 14) hydrogen bonds : bond 0.03803 ( 426) hydrogen bonds : angle 4.10996 ( 1206) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 151 time to evaluate : 0.375 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 LYS cc_start: 0.8366 (mttp) cc_final: 0.7716 (mmtm) REVERT: A 311 TYR cc_start: 0.7014 (m-80) cc_final: 0.6473 (m-80) REVERT: A 343 ASP cc_start: 0.8081 (m-30) cc_final: 0.7760 (m-30) REVERT: G 17 GLU cc_start: 0.7815 (tt0) cc_final: 0.7538 (tm-30) REVERT: G 42 GLU cc_start: 0.7954 (mt-10) cc_final: 0.7342 (mm-30) REVERT: N 77 ASN cc_start: 0.8851 (m-40) cc_final: 0.8650 (m-40) REVERT: P 3 ASP cc_start: 0.8606 (m-30) cc_final: 0.8247 (m-30) REVERT: R 42 MET cc_start: 0.8167 (mpp) cc_final: 0.6725 (ppp) REVERT: R 134 GLN cc_start: 0.8409 (OUTLIER) cc_final: 0.8143 (pm20) REVERT: R 252 ARG cc_start: 0.7538 (tpt170) cc_final: 0.6482 (tpm170) REVERT: R 261 ILE cc_start: 0.8562 (tt) cc_final: 0.8347 (tp) REVERT: R 344 LEU cc_start: 0.8360 (tp) cc_final: 0.8138 (mm) outliers start: 26 outliers final: 15 residues processed: 169 average time/residue: 0.7023 time to fit residues: 125.5531 Evaluate side-chains 158 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 142 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 GLU Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 96 CYS Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain P residue 19 VAL Chi-restraints excluded: chain R residue 134 GLN Chi-restraints excluded: chain R residue 158 LEU Chi-restraints excluded: chain R residue 159 VAL Chi-restraints excluded: chain R residue 260 LEU Chi-restraints excluded: chain R residue 341 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 108 optimal weight: 5.9990 chunk 50 optimal weight: 0.1980 chunk 1 optimal weight: 0.9980 chunk 109 optimal weight: 3.9990 chunk 3 optimal weight: 0.9980 chunk 94 optimal weight: 3.9990 chunk 2 optimal weight: 0.8980 chunk 49 optimal weight: 1.9990 chunk 61 optimal weight: 0.8980 chunk 65 optimal weight: 0.0000 chunk 64 optimal weight: 0.9990 overall best weight: 0.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 156 GLN B 268 ASN N 53 GLN N 84 ASN R 223 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.155663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.113354 restraints weight = 22869.835| |-----------------------------------------------------------------------------| r_work (start): 0.3443 rms_B_bonded: 2.95 r_work: 0.3326 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3325 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3325 r_free = 0.3325 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3324 r_free = 0.3324 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3324 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.3059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9090 Z= 0.114 Angle : 0.504 7.178 12308 Z= 0.269 Chirality : 0.041 0.148 1362 Planarity : 0.004 0.059 1572 Dihedral : 4.646 81.452 1235 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 2.13 % Allowed : 18.23 % Favored : 79.64 % 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 aren not related in a simple way. whole: 1.20 (0.25), residues: 1115 helix: 2.55 (0.25), residues: 416 sheet: 0.73 (0.33), residues: 201 loop : -0.72 (0.27), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 232 TYR 0.018 0.001 TYR P 22 PHE 0.016 0.001 PHE A 212 TRP 0.028 0.001 TRP R 256 HIS 0.008 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00261 ( 9083) covalent geometry : angle 0.50211 (12294) SS BOND : bond 0.00197 ( 7) SS BOND : angle 1.38526 ( 14) hydrogen bonds : bond 0.03410 ( 426) hydrogen bonds : angle 4.01266 ( 1206) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 146 time to evaluate : 0.361 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 311 TYR cc_start: 0.6998 (m-80) cc_final: 0.6477 (m-80) REVERT: A 343 ASP cc_start: 0.8130 (m-30) cc_final: 0.7798 (m-30) REVERT: G 17 GLU cc_start: 0.7820 (tt0) cc_final: 0.7576 (tm-30) REVERT: G 42 GLU cc_start: 0.7909 (mt-10) cc_final: 0.7366 (mm-30) REVERT: N 82 GLN cc_start: 0.7905 (tp40) cc_final: 0.7668 (tp40) REVERT: P 3 ASP cc_start: 0.8576 (m-30) cc_final: 0.8267 (m-30) REVERT: P 21 LYS cc_start: 0.8915 (ttpp) cc_final: 0.8713 (tmmm) REVERT: R 42 MET cc_start: 0.8194 (mpp) cc_final: 0.6725 (ppp) REVERT: R 134 GLN cc_start: 0.8391 (OUTLIER) cc_final: 0.8137 (pm20) REVERT: R 158 LEU cc_start: 0.7808 (OUTLIER) cc_final: 0.7505 (mm) REVERT: R 252 ARG cc_start: 0.7348 (tpt170) cc_final: 0.6287 (tpm170) REVERT: R 344 LEU cc_start: 0.8404 (tp) cc_final: 0.8148 (mm) REVERT: R 367 GLU cc_start: 0.6542 (mp0) cc_final: 0.5136 (mm-30) outliers start: 20 outliers final: 11 residues processed: 158 average time/residue: 0.7459 time to fit residues: 124.1806 Evaluate side-chains 154 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 141 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 GLU Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain R residue 134 GLN Chi-restraints excluded: chain R residue 158 LEU Chi-restraints excluded: chain R residue 159 VAL Chi-restraints excluded: chain R residue 341 ARG Chi-restraints excluded: chain R residue 345 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 2 optimal weight: 3.9990 chunk 104 optimal weight: 0.9980 chunk 17 optimal weight: 0.0070 chunk 63 optimal weight: 0.0050 chunk 20 optimal weight: 0.8980 chunk 101 optimal weight: 0.7980 chunk 57 optimal weight: 0.8980 chunk 45 optimal weight: 2.9990 chunk 13 optimal weight: 0.8980 chunk 52 optimal weight: 2.9990 chunk 24 optimal weight: 5.9990 overall best weight: 0.5212 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 268 ASN N 53 GLN R 223 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.156324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.112250 restraints weight = 24367.760| |-----------------------------------------------------------------------------| r_work (start): 0.3431 rms_B_bonded: 3.14 r_work: 0.3311 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3318 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3318 r_free = 0.3318 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3318 r_free = 0.3318 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3318 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.3139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 9090 Z= 0.107 Angle : 0.488 5.499 12308 Z= 0.261 Chirality : 0.040 0.147 1362 Planarity : 0.003 0.039 1572 Dihedral : 4.560 81.484 1235 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 2.45 % Allowed : 18.02 % Favored : 79.53 % 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 aren not related in a simple way. whole: 1.22 (0.25), residues: 1115 helix: 2.61 (0.25), residues: 416 sheet: 0.69 (0.33), residues: 201 loop : -0.73 (0.27), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 232 TYR 0.015 0.001 TYR R 146 PHE 0.015 0.001 PHE A 212 TRP 0.034 0.001 TRP R 256 HIS 0.008 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00243 ( 9083) covalent geometry : angle 0.48680 (12294) SS BOND : bond 0.00182 ( 7) SS BOND : angle 1.28714 ( 14) hydrogen bonds : bond 0.03294 ( 426) hydrogen bonds : angle 3.93036 ( 1206) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 147 time to evaluate : 0.379 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 58 LYS cc_start: 0.8316 (mttp) cc_final: 0.7682 (mmtm) REVERT: A 343 ASP cc_start: 0.8133 (m-30) cc_final: 0.7773 (m-30) REVERT: B 215 GLU cc_start: 0.8479 (pp20) cc_final: 0.7826 (pp20) REVERT: G 17 GLU cc_start: 0.7807 (tt0) cc_final: 0.7511 (tm-30) REVERT: G 42 GLU cc_start: 0.7881 (mt-10) cc_final: 0.7321 (mm-30) REVERT: N 96 CYS cc_start: 0.8436 (OUTLIER) cc_final: 0.8060 (p) REVERT: P 3 ASP cc_start: 0.8541 (m-30) cc_final: 0.8228 (m-30) REVERT: R 42 MET cc_start: 0.8172 (mpp) cc_final: 0.6724 (ppp) REVERT: R 134 GLN cc_start: 0.8394 (OUTLIER) cc_final: 0.8133 (pm20) REVERT: R 158 LEU cc_start: 0.7662 (OUTLIER) cc_final: 0.7356 (mm) REVERT: R 252 ARG cc_start: 0.7304 (tpt170) cc_final: 0.6202 (tpm170) REVERT: R 344 LEU cc_start: 0.8325 (tp) cc_final: 0.8071 (mm) REVERT: R 367 GLU cc_start: 0.6475 (mp0) cc_final: 0.5042 (mm-30) outliers start: 23 outliers final: 10 residues processed: 165 average time/residue: 0.7236 time to fit residues: 125.8912 Evaluate side-chains 156 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 143 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 GLU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 96 CYS Chi-restraints excluded: chain R residue 134 GLN Chi-restraints excluded: chain R residue 158 LEU Chi-restraints excluded: chain R residue 159 VAL Chi-restraints excluded: chain R residue 341 ARG Chi-restraints excluded: chain R residue 345 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 2 optimal weight: 3.9990 chunk 90 optimal weight: 10.0000 chunk 47 optimal weight: 0.0870 chunk 21 optimal weight: 1.9990 chunk 71 optimal weight: 3.9990 chunk 18 optimal weight: 4.9990 chunk 5 optimal weight: 0.0270 chunk 35 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 85 optimal weight: 0.8980 chunk 93 optimal weight: 1.9990 overall best weight: 1.0020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 390 GLN B 268 ASN R 223 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.153706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.110490 restraints weight = 19677.976| |-----------------------------------------------------------------------------| r_work (start): 0.3404 rms_B_bonded: 2.77 r_work: 0.3291 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3298 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3298 r_free = 0.3298 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3298 r_free = 0.3298 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3298 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.3382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 9090 Z= 0.150 Angle : 0.540 7.000 12308 Z= 0.289 Chirality : 0.042 0.149 1362 Planarity : 0.004 0.041 1572 Dihedral : 4.767 81.302 1235 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 2.13 % Allowed : 19.19 % Favored : 78.68 % 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 aren not related in a simple way. whole: 1.13 (0.25), residues: 1115 helix: 2.54 (0.25), residues: 416 sheet: 0.62 (0.34), residues: 197 loop : -0.76 (0.27), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 380 TYR 0.021 0.002 TYR P 22 PHE 0.016 0.001 PHE A 212 TRP 0.034 0.002 TRP R 256 HIS 0.009 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00352 ( 9083) covalent geometry : angle 0.53693 (12294) SS BOND : bond 0.00322 ( 7) SS BOND : angle 1.79276 ( 14) hydrogen bonds : bond 0.03552 ( 426) hydrogen bonds : angle 4.01562 ( 1206) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 145 time to evaluate : 0.391 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 LYS cc_start: 0.8339 (mttp) cc_final: 0.7708 (mmtm) REVERT: A 343 ASP cc_start: 0.8109 (m-30) cc_final: 0.7909 (m-30) REVERT: A 380 ARG cc_start: 0.7946 (ttm-80) cc_final: 0.7248 (ttp80) REVERT: G 17 GLU cc_start: 0.7809 (tt0) cc_final: 0.7546 (tm-30) REVERT: G 42 GLU cc_start: 0.7870 (mt-10) cc_final: 0.7363 (mm-30) REVERT: R 42 MET cc_start: 0.8103 (mpp) cc_final: 0.6611 (ppp) REVERT: R 44 GLU cc_start: 0.6650 (pm20) cc_final: 0.6044 (pm20) REVERT: R 134 GLN cc_start: 0.8314 (OUTLIER) cc_final: 0.8069 (pm20) REVERT: R 158 LEU cc_start: 0.7697 (OUTLIER) cc_final: 0.7342 (mm) REVERT: R 252 ARG cc_start: 0.7316 (tpt170) cc_final: 0.6304 (tpm170) REVERT: R 344 LEU cc_start: 0.8423 (tp) cc_final: 0.8169 (mm) REVERT: R 367 GLU cc_start: 0.6315 (mp0) cc_final: 0.4811 (mm-30) outliers start: 20 outliers final: 15 residues processed: 158 average time/residue: 0.7705 time to fit residues: 128.3009 Evaluate side-chains 154 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 137 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 GLU Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 96 CYS Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain R residue 134 GLN Chi-restraints excluded: chain R residue 158 LEU Chi-restraints excluded: chain R residue 159 VAL Chi-restraints excluded: chain R residue 341 ARG Chi-restraints excluded: chain R residue 345 LEU Chi-restraints excluded: chain R residue 368 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 32 optimal weight: 0.0010 chunk 82 optimal weight: 6.9990 chunk 33 optimal weight: 1.9990 chunk 39 optimal weight: 0.9980 chunk 13 optimal weight: 0.7980 chunk 96 optimal weight: 0.9980 chunk 21 optimal weight: 0.9980 chunk 87 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 64 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 overall best weight: 0.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 390 GLN B 268 ASN R 223 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.154461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.110588 restraints weight = 21011.963| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 2.90 r_work: 0.3290 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3297 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3297 r_free = 0.3297 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3297 r_free = 0.3297 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3297 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.3490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9090 Z= 0.127 Angle : 0.528 6.910 12308 Z= 0.282 Chirality : 0.041 0.149 1362 Planarity : 0.003 0.040 1572 Dihedral : 4.744 81.259 1235 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 2.35 % Allowed : 19.40 % Favored : 78.25 % 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 aren not related in a simple way. whole: 1.16 (0.25), residues: 1115 helix: 2.56 (0.25), residues: 416 sheet: 0.58 (0.34), residues: 197 loop : -0.73 (0.27), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 380 TYR 0.020 0.001 TYR R 254 PHE 0.015 0.001 PHE A 212 TRP 0.041 0.002 TRP R 256 HIS 0.009 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00295 ( 9083) covalent geometry : angle 0.52583 (12294) SS BOND : bond 0.00212 ( 7) SS BOND : angle 1.36965 ( 14) hydrogen bonds : bond 0.03444 ( 426) hydrogen bonds : angle 3.98740 ( 1206) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 142 time to evaluate : 0.389 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 58 LYS cc_start: 0.8341 (mttp) cc_final: 0.7696 (mmtm) REVERT: A 343 ASP cc_start: 0.8115 (m-30) cc_final: 0.7913 (m-30) REVERT: A 380 ARG cc_start: 0.7934 (ttm-80) cc_final: 0.7222 (ttp80) REVERT: G 17 GLU cc_start: 0.7823 (tt0) cc_final: 0.7528 (tm-30) REVERT: G 42 GLU cc_start: 0.7864 (mt-10) cc_final: 0.7360 (mm-30) REVERT: N 82 GLN cc_start: 0.7823 (tp40) cc_final: 0.7591 (tp40) REVERT: N 96 CYS cc_start: 0.8399 (OUTLIER) cc_final: 0.7959 (p) REVERT: P 21 LYS cc_start: 0.8941 (ttpp) cc_final: 0.8728 (tmmm) REVERT: R 42 MET cc_start: 0.8101 (mpp) cc_final: 0.6623 (ppp) REVERT: R 44 GLU cc_start: 0.6687 (pm20) cc_final: 0.6065 (pm20) REVERT: R 134 GLN cc_start: 0.8332 (OUTLIER) cc_final: 0.8083 (pm20) REVERT: R 158 LEU cc_start: 0.7654 (OUTLIER) cc_final: 0.7338 (mm) REVERT: R 252 ARG cc_start: 0.7219 (tpt170) cc_final: 0.6104 (tpm170) REVERT: R 344 LEU cc_start: 0.8394 (tp) cc_final: 0.8150 (mm) REVERT: R 356 MET cc_start: 0.8120 (ttm) cc_final: 0.7734 (ttm) REVERT: R 357 PHE cc_start: 0.8416 (m-80) cc_final: 0.7873 (m-80) REVERT: R 367 GLU cc_start: 0.6440 (mp0) cc_final: 0.4813 (mm-30) outliers start: 22 outliers final: 12 residues processed: 155 average time/residue: 0.7393 time to fit residues: 120.7038 Evaluate side-chains 153 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 138 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 GLU Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 96 CYS Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain R residue 134 GLN Chi-restraints excluded: chain R residue 158 LEU Chi-restraints excluded: chain R residue 159 VAL Chi-restraints excluded: chain R residue 341 ARG Chi-restraints excluded: chain R residue 345 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 56 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 96 optimal weight: 0.7980 chunk 51 optimal weight: 0.9990 chunk 91 optimal weight: 0.7980 chunk 55 optimal weight: 3.9990 chunk 102 optimal weight: 10.0000 chunk 43 optimal weight: 0.9990 chunk 4 optimal weight: 0.0870 chunk 94 optimal weight: 5.9990 chunk 24 optimal weight: 0.3980 overall best weight: 0.6160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 268 ASN R 223 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.154812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.109658 restraints weight = 31003.346| |-----------------------------------------------------------------------------| r_work (start): 0.3386 rms_B_bonded: 3.48 r_work: 0.3257 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3270 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3270 r_free = 0.3270 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3270 r_free = 0.3270 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3270 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.3567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9090 Z= 0.117 Angle : 0.509 6.524 12308 Z= 0.274 Chirality : 0.041 0.148 1362 Planarity : 0.004 0.043 1572 Dihedral : 4.686 82.133 1235 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 2.35 % Allowed : 20.04 % Favored : 77.61 % 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 aren not related in a simple way. whole: 1.19 (0.25), residues: 1115 helix: 2.61 (0.25), residues: 415 sheet: 0.61 (0.34), residues: 201 loop : -0.74 (0.27), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG P 12 TYR 0.023 0.001 TYR P 22 PHE 0.017 0.001 PHE A 212 TRP 0.042 0.001 TRP R 256 HIS 0.006 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00269 ( 9083) covalent geometry : angle 0.50777 (12294) SS BOND : bond 0.00187 ( 7) SS BOND : angle 1.16865 ( 14) hydrogen bonds : bond 0.03347 ( 426) hydrogen bonds : angle 3.94615 ( 1206) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 138 time to evaluate : 0.340 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 58 LYS cc_start: 0.8323 (mttp) cc_final: 0.7678 (mmtm) REVERT: A 343 ASP cc_start: 0.8175 (m-30) cc_final: 0.7968 (m-30) REVERT: A 380 ARG cc_start: 0.7989 (ttm-80) cc_final: 0.7271 (ttp80) REVERT: G 17 GLU cc_start: 0.7848 (tt0) cc_final: 0.7539 (tm-30) REVERT: G 42 GLU cc_start: 0.7891 (mt-10) cc_final: 0.7352 (mm-30) REVERT: N 82 GLN cc_start: 0.7823 (tp40) cc_final: 0.7572 (tp40) REVERT: N 96 CYS cc_start: 0.8486 (OUTLIER) cc_final: 0.8040 (p) REVERT: P 21 LYS cc_start: 0.8942 (ttpp) cc_final: 0.8735 (tmmm) REVERT: R 42 MET cc_start: 0.8100 (mpp) cc_final: 0.6612 (ppp) REVERT: R 44 GLU cc_start: 0.6690 (pm20) cc_final: 0.6124 (pm20) REVERT: R 134 GLN cc_start: 0.8351 (OUTLIER) cc_final: 0.8124 (pm20) REVERT: R 252 ARG cc_start: 0.7106 (tpt170) cc_final: 0.5961 (tpm170) REVERT: R 344 LEU cc_start: 0.8435 (tp) cc_final: 0.8146 (mm) REVERT: R 367 GLU cc_start: 0.6407 (mp0) cc_final: 0.4743 (mm-30) outliers start: 22 outliers final: 13 residues processed: 152 average time/residue: 0.6662 time to fit residues: 106.7066 Evaluate side-chains 151 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 136 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 GLU Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 96 CYS Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain R residue 134 GLN Chi-restraints excluded: chain R residue 159 VAL Chi-restraints excluded: chain R residue 341 ARG Chi-restraints excluded: chain R residue 345 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 37 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 60 optimal weight: 0.3980 chunk 107 optimal weight: 4.9990 chunk 90 optimal weight: 3.9990 chunk 79 optimal weight: 2.9990 chunk 55 optimal weight: 4.9990 chunk 34 optimal weight: 3.9990 chunk 93 optimal weight: 1.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 268 ASN N 82 GLN R 178 HIS R 223 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.152324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.105196 restraints weight = 19241.023| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 2.95 r_work: 0.3195 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3204 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3204 r_free = 0.3204 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3204 r_free = 0.3204 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3204 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.3806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 9090 Z= 0.173 Angle : 0.563 6.913 12308 Z= 0.303 Chirality : 0.043 0.151 1362 Planarity : 0.004 0.041 1572 Dihedral : 4.911 80.506 1235 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 2.13 % Allowed : 20.47 % Favored : 77.40 % 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 aren not related in a simple way. whole: 0.95 (0.25), residues: 1115 helix: 2.32 (0.25), residues: 423 sheet: 0.23 (0.33), residues: 221 loop : -0.74 (0.28), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 380 TYR 0.019 0.002 TYR R 146 PHE 0.018 0.002 PHE A 212 TRP 0.045 0.002 TRP R 256 HIS 0.009 0.002 HIS B 62 Details of bonding type rmsd covalent geometry : bond 0.00410 ( 9083) covalent geometry : angle 0.56218 (12294) SS BOND : bond 0.00235 ( 7) SS BOND : angle 1.23327 ( 14) hydrogen bonds : bond 0.03848 ( 426) hydrogen bonds : angle 4.12980 ( 1206) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 141 time to evaluate : 0.375 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 58 LYS cc_start: 0.8291 (mttp) cc_final: 0.7674 (mmtm) REVERT: A 343 ASP cc_start: 0.8110 (m-30) cc_final: 0.7904 (m-30) REVERT: A 380 ARG cc_start: 0.7930 (ttm-80) cc_final: 0.7223 (ttp80) REVERT: G 17 GLU cc_start: 0.7807 (tt0) cc_final: 0.7484 (tm-30) REVERT: G 42 GLU cc_start: 0.7924 (mt-10) cc_final: 0.7372 (mm-30) REVERT: P 12 ARG cc_start: 0.8105 (mtt90) cc_final: 0.7869 (mtt-85) REVERT: R 42 MET cc_start: 0.8109 (mpp) cc_final: 0.6643 (ppp) REVERT: R 134 GLN cc_start: 0.8352 (OUTLIER) cc_final: 0.8147 (pm20) REVERT: R 344 LEU cc_start: 0.8482 (tp) cc_final: 0.8219 (mm) REVERT: R 367 GLU cc_start: 0.6507 (mp0) cc_final: 0.4827 (mm-30) outliers start: 20 outliers final: 13 residues processed: 153 average time/residue: 0.6960 time to fit residues: 112.4165 Evaluate side-chains 150 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 136 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 GLU Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 96 CYS Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain R residue 134 GLN Chi-restraints excluded: chain R residue 159 VAL Chi-restraints excluded: chain R residue 345 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 38 optimal weight: 0.6980 chunk 48 optimal weight: 2.9990 chunk 79 optimal weight: 0.5980 chunk 51 optimal weight: 0.0170 chunk 82 optimal weight: 0.0170 chunk 92 optimal weight: 1.9990 chunk 63 optimal weight: 0.0870 chunk 7 optimal weight: 0.8980 chunk 3 optimal weight: 0.4980 chunk 97 optimal weight: 1.9990 chunk 57 optimal weight: 0.8980 overall best weight: 0.2434 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 295 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.157042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.108063 restraints weight = 30421.480| |-----------------------------------------------------------------------------| r_work (start): 0.3369 rms_B_bonded: 3.74 r_work: 0.3223 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3228 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3228 r_free = 0.3228 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3228 r_free = 0.3228 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3228 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.3716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 9090 Z= 0.103 Angle : 0.513 7.192 12308 Z= 0.278 Chirality : 0.041 0.153 1362 Planarity : 0.003 0.039 1572 Dihedral : 4.660 80.107 1235 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.71 % Allowed : 21.22 % Favored : 77.08 % 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 aren not related in a simple way. whole: 1.15 (0.25), residues: 1115 helix: 2.55 (0.25), residues: 416 sheet: 0.56 (0.35), residues: 201 loop : -0.73 (0.27), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 380 TYR 0.023 0.001 TYR P 22 PHE 0.016 0.001 PHE A 212 TRP 0.049 0.002 TRP R 256 HIS 0.004 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00230 ( 9083) covalent geometry : angle 0.51211 (12294) SS BOND : bond 0.00179 ( 7) SS BOND : angle 1.06116 ( 14) hydrogen bonds : bond 0.03233 ( 426) hydrogen bonds : angle 3.96808 ( 1206) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4426.41 seconds wall clock time: 76 minutes 3.17 seconds (4563.17 seconds total)