Starting phenix.real_space_refine on Thu Mar 13 12:15:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8e3z_27874/03_2025/8e3z_27874.cif Found real_map, /net/cci-nas-00/data/ceres_data/8e3z_27874/03_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_27874/03_2025/8e3z_27874.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8e3z_27874/03_2025/8e3z_27874.map" model { file = "/net/cci-nas-00/data/ceres_data/8e3z_27874/03_2025/8e3z_27874.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8e3z_27874/03_2025/8e3z_27874.cif" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: {'GLN:plan1': 3, 'HIS:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 2, 'ASP:plan': 1, 'GLU:plan': 6, 'ARG:plan': 2} 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: 6.67, per 1000 atoms: 0.75 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: 2.87 Conformation dependent library (CDL) restraints added in 1.2 seconds 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: 0.90 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: 2.45 Time building geometry restraints manager: 2.73 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: 1.400 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: 0.010 Extract box with map and model: 0.440 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 24.830 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.040 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:12.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.970 ------------------------------------------------------------------------------- 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 9083 Z= 0.197 Angle : 0.588 7.466 12294 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 : 7.18 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.013 0.001 TRP B 82 HIS 0.003 0.001 HIS A 357 PHE 0.015 0.001 PHE B 335 TYR 0.012 0.001 TYR B 59 ARG 0.009 0.000 ARG A 38 *********************** 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 : 0.957 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: 0.7580 (m-30) REVERT: P 11 THR cc_start: 0.8235 (t) cc_final: 0.7966 (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: 0.6616 (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: 1.2760 time to fit residues: 303.7838 Evaluate side-chains 140 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 140 time to evaluate : 1.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 0.5980 chunk 83 optimal weight: 0.7980 chunk 46 optimal weight: 5.9990 chunk 28 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 44 optimal weight: 4.9990 chunk 86 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 52 optimal weight: 0.9990 chunk 64 optimal weight: 3.9990 chunk 99 optimal weight: 3.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- 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 44 GLN B 125 ASN B 156 GLN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 295 ASN N 53 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.156244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.110852 restraints weight = 16796.121| |-----------------------------------------------------------------------------| r_work (start): 0.3408 rms_B_bonded: 2.72 r_work: 0.3281 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3287 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3287 r_free = 0.3287 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3287 r_free = 0.3287 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3287 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.2522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9083 Z= 0.284 Angle : 0.588 6.253 12294 Z= 0.314 Chirality : 0.044 0.170 1362 Planarity : 0.004 0.044 1572 Dihedral : 4.840 81.572 1235 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 2.45 % Allowed : 12.26 % Favored : 85.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.25), residues: 1115 helix: 2.24 (0.25), residues: 424 sheet: 0.61 (0.34), residues: 213 loop : -0.69 (0.27), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP R 232 HIS 0.013 0.002 HIS A 357 PHE 0.016 0.002 PHE N 108 TYR 0.024 0.002 TYR R 146 ARG 0.011 0.001 ARG A 283 *********************** 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 179 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 156 time to evaluate : 1.018 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 GLU cc_start: 0.7456 (tp30) cc_final: 0.7170 (tp30) REVERT: A 232 ARG cc_start: 0.8789 (ttp-110) cc_final: 0.8466 (ptp-170) REVERT: A 311 TYR cc_start: 0.6890 (m-80) cc_final: 0.6378 (m-80) REVERT: A 343 ASP cc_start: 0.8092 (m-30) cc_final: 0.7800 (m-30) REVERT: B 267 ASP cc_start: 0.8935 (m-30) cc_final: 0.8731 (m-30) REVERT: N 76 LYS cc_start: 0.8639 (mtpp) cc_final: 0.8403 (mtmm) REVERT: N 77 ASN cc_start: 0.8815 (m-40) cc_final: 0.8583 (m-40) REVERT: P 3 ASP cc_start: 0.8582 (m-30) cc_final: 0.8148 (m-30) REVERT: P 11 THR cc_start: 0.8683 (t) cc_final: 0.8358 (p) REVERT: R 42 MET cc_start: 0.8243 (mpp) cc_final: 0.6860 (ppp) REVERT: R 252 ARG cc_start: 0.7562 (tpt170) cc_final: 0.6585 (tpm170) REVERT: R 254 TYR cc_start: 0.7306 (m-80) cc_final: 0.6632 (m-80) REVERT: R 261 ILE cc_start: 0.8515 (tt) cc_final: 0.8274 (tp) outliers start: 23 outliers final: 11 residues processed: 173 average time/residue: 1.4461 time to fit residues: 264.3343 Evaluate side-chains 153 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 142 time to evaluate : 1.064 ------------------------------------------------------------------------------- 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 G residue 16 VAL Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain P residue 19 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 57 optimal weight: 1.9990 chunk 30 optimal weight: 3.9990 chunk 78 optimal weight: 7.9990 chunk 14 optimal weight: 2.9990 chunk 56 optimal weight: 0.9990 chunk 106 optimal weight: 4.9990 chunk 81 optimal weight: 7.9990 chunk 102 optimal weight: 0.0770 chunk 107 optimal weight: 0.8980 chunk 6 optimal weight: 3.9990 chunk 90 optimal weight: 10.0000 overall best weight: 1.3944 ------------------------------------------------------------------------------- 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 R 223 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.152660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.107024 restraints weight = 25781.993| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 3.25 r_work: 0.3227 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3237 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3237 r_free = 0.3237 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3237 r_free = 0.3237 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3237 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.3163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9083 Z= 0.291 Angle : 0.564 6.164 12294 Z= 0.302 Chirality : 0.043 0.152 1362 Planarity : 0.004 0.040 1572 Dihedral : 4.892 80.268 1235 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 3.41 % Allowed : 14.61 % Favored : 81.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.25), residues: 1115 helix: 2.20 (0.25), residues: 421 sheet: 0.42 (0.34), residues: 200 loop : -0.81 (0.27), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP R 232 HIS 0.011 0.002 HIS B 62 PHE 0.017 0.002 PHE N 108 TYR 0.022 0.002 TYR R 146 ARG 0.009 0.001 ARG A 283 *********************** 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 186 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 154 time to evaluate : 0.925 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 GLU cc_start: 0.7568 (tp30) cc_final: 0.7267 (tp30) REVERT: A 311 TYR cc_start: 0.7005 (m-80) cc_final: 0.6416 (m-80) REVERT: A 343 ASP cc_start: 0.8097 (m-30) cc_final: 0.7808 (m-30) REVERT: B 10 GLU cc_start: 0.8468 (OUTLIER) cc_final: 0.8249 (pt0) REVERT: B 267 ASP cc_start: 0.9001 (m-30) cc_final: 0.8790 (m-30) REVERT: G 17 GLU cc_start: 0.7794 (tt0) cc_final: 0.7507 (tm-30) REVERT: G 42 GLU cc_start: 0.7952 (mt-10) cc_final: 0.7340 (mm-30) REVERT: N 12 VAL cc_start: 0.8402 (m) cc_final: 0.8122 (p) REVERT: N 77 ASN cc_start: 0.8805 (m-40) cc_final: 0.8599 (m-40) REVERT: P 3 ASP cc_start: 0.8640 (m-30) cc_final: 0.8298 (m-30) REVERT: P 12 ARG cc_start: 0.8116 (mtt90) cc_final: 0.7793 (mtt-85) REVERT: R 42 MET cc_start: 0.8119 (mpp) cc_final: 0.6679 (ppp) REVERT: R 134 GLN cc_start: 0.8453 (pt0) cc_final: 0.8114 (pm20) REVERT: R 252 ARG cc_start: 0.7709 (tpt170) cc_final: 0.6721 (tpm170) REVERT: R 254 TYR cc_start: 0.7170 (m-80) cc_final: 0.6913 (m-80) REVERT: R 261 ILE cc_start: 0.8671 (tt) cc_final: 0.8433 (tp) REVERT: R 344 LEU cc_start: 0.8378 (tp) cc_final: 0.8138 (mm) outliers start: 32 outliers final: 17 residues processed: 175 average time/residue: 1.3890 time to fit residues: 257.1505 Evaluate side-chains 157 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 139 time to evaluate : 0.965 ------------------------------------------------------------------------------- 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 10 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 321 THR Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 64 VAL 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 158 LEU Chi-restraints excluded: chain R residue 159 VAL Chi-restraints excluded: chain R residue 183 ILE Chi-restraints excluded: chain R residue 260 LEU 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 45 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 107 optimal weight: 0.8980 chunk 101 optimal weight: 0.8980 chunk 11 optimal weight: 0.9990 chunk 97 optimal weight: 3.9990 chunk 79 optimal weight: 0.8980 chunk 54 optimal weight: 2.9990 chunk 12 optimal weight: 0.5980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 259 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 = 0.3945 r_free = 0.3945 target = 0.152879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.106446 restraints weight = 23605.293| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 3.18 r_work: 0.3201 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3212 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3212 r_free = 0.3212 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3212 r_free = 0.3212 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3212 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.3295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9083 Z= 0.211 Angle : 0.517 6.096 12294 Z= 0.279 Chirality : 0.042 0.167 1362 Planarity : 0.004 0.059 1572 Dihedral : 4.789 80.914 1235 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 2.45 % Allowed : 17.80 % Favored : 79.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.25), residues: 1115 helix: 2.43 (0.25), residues: 415 sheet: 0.49 (0.34), residues: 198 loop : -0.77 (0.27), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP R 256 HIS 0.008 0.001 HIS A 220 PHE 0.016 0.001 PHE A 212 TYR 0.018 0.001 TYR R 146 ARG 0.007 0.001 ARG A 317 *********************** 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 168 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 145 time to evaluate : 1.088 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 GLU cc_start: 0.7475 (tp30) cc_final: 0.7243 (tp30) REVERT: A 58 LYS cc_start: 0.8395 (mttp) cc_final: 0.7744 (mmtm) REVERT: A 311 TYR cc_start: 0.6967 (m-80) cc_final: 0.6371 (m-80) REVERT: A 343 ASP cc_start: 0.8099 (m-30) cc_final: 0.7785 (m-30) REVERT: G 17 GLU cc_start: 0.7788 (tt0) cc_final: 0.7466 (tm-30) REVERT: G 42 GLU cc_start: 0.7938 (mt-10) cc_final: 0.7350 (mm-30) REVERT: P 3 ASP cc_start: 0.8566 (m-30) cc_final: 0.8193 (m-30) REVERT: R 42 MET cc_start: 0.8158 (mpp) cc_final: 0.6780 (ppp) REVERT: R 134 GLN cc_start: 0.8443 (pt0) cc_final: 0.8125 (pm20) REVERT: R 158 LEU cc_start: 0.7714 (OUTLIER) cc_final: 0.7382 (mm) REVERT: R 252 ARG cc_start: 0.7738 (tpt170) cc_final: 0.6651 (tpm170) REVERT: R 261 ILE cc_start: 0.8622 (tt) cc_final: 0.8400 (tp) REVERT: R 344 LEU cc_start: 0.8402 (tp) cc_final: 0.8155 (mm) REVERT: R 365 LYS cc_start: 0.8160 (pmmt) cc_final: 0.7102 (tppt) outliers start: 23 outliers final: 14 residues processed: 160 average time/residue: 1.3838 time to fit residues: 234.5752 Evaluate side-chains 157 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 142 time to evaluate : 1.020 ------------------------------------------------------------------------------- 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 76 ASP 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 110 VAL Chi-restraints excluded: chain R residue 158 LEU Chi-restraints excluded: chain R residue 159 VAL Chi-restraints excluded: chain R residue 179 MET Chi-restraints excluded: chain R residue 183 ILE 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 98 optimal weight: 8.9990 chunk 30 optimal weight: 5.9990 chunk 32 optimal weight: 0.9990 chunk 66 optimal weight: 5.9990 chunk 63 optimal weight: 0.6980 chunk 60 optimal weight: 0.0970 chunk 34 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 43 optimal weight: 0.8980 chunk 68 optimal weight: 7.9990 chunk 53 optimal weight: 4.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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 = 0.3943 r_free = 0.3943 target = 0.152893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.105871 restraints weight = 20122.719| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 3.01 r_work: 0.3203 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3210 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3210 r_free = 0.3210 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3210 r_free = 0.3210 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3210 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.3413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9083 Z= 0.222 Angle : 0.514 6.082 12294 Z= 0.278 Chirality : 0.042 0.149 1362 Planarity : 0.004 0.051 1572 Dihedral : 4.785 80.924 1235 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.25), residues: 1115 helix: 2.31 (0.25), residues: 421 sheet: 0.44 (0.34), residues: 199 loop : -0.84 (0.26), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP R 256 HIS 0.008 0.001 HIS A 220 PHE 0.017 0.001 PHE A 212 TYR 0.020 0.002 TYR P 22 ARG 0.007 0.000 ARG A 317 *********************** 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: 23 poor density : 143 time to evaluate : 1.023 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 27 GLU cc_start: 0.7422 (tp30) cc_final: 0.7214 (tp30) REVERT: A 58 LYS cc_start: 0.8402 (mttp) cc_final: 0.7756 (mmtm) REVERT: A 311 TYR cc_start: 0.6994 (m-80) cc_final: 0.6395 (m-80) REVERT: G 17 GLU cc_start: 0.7793 (tt0) cc_final: 0.7473 (tm-30) REVERT: G 42 GLU cc_start: 0.7889 (mt-10) cc_final: 0.7321 (mm-30) REVERT: R 42 MET cc_start: 0.8107 (mpp) cc_final: 0.6662 (ppp) REVERT: R 44 GLU cc_start: 0.6629 (pm20) cc_final: 0.6042 (pm20) REVERT: R 134 GLN cc_start: 0.8422 (pt0) cc_final: 0.8103 (pm20) REVERT: R 158 LEU cc_start: 0.7703 (OUTLIER) cc_final: 0.7354 (mm) REVERT: R 252 ARG cc_start: 0.7672 (tpt170) cc_final: 0.6596 (tpm170) REVERT: R 261 ILE cc_start: 0.8629 (tt) cc_final: 0.8409 (tp) REVERT: R 344 LEU cc_start: 0.8465 (tp) cc_final: 0.8179 (mm) REVERT: R 357 PHE cc_start: 0.8082 (m-10) cc_final: 0.7860 (m-80) outliers start: 23 outliers final: 17 residues processed: 161 average time/residue: 1.4087 time to fit residues: 239.8604 Evaluate side-chains 159 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 141 time to evaluate : 0.973 ------------------------------------------------------------------------------- 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 76 ASP 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 158 LEU Chi-restraints excluded: chain R residue 159 VAL Chi-restraints excluded: chain R residue 179 MET Chi-restraints excluded: chain R residue 183 ILE Chi-restraints excluded: chain R residue 260 LEU Chi-restraints excluded: chain R residue 341 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 14 optimal weight: 8.9990 chunk 9 optimal weight: 0.7980 chunk 7 optimal weight: 0.9980 chunk 24 optimal weight: 2.9990 chunk 12 optimal weight: 0.8980 chunk 109 optimal weight: 0.9980 chunk 96 optimal weight: 0.9990 chunk 97 optimal weight: 3.9990 chunk 62 optimal weight: 0.7980 chunk 71 optimal weight: 3.9990 chunk 19 optimal weight: 0.0070 overall best weight: 0.6998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 223 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.153955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.106074 restraints weight = 23775.313| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 3.29 r_work: 0.3202 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3207 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3207 r_free = 0.3207 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3207 r_free = 0.3207 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3207 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.3459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 9083 Z= 0.187 Angle : 0.496 5.907 12294 Z= 0.268 Chirality : 0.041 0.161 1362 Planarity : 0.004 0.041 1572 Dihedral : 4.721 80.920 1235 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 2.77 % Allowed : 18.87 % Favored : 78.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.25), residues: 1115 helix: 2.50 (0.25), residues: 415 sheet: 0.51 (0.34), residues: 198 loop : -0.77 (0.27), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP R 256 HIS 0.008 0.001 HIS A 220 PHE 0.016 0.001 PHE A 212 TYR 0.017 0.001 TYR R 146 ARG 0.006 0.000 ARG A 317 *********************** 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 174 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 148 time to evaluate : 0.974 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 LYS cc_start: 0.8378 (mttp) cc_final: 0.7740 (mmtm) REVERT: A 229 ASP cc_start: 0.8327 (p0) cc_final: 0.8123 (p0) REVERT: A 311 TYR cc_start: 0.7004 (m-80) cc_final: 0.6400 (m-80) REVERT: A 343 ASP cc_start: 0.8230 (m-30) cc_final: 0.7934 (m-30) REVERT: G 17 GLU cc_start: 0.7806 (tt0) cc_final: 0.7484 (tm-30) REVERT: G 42 GLU cc_start: 0.7895 (mt-10) cc_final: 0.7313 (mm-30) REVERT: R 42 MET cc_start: 0.8147 (mpp) cc_final: 0.6712 (ppp) REVERT: R 158 LEU cc_start: 0.7678 (OUTLIER) cc_final: 0.7336 (mm) REVERT: R 252 ARG cc_start: 0.7656 (tpt170) cc_final: 0.6442 (tpm170) REVERT: R 261 ILE cc_start: 0.8607 (tt) cc_final: 0.8396 (tp) REVERT: R 344 LEU cc_start: 0.8470 (tp) cc_final: 0.8186 (mm) REVERT: R 357 PHE cc_start: 0.8128 (m-10) cc_final: 0.7913 (m-80) REVERT: R 365 LYS cc_start: 0.8209 (pmmt) cc_final: 0.7173 (tppt) REVERT: R 367 GLU cc_start: 0.6567 (mp0) cc_final: 0.5149 (mm-30) REVERT: R 398 GLU cc_start: 0.6594 (OUTLIER) cc_final: 0.6213 (tm-30) outliers start: 26 outliers final: 15 residues processed: 168 average time/residue: 1.8926 time to fit residues: 336.3005 Evaluate side-chains 153 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 136 time to evaluate : 1.236 ------------------------------------------------------------------------------- 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 76 ASP 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 158 LEU Chi-restraints excluded: chain R residue 159 VAL Chi-restraints excluded: chain R residue 183 ILE Chi-restraints excluded: chain R residue 341 ARG Chi-restraints excluded: chain R residue 398 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 29 optimal weight: 1.9990 chunk 88 optimal weight: 3.9990 chunk 66 optimal weight: 0.7980 chunk 12 optimal weight: 4.9990 chunk 6 optimal weight: 2.9990 chunk 92 optimal weight: 2.9990 chunk 58 optimal weight: 0.6980 chunk 108 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 chunk 27 optimal weight: 0.7980 chunk 73 optimal weight: 6.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 223 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.152728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.104038 restraints weight = 27119.100| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 3.48 r_work: 0.3167 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3173 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3173 r_free = 0.3173 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3173 r_free = 0.3173 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3173 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.3600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9083 Z= 0.246 Angle : 0.538 6.643 12294 Z= 0.289 Chirality : 0.042 0.151 1362 Planarity : 0.004 0.043 1572 Dihedral : 4.862 81.161 1235 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 2.88 % Allowed : 19.51 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.25), residues: 1115 helix: 2.34 (0.25), residues: 421 sheet: 0.47 (0.35), residues: 194 loop : -0.87 (0.26), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP R 256 HIS 0.009 0.001 HIS A 220 PHE 0.017 0.001 PHE A 212 TYR 0.021 0.002 TYR P 22 ARG 0.007 0.001 ARG A 380 *********************** 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 171 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 144 time to evaluate : 1.062 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 LYS cc_start: 0.8395 (mttp) cc_final: 0.7745 (mmtm) REVERT: A 311 TYR cc_start: 0.7029 (m-80) cc_final: 0.6422 (m-80) REVERT: A 343 ASP cc_start: 0.8275 (m-30) cc_final: 0.7991 (m-30) REVERT: A 380 ARG cc_start: 0.7911 (ttm-80) cc_final: 0.7249 (ttp80) REVERT: B 44 GLN cc_start: 0.8579 (mm110) cc_final: 0.8110 (mp10) REVERT: G 17 GLU cc_start: 0.7806 (tt0) cc_final: 0.7471 (tm-30) REVERT: G 42 GLU cc_start: 0.7923 (mt-10) cc_final: 0.7341 (mm-30) REVERT: N 77 ASN cc_start: 0.9026 (m-40) cc_final: 0.8824 (m-40) REVERT: R 42 MET cc_start: 0.8160 (mpp) cc_final: 0.6675 (ppp) REVERT: R 44 GLU cc_start: 0.7099 (pm20) cc_final: 0.6664 (pm20) REVERT: R 158 LEU cc_start: 0.7673 (OUTLIER) cc_final: 0.7319 (mm) REVERT: R 252 ARG cc_start: 0.7569 (tpt170) cc_final: 0.6345 (tpm170) REVERT: R 261 ILE cc_start: 0.8599 (tt) cc_final: 0.8386 (tp) REVERT: R 344 LEU cc_start: 0.8476 (tp) cc_final: 0.8199 (mm) REVERT: R 357 PHE cc_start: 0.8188 (m-10) cc_final: 0.7949 (m-80) REVERT: R 367 GLU cc_start: 0.6620 (mp0) cc_final: 0.5164 (mm-30) REVERT: R 398 GLU cc_start: 0.6561 (OUTLIER) cc_final: 0.6174 (tm-30) outliers start: 27 outliers final: 17 residues processed: 163 average time/residue: 1.5625 time to fit residues: 269.0747 Evaluate side-chains 157 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 138 time to evaluate : 0.979 ------------------------------------------------------------------------------- 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 76 ASP 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 P residue 19 VAL Chi-restraints excluded: chain R residue 158 LEU Chi-restraints excluded: chain R residue 159 VAL Chi-restraints excluded: chain R residue 179 MET Chi-restraints excluded: chain R residue 183 ILE Chi-restraints excluded: chain R residue 341 ARG Chi-restraints excluded: chain R residue 398 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 63 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.7980 chunk 93 optimal weight: 0.7980 chunk 102 optimal weight: 6.9990 chunk 33 optimal weight: 0.0770 chunk 101 optimal weight: 0.7980 chunk 12 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 overall best weight: 0.6940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 223 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.153726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.106993 restraints weight = 30380.760| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 3.57 r_work: 0.3225 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3243 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3243 r_free = 0.3243 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3243 r_free = 0.3243 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3243 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.3642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9083 Z= 0.193 Angle : 0.512 5.921 12294 Z= 0.277 Chirality : 0.041 0.149 1362 Planarity : 0.004 0.046 1572 Dihedral : 4.778 81.875 1235 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.13 % Allowed : 20.36 % Favored : 77.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.25), residues: 1115 helix: 2.52 (0.25), residues: 415 sheet: 0.49 (0.35), residues: 199 loop : -0.78 (0.27), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP R 256 HIS 0.008 0.001 HIS A 220 PHE 0.016 0.001 PHE A 212 TYR 0.017 0.001 TYR R 146 ARG 0.014 0.001 ARG A 232 *********************** 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 161 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 141 time to evaluate : 1.044 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 LYS cc_start: 0.8401 (mttp) cc_final: 0.7740 (mmtm) REVERT: A 343 ASP cc_start: 0.8286 (m-30) cc_final: 0.7973 (m-30) REVERT: A 380 ARG cc_start: 0.7891 (ttm-80) cc_final: 0.7206 (ttp80) REVERT: G 17 GLU cc_start: 0.7827 (tt0) cc_final: 0.7482 (tm-30) REVERT: G 42 GLU cc_start: 0.7903 (mt-10) cc_final: 0.7344 (mm-30) REVERT: P 12 ARG cc_start: 0.8151 (mtt90) cc_final: 0.7908 (mtt-85) REVERT: R 42 MET cc_start: 0.8177 (mpp) cc_final: 0.6635 (ppp) REVERT: R 44 GLU cc_start: 0.7085 (pm20) cc_final: 0.6607 (pm20) REVERT: R 261 ILE cc_start: 0.8586 (tt) cc_final: 0.8374 (tp) REVERT: R 344 LEU cc_start: 0.8439 (tp) cc_final: 0.8158 (mm) REVERT: R 357 PHE cc_start: 0.8178 (m-10) cc_final: 0.7930 (m-80) REVERT: R 367 GLU cc_start: 0.6489 (mp0) cc_final: 0.4955 (mm-30) REVERT: R 398 GLU cc_start: 0.6605 (OUTLIER) cc_final: 0.6275 (tm-30) outliers start: 20 outliers final: 14 residues processed: 155 average time/residue: 1.4482 time to fit residues: 237.7294 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 : 1.079 ------------------------------------------------------------------------------- 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 159 VAL Chi-restraints excluded: chain R residue 179 MET Chi-restraints excluded: chain R residue 183 ILE Chi-restraints excluded: chain R residue 341 ARG Chi-restraints excluded: chain R residue 398 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 103 optimal weight: 2.9990 chunk 65 optimal weight: 0.6980 chunk 42 optimal weight: 4.9990 chunk 0 optimal weight: 6.9990 chunk 64 optimal weight: 0.2980 chunk 71 optimal weight: 2.9990 chunk 59 optimal weight: 0.8980 chunk 3 optimal weight: 0.8980 chunk 61 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 390 GLN R 223 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.153456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.107586 restraints weight = 23351.662| |-----------------------------------------------------------------------------| r_work (start): 0.3369 rms_B_bonded: 3.16 r_work: 0.3246 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3267 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3267 r_free = 0.3267 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3267 r_free = 0.3267 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3267 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.3695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9083 Z= 0.200 Angle : 0.520 7.269 12294 Z= 0.281 Chirality : 0.041 0.152 1362 Planarity : 0.004 0.042 1572 Dihedral : 4.777 81.135 1235 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.03 % Allowed : 20.90 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.25), residues: 1115 helix: 2.53 (0.25), residues: 415 sheet: 0.52 (0.35), residues: 199 loop : -0.78 (0.27), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP R 256 HIS 0.010 0.001 HIS A 220 PHE 0.016 0.001 PHE A 212 TYR 0.023 0.002 TYR P 22 ARG 0.014 0.001 ARG A 232 *********************** 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 157 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 138 time to evaluate : 0.950 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 LYS cc_start: 0.8359 (mttp) cc_final: 0.7716 (mmtm) REVERT: A 343 ASP cc_start: 0.8267 (m-30) cc_final: 0.7955 (m-30) REVERT: A 380 ARG cc_start: 0.7863 (ttm-80) cc_final: 0.7183 (ttp80) REVERT: B 44 GLN cc_start: 0.8502 (mm110) cc_final: 0.7700 (mm110) REVERT: B 171 ILE cc_start: 0.8131 (mm) cc_final: 0.7931 (mm) REVERT: G 17 GLU cc_start: 0.7808 (tt0) cc_final: 0.7479 (tm-30) REVERT: G 42 GLU cc_start: 0.7867 (mt-10) cc_final: 0.7339 (mm-30) REVERT: P 12 ARG cc_start: 0.8123 (mtt90) cc_final: 0.7870 (mtt-85) REVERT: R 42 MET cc_start: 0.8215 (mpp) cc_final: 0.6666 (ppp) REVERT: R 344 LEU cc_start: 0.8442 (tp) cc_final: 0.8179 (mm) REVERT: R 357 PHE cc_start: 0.8185 (m-10) cc_final: 0.7935 (m-80) REVERT: R 367 GLU cc_start: 0.6470 (mp0) cc_final: 0.4991 (mm-30) REVERT: R 398 GLU cc_start: 0.6659 (OUTLIER) cc_final: 0.6311 (tm-30) outliers start: 19 outliers final: 16 residues processed: 152 average time/residue: 1.4776 time to fit residues: 237.6221 Evaluate side-chains 153 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 136 time to evaluate : 1.082 ------------------------------------------------------------------------------- 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 159 VAL Chi-restraints excluded: chain R residue 179 MET Chi-restraints excluded: chain R residue 183 ILE Chi-restraints excluded: chain R residue 341 ARG Chi-restraints excluded: chain R residue 368 VAL Chi-restraints excluded: chain R residue 398 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 42 optimal weight: 0.8980 chunk 74 optimal weight: 0.5980 chunk 17 optimal weight: 0.0370 chunk 32 optimal weight: 0.4980 chunk 87 optimal weight: 2.9990 chunk 52 optimal weight: 0.0370 chunk 91 optimal weight: 0.9980 chunk 43 optimal weight: 2.9990 chunk 58 optimal weight: 0.0670 chunk 35 optimal weight: 0.9990 chunk 61 optimal weight: 0.9990 overall best weight: 0.2474 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN B 295 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 = 0.3991 r_free = 0.3991 target = 0.157116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.110950 restraints weight = 16369.894| |-----------------------------------------------------------------------------| r_work (start): 0.3410 rms_B_bonded: 2.78 r_work: 0.3285 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3290 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3290 r_free = 0.3290 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3290 r_free = 0.3290 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3290 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.3649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 9083 Z= 0.145 Angle : 0.495 7.262 12294 Z= 0.267 Chirality : 0.040 0.159 1362 Planarity : 0.004 0.058 1572 Dihedral : 4.594 80.385 1235 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 1.49 % Allowed : 21.64 % Favored : 76.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.25), residues: 1115 helix: 2.61 (0.25), residues: 415 sheet: 0.56 (0.34), residues: 202 loop : -0.74 (0.27), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.001 TRP R 256 HIS 0.003 0.001 HIS A 357 PHE 0.015 0.001 PHE A 212 TYR 0.028 0.001 TYR R 254 ARG 0.014 0.001 ARG A 232 ********************** 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 158 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 144 time to evaluate : 0.958 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 LYS cc_start: 0.8327 (mttp) cc_final: 0.7675 (mmtm) REVERT: A 343 ASP cc_start: 0.8236 (m-30) cc_final: 0.7899 (m-30) REVERT: B 44 GLN cc_start: 0.8414 (mm110) cc_final: 0.8182 (mm-40) REVERT: G 17 GLU cc_start: 0.7806 (tt0) cc_final: 0.7484 (tm-30) REVERT: G 42 GLU cc_start: 0.7817 (mt-10) cc_final: 0.7297 (mm-30) REVERT: N 96 CYS cc_start: 0.8297 (OUTLIER) cc_final: 0.7958 (p) REVERT: R 42 MET cc_start: 0.8244 (mpp) cc_final: 0.6690 (ppp) REVERT: R 281 GLU cc_start: 0.7585 (mt-10) cc_final: 0.7071 (mp0) REVERT: R 344 LEU cc_start: 0.8417 (tp) cc_final: 0.8155 (mm) REVERT: R 357 PHE cc_start: 0.8144 (m-10) cc_final: 0.7906 (m-80) REVERT: R 367 GLU cc_start: 0.6475 (mp0) cc_final: 0.4981 (mm-30) REVERT: R 398 GLU cc_start: 0.6690 (OUTLIER) cc_final: 0.6434 (tm-30) outliers start: 14 outliers final: 11 residues processed: 153 average time/residue: 1.6079 time to fit residues: 260.1158 Evaluate side-chains 149 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 136 time to evaluate : 1.193 ------------------------------------------------------------------------------- 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 195 ASP 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 R residue 179 MET Chi-restraints excluded: chain R residue 183 ILE Chi-restraints excluded: chain R residue 290 ASN Chi-restraints excluded: chain R residue 341 ARG Chi-restraints excluded: chain R residue 398 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 61 optimal weight: 0.7980 chunk 47 optimal weight: 5.9990 chunk 37 optimal weight: 2.9990 chunk 63 optimal weight: 0.0770 chunk 59 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 chunk 2 optimal weight: 0.5980 chunk 30 optimal weight: 0.0970 chunk 99 optimal weight: 0.6980 chunk 8 optimal weight: 0.9990 chunk 46 optimal weight: 4.9990 overall best weight: 0.4536 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 390 GLN R 223 GLN R 380 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.156286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.109337 restraints weight = 19295.105| |-----------------------------------------------------------------------------| r_work (start): 0.3390 rms_B_bonded: 3.01 r_work: 0.3259 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3268 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3268 r_free = 0.3268 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3268 r_free = 0.3268 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3268 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.3627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 9083 Z= 0.166 Angle : 0.511 7.511 12294 Z= 0.274 Chirality : 0.041 0.152 1362 Planarity : 0.004 0.047 1572 Dihedral : 4.608 79.925 1235 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 1.60 % Allowed : 22.07 % Favored : 76.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.25), residues: 1115 helix: 2.58 (0.25), residues: 416 sheet: 0.59 (0.34), residues: 202 loop : -0.70 (0.28), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.001 TRP R 256 HIS 0.005 0.001 HIS A 220 PHE 0.015 0.001 PHE A 212 TYR 0.023 0.001 TYR P 22 ARG 0.014 0.001 ARG A 232 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8774.94 seconds wall clock time: 152 minutes 27.26 seconds (9147.26 seconds total)