Starting phenix.real_space_refine on Thu Feb 13 09:56:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8e3z_27874/02_2025/8e3z_27874.cif Found real_map, /net/cci-nas-00/data/ceres_data/8e3z_27874/02_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_27874/02_2025/8e3z_27874.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8e3z_27874/02_2025/8e3z_27874.map" model { file = "/net/cci-nas-00/data/ceres_data/8e3z_27874/02_2025/8e3z_27874.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8e3z_27874/02_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-5592/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: 5.97, per 1000 atoms: 0.67 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: 2.39 Conformation dependent library (CDL) restraints added in 1.3 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: 0.88 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: 2.51 Time building geometry restraints manager: 2.74 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: 1.340 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: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 23.260 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:12.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.300 ------------------------------------------------------------------------------- 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 : 0.946 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: 1.3448 time to fit residues: 320.1156 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 : 1.126 ------------------------------------------------------------------------------- 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 = 0.156235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.110846 restraints weight = 16795.611| |-----------------------------------------------------------------------------| r_work (start): 0.3408 rms_B_bonded: 2.72 r_work: 0.3280 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3289 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3289 r_free = 0.3289 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 = 0.3289 r_free = 0.3289 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3289 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.2524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9083 Z= 0.283 Angle : 0.588 6.267 12294 Z= 0.314 Chirality : 0.044 0.170 1362 Planarity : 0.004 0.044 1572 Dihedral : 4.840 81.565 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 : 1.023 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 GLU cc_start: 0.7461 (tp30) cc_final: 0.7176 (tp30) REVERT: A 232 ARG cc_start: 0.8790 (ttp-110) cc_final: 0.8468 (ptp-170) REVERT: A 311 TYR cc_start: 0.6881 (m-80) cc_final: 0.6372 (m-80) REVERT: A 343 ASP cc_start: 0.8090 (m-30) cc_final: 0.7792 (m-30) REVERT: B 267 ASP cc_start: 0.8931 (m-30) cc_final: 0.8727 (m-30) REVERT: N 76 LYS cc_start: 0.8640 (mtpp) cc_final: 0.8404 (mtmm) REVERT: N 77 ASN cc_start: 0.8815 (m-40) cc_final: 0.8583 (m-40) REVERT: P 3 ASP cc_start: 0.8574 (m-30) cc_final: 0.8138 (m-30) REVERT: P 11 THR cc_start: 0.8663 (t) cc_final: 0.8338 (p) REVERT: R 42 MET cc_start: 0.8243 (mpp) cc_final: 0.6860 (ppp) REVERT: R 252 ARG cc_start: 0.7563 (tpt170) cc_final: 0.6585 (tpm170) REVERT: R 254 TYR cc_start: 0.7296 (m-80) cc_final: 0.6618 (m-80) REVERT: R 261 ILE cc_start: 0.8513 (tt) cc_final: 0.8272 (tp) outliers start: 23 outliers final: 11 residues processed: 173 average time/residue: 1.4676 time to fit residues: 268.7944 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 : 0.984 ------------------------------------------------------------------------------- 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: 0.1980 chunk 30 optimal weight: 3.9990 chunk 78 optimal weight: 5.9990 chunk 14 optimal weight: 1.9990 chunk 56 optimal weight: 0.8980 chunk 106 optimal weight: 3.9990 chunk 81 optimal weight: 20.0000 chunk 102 optimal weight: 0.0980 chunk 107 optimal weight: 0.7980 chunk 6 optimal weight: 3.9990 chunk 90 optimal weight: 10.0000 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 = 0.3989 r_free = 0.3989 target = 0.155996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.111497 restraints weight = 26240.787| |-----------------------------------------------------------------------------| r_work (start): 0.3419 rms_B_bonded: 3.26 r_work: 0.3293 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3296 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3296 r_free = 0.3296 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 = 0.3296 r_free = 0.3296 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3296 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.2778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9083 Z= 0.203 Angle : 0.511 6.303 12294 Z= 0.273 Chirality : 0.041 0.150 1362 Planarity : 0.004 0.039 1572 Dihedral : 4.629 80.787 1235 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 2.88 % Allowed : 14.71 % Favored : 82.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.14 (0.25), residues: 1115 helix: 2.45 (0.25), residues: 416 sheet: 0.77 (0.34), residues: 195 loop : -0.74 (0.27), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP R 232 HIS 0.006 0.001 HIS A 357 PHE 0.016 0.001 PHE A 212 TYR 0.019 0.001 TYR R 146 ARG 0.008 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 176 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 149 time to evaluate : 1.017 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 GLU cc_start: 0.7496 (tp30) cc_final: 0.7215 (tp30) REVERT: A 232 ARG cc_start: 0.8757 (ttp-110) cc_final: 0.8460 (ptp-170) REVERT: A 311 TYR cc_start: 0.6959 (m-80) cc_final: 0.6427 (m-80) REVERT: A 343 ASP cc_start: 0.8107 (m-30) cc_final: 0.7779 (m-30) REVERT: B 267 ASP cc_start: 0.8976 (m-30) cc_final: 0.8759 (m-30) REVERT: G 17 GLU cc_start: 0.7807 (tt0) cc_final: 0.7513 (tm-30) REVERT: G 42 GLU cc_start: 0.7885 (mt-10) cc_final: 0.7254 (mm-30) REVERT: N 77 ASN cc_start: 0.8793 (m-40) cc_final: 0.8569 (m-40) REVERT: P 3 ASP cc_start: 0.8611 (m-30) cc_final: 0.8269 (m-30) REVERT: R 42 MET cc_start: 0.8133 (mpp) cc_final: 0.6702 (ppp) REVERT: R 252 ARG cc_start: 0.7628 (tpt170) cc_final: 0.6616 (tpm170) REVERT: R 253 LYS cc_start: 0.7865 (tmtp) cc_final: 0.7587 (tmmm) REVERT: R 254 TYR cc_start: 0.7170 (m-80) cc_final: 0.6946 (m-80) REVERT: R 261 ILE cc_start: 0.8590 (tt) cc_final: 0.8353 (tp) outliers start: 27 outliers final: 13 residues processed: 167 average time/residue: 1.4596 time to fit residues: 257.8483 Evaluate side-chains 151 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 138 time to evaluate : 1.037 ------------------------------------------------------------------------------- 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 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 110 VAL Chi-restraints excluded: chain N residue 126 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 45 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 34 optimal weight: 0.7980 chunk 21 optimal weight: 1.9990 chunk 107 optimal weight: 3.9990 chunk 101 optimal weight: 0.9980 chunk 11 optimal weight: 2.9990 chunk 97 optimal weight: 5.9990 chunk 79 optimal weight: 40.0000 chunk 54 optimal weight: 0.6980 chunk 12 optimal weight: 2.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- 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 B 268 ASN N 53 GLN R 223 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.152716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.108049 restraints weight = 25256.346| |-----------------------------------------------------------------------------| r_work (start): 0.3362 rms_B_bonded: 3.13 r_work: 0.3238 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3247 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3247 r_free = 0.3247 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3247 r_free = 0.3247 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3247 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.3227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9083 Z= 0.277 Angle : 0.535 6.070 12294 Z= 0.288 Chirality : 0.043 0.169 1362 Planarity : 0.004 0.044 1572 Dihedral : 4.855 80.940 1235 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 2.88 % Allowed : 16.63 % Favored : 80.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.29 (0.25), residues: 421 sheet: 0.21 (0.33), residues: 218 loop : -0.74 (0.27), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP R 256 HIS 0.009 0.002 HIS B 62 PHE 0.016 0.002 PHE N 108 TYR 0.020 0.002 TYR R 146 ARG 0.007 0.000 ARG B 134 *********************** 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: 27 poor density : 150 time to evaluate : 1.038 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 27 GLU cc_start: 0.7486 (tp30) cc_final: 0.7245 (tp30) REVERT: A 58 LYS cc_start: 0.8369 (mttp) cc_final: 0.7739 (mmtm) REVERT: A 232 ARG cc_start: 0.8805 (ttp-110) cc_final: 0.8535 (ptp-170) REVERT: A 311 TYR cc_start: 0.6989 (m-80) cc_final: 0.6406 (m-80) REVERT: A 343 ASP cc_start: 0.8096 (m-30) cc_final: 0.7788 (m-30) REVERT: B 267 ASP cc_start: 0.9003 (m-30) cc_final: 0.8801 (m-30) REVERT: G 17 GLU cc_start: 0.7831 (tt0) cc_final: 0.7515 (tm-30) REVERT: G 42 GLU cc_start: 0.7963 (mt-10) cc_final: 0.7371 (mm-30) REVERT: N 12 VAL cc_start: 0.8417 (m) cc_final: 0.8138 (p) REVERT: N 77 ASN cc_start: 0.8821 (m-40) cc_final: 0.8612 (m-40) REVERT: R 42 MET cc_start: 0.8169 (mpp) cc_final: 0.6801 (ppp) REVERT: R 134 GLN cc_start: 0.8331 (OUTLIER) cc_final: 0.8063 (pm20) REVERT: R 252 ARG cc_start: 0.7686 (tpt170) cc_final: 0.6738 (tpm170) REVERT: R 256 TRP cc_start: 0.6942 (p-90) cc_final: 0.6731 (p-90) REVERT: R 261 ILE cc_start: 0.8650 (tt) cc_final: 0.8411 (tp) REVERT: R 344 LEU cc_start: 0.8374 (tp) cc_final: 0.8140 (mm) REVERT: R 365 LYS cc_start: 0.8213 (pmmt) cc_final: 0.7154 (tppt) outliers start: 27 outliers final: 18 residues processed: 168 average time/residue: 1.4390 time to fit residues: 255.8501 Evaluate side-chains 161 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 142 time to evaluate : 0.956 ------------------------------------------------------------------------------- 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 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 134 GLN 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 7.9990 chunk 30 optimal weight: 0.6980 chunk 32 optimal weight: 0.8980 chunk 66 optimal weight: 1.9990 chunk 63 optimal weight: 0.0070 chunk 60 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 29 optimal weight: 0.9980 chunk 43 optimal weight: 1.9990 chunk 68 optimal weight: 0.9990 chunk 53 optimal weight: 3.9990 overall best weight: 0.7200 ------------------------------------------------------------------------------- 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 = 0.3969 r_free = 0.3969 target = 0.154527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.109169 restraints weight = 20490.424| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 2.96 r_work: 0.3267 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3274 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3274 r_free = 0.3274 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3274 r_free = 0.3274 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3274 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.3294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9083 Z= 0.193 Angle : 0.503 6.013 12294 Z= 0.270 Chirality : 0.041 0.148 1362 Planarity : 0.004 0.062 1572 Dihedral : 4.704 80.998 1235 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 2.35 % Allowed : 18.34 % Favored : 79.32 % 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: 2.48 (0.25), residues: 415 sheet: 0.51 (0.34), residues: 198 loop : -0.75 (0.27), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP R 232 HIS 0.008 0.001 HIS A 220 PHE 0.016 0.001 PHE A 212 TYR 0.020 0.001 TYR P 22 ARG 0.008 0.000 ARG P 12 *********************** 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 170 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 148 time to evaluate : 1.074 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 311 TYR cc_start: 0.6942 (m-80) cc_final: 0.6356 (m-80) REVERT: A 343 ASP cc_start: 0.8095 (m-30) cc_final: 0.7747 (m-30) REVERT: G 17 GLU cc_start: 0.7780 (tt0) cc_final: 0.7465 (tm-30) REVERT: G 42 GLU cc_start: 0.7864 (mt-10) cc_final: 0.7271 (mm-30) REVERT: N 96 CYS cc_start: 0.8352 (OUTLIER) cc_final: 0.7931 (p) REVERT: R 42 MET cc_start: 0.8117 (mpp) cc_final: 0.6676 (ppp) REVERT: R 44 GLU cc_start: 0.6676 (pm20) cc_final: 0.6049 (pm20) REVERT: R 134 GLN cc_start: 0.8362 (OUTLIER) cc_final: 0.8099 (pm20) REVERT: R 158 LEU cc_start: 0.7646 (OUTLIER) cc_final: 0.7304 (mm) REVERT: R 252 ARG cc_start: 0.7728 (tpt170) cc_final: 0.6693 (tpm170) REVERT: R 261 ILE cc_start: 0.8598 (tt) cc_final: 0.8387 (tp) REVERT: R 344 LEU cc_start: 0.8390 (tp) cc_final: 0.8143 (mm) REVERT: R 357 PHE cc_start: 0.8062 (m-10) cc_final: 0.7796 (m-80) REVERT: R 360 PHE cc_start: 0.6739 (m-10) cc_final: 0.6489 (m-10) REVERT: R 365 LYS cc_start: 0.8188 (pmmt) cc_final: 0.7193 (tppt) outliers start: 22 outliers final: 13 residues processed: 164 average time/residue: 1.4585 time to fit residues: 253.4720 Evaluate side-chains 156 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 140 time to evaluate : 1.013 ------------------------------------------------------------------------------- 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 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 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: 5.9990 chunk 9 optimal weight: 0.0980 chunk 7 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 109 optimal weight: 0.6980 chunk 96 optimal weight: 0.7980 chunk 97 optimal weight: 3.9990 chunk 62 optimal weight: 0.9980 chunk 71 optimal weight: 4.9990 chunk 19 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 = 0.3958 r_free = 0.3958 target = 0.152966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.108709 restraints weight = 25365.706| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 3.14 r_work: 0.3247 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3262 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3262 r_free = 0.3262 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3262 r_free = 0.3262 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3262 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.3422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9083 Z= 0.221 Angle : 0.523 5.952 12294 Z= 0.281 Chirality : 0.042 0.148 1362 Planarity : 0.004 0.041 1572 Dihedral : 4.748 80.971 1235 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.56 % Allowed : 18.44 % Favored : 79.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.06 (0.25), residues: 1115 helix: 2.49 (0.25), residues: 415 sheet: 0.51 (0.34), residues: 198 loop : -0.78 (0.27), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP R 256 HIS 0.009 0.001 HIS A 220 PHE 0.016 0.001 PHE A 212 TYR 0.018 0.001 TYR R 146 ARG 0.013 0.001 ARG A 232 *********************** 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: 24 poor density : 146 time to evaluate : 0.980 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 311 TYR cc_start: 0.6996 (m-80) cc_final: 0.6407 (m-80) REVERT: G 17 GLU cc_start: 0.7828 (tt0) cc_final: 0.7527 (tm-30) REVERT: G 42 GLU cc_start: 0.7904 (mt-10) cc_final: 0.7356 (mm-30) REVERT: R 42 MET cc_start: 0.8136 (mpp) cc_final: 0.6700 (ppp) REVERT: R 134 GLN cc_start: 0.8349 (OUTLIER) cc_final: 0.8094 (pm20) REVERT: R 158 LEU cc_start: 0.7717 (OUTLIER) cc_final: 0.7363 (mm) REVERT: R 252 ARG cc_start: 0.7691 (tpt170) cc_final: 0.6666 (tpm170) REVERT: R 261 ILE cc_start: 0.8615 (tt) cc_final: 0.8403 (tp) REVERT: R 344 LEU cc_start: 0.8466 (tp) cc_final: 0.8167 (mm) REVERT: R 357 PHE cc_start: 0.8132 (m-10) cc_final: 0.7895 (m-80) REVERT: R 367 GLU cc_start: 0.6589 (mp0) cc_final: 0.5141 (mm-30) outliers start: 24 outliers final: 16 residues processed: 162 average time/residue: 1.5114 time to fit residues: 258.8261 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 : 1.052 ------------------------------------------------------------------------------- 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 134 GLN 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 29 optimal weight: 0.8980 chunk 88 optimal weight: 2.9990 chunk 66 optimal weight: 0.5980 chunk 12 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 chunk 92 optimal weight: 0.9980 chunk 58 optimal weight: 0.9990 chunk 108 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 27 optimal weight: 0.5980 chunk 73 optimal weight: 4.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 = 0.3961 r_free = 0.3961 target = 0.153646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.107009 restraints weight = 28507.228| |-----------------------------------------------------------------------------| r_work (start): 0.3355 rms_B_bonded: 3.46 r_work: 0.3224 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3244 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3244 r_free = 0.3244 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3244 r_free = 0.3244 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3244 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.3541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9083 Z= 0.211 Angle : 0.529 6.829 12294 Z= 0.284 Chirality : 0.041 0.158 1362 Planarity : 0.004 0.048 1572 Dihedral : 4.803 81.217 1235 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.77 % Allowed : 19.30 % Favored : 77.93 % 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: 1.08 (0.25), residues: 1115 helix: 2.51 (0.25), residues: 415 sheet: 0.52 (0.34), residues: 204 loop : -0.78 (0.27), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP R 256 HIS 0.008 0.001 HIS A 220 PHE 0.016 0.001 PHE A 212 TYR 0.021 0.001 TYR P 22 ARG 0.014 0.001 ARG A 232 *********************** 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 168 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 142 time to evaluate : 1.069 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 311 TYR cc_start: 0.7013 (m-80) cc_final: 0.6408 (m-80) REVERT: A 343 ASP cc_start: 0.8245 (m-30) cc_final: 0.7951 (m-30) REVERT: A 380 ARG cc_start: 0.7868 (ttm-80) cc_final: 0.7202 (ttp80) REVERT: B 44 GLN cc_start: 0.8530 (mm110) cc_final: 0.8066 (mp10) REVERT: G 17 GLU cc_start: 0.7798 (tt0) cc_final: 0.7463 (tm-30) REVERT: G 42 GLU cc_start: 0.7907 (mt-10) cc_final: 0.7312 (mm-30) REVERT: R 42 MET cc_start: 0.8181 (mpp) cc_final: 0.6677 (ppp) REVERT: R 44 GLU cc_start: 0.7142 (pm20) cc_final: 0.6761 (pm20) REVERT: R 134 GLN cc_start: 0.8308 (OUTLIER) cc_final: 0.8086 (pm20) REVERT: R 158 LEU cc_start: 0.7618 (OUTLIER) cc_final: 0.7269 (mm) REVERT: R 252 ARG cc_start: 0.7759 (tpt170) cc_final: 0.6629 (tpm170) REVERT: R 261 ILE cc_start: 0.8592 (tt) cc_final: 0.8378 (tp) REVERT: R 344 LEU cc_start: 0.8474 (tp) cc_final: 0.8183 (mm) REVERT: R 357 PHE cc_start: 0.8179 (m-10) cc_final: 0.7932 (m-80) REVERT: R 360 PHE cc_start: 0.6774 (m-10) cc_final: 0.6557 (m-10) REVERT: R 365 LYS cc_start: 0.8286 (pmmt) cc_final: 0.7512 (mtpp) REVERT: R 367 GLU cc_start: 0.6558 (mp0) cc_final: 0.5090 (mm-30) outliers start: 26 outliers final: 19 residues processed: 160 average time/residue: 1.4936 time to fit residues: 252.4692 Evaluate side-chains 159 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 138 time to evaluate : 1.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 GLU Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 386 MET 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 134 GLN 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 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 63 optimal weight: 0.5980 chunk 21 optimal weight: 1.9990 chunk 65 optimal weight: 0.1980 chunk 62 optimal weight: 0.7980 chunk 93 optimal weight: 2.9990 chunk 102 optimal weight: 0.0010 chunk 33 optimal weight: 0.0870 chunk 101 optimal weight: 0.9980 chunk 12 optimal weight: 4.9990 chunk 28 optimal weight: 2.9990 chunk 22 optimal weight: 0.8980 overall best weight: 0.3364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 390 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 = 0.3986 r_free = 0.3986 target = 0.155832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.109527 restraints weight = 30359.306| |-----------------------------------------------------------------------------| r_work (start): 0.3392 rms_B_bonded: 3.57 r_work: 0.3260 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3281 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3281 r_free = 0.3281 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3281 r_free = 0.3281 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3281 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.3492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 9083 Z= 0.154 Angle : 0.499 6.365 12294 Z= 0.268 Chirality : 0.040 0.149 1362 Planarity : 0.004 0.040 1572 Dihedral : 4.620 81.218 1235 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 2.24 % Allowed : 19.51 % 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 (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: 1.17 (0.25), residues: 1115 helix: 2.61 (0.25), residues: 415 sheet: 0.60 (0.34), residues: 202 loop : -0.76 (0.27), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP R 256 HIS 0.008 0.001 HIS A 220 PHE 0.015 0.001 PHE A 212 TYR 0.016 0.001 TYR R 146 ARG 0.012 0.000 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 162 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 141 time to evaluate : 0.984 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 343 ASP cc_start: 0.8234 (m-30) cc_final: 0.7871 (m-30) REVERT: A 380 ARG cc_start: 0.7854 (ttm-80) cc_final: 0.7194 (ttp80) REVERT: B 44 GLN cc_start: 0.8525 (mm110) cc_final: 0.8093 (mp10) REVERT: G 17 GLU cc_start: 0.7819 (tt0) cc_final: 0.7487 (tm-30) REVERT: G 42 GLU cc_start: 0.7889 (mt-10) cc_final: 0.7309 (mm-30) REVERT: N 77 ASN cc_start: 0.8971 (m-40) cc_final: 0.8770 (m-40) REVERT: N 96 CYS cc_start: 0.8412 (OUTLIER) cc_final: 0.7983 (p) REVERT: R 42 MET cc_start: 0.8173 (mpp) cc_final: 0.6668 (ppp) REVERT: R 134 GLN cc_start: 0.8327 (OUTLIER) cc_final: 0.8124 (pm20) REVERT: R 252 ARG cc_start: 0.7673 (tpt170) cc_final: 0.6472 (tpm170) REVERT: R 344 LEU cc_start: 0.8433 (tp) cc_final: 0.8145 (mm) REVERT: R 357 PHE cc_start: 0.8164 (m-10) cc_final: 0.7926 (m-80) REVERT: R 365 LYS cc_start: 0.8269 (pmmt) cc_final: 0.7193 (ttmm) REVERT: R 367 GLU cc_start: 0.6546 (mp0) cc_final: 0.5088 (mm-30) REVERT: R 398 GLU cc_start: 0.6608 (OUTLIER) cc_final: 0.6315 (tm-30) outliers start: 21 outliers final: 15 residues processed: 155 average time/residue: 1.4833 time to fit residues: 243.0410 Evaluate side-chains 155 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 137 time to evaluate : 1.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 GLU Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 386 MET 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 R residue 134 GLN 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=1.50 ------------------------------------------------------------------------------- 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: 1.9990 chunk 0 optimal weight: 6.9990 chunk 64 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 59 optimal weight: 3.9990 chunk 3 optimal weight: 0.9990 chunk 61 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 25 optimal weight: 4.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 390 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 = 0.3935 r_free = 0.3935 target = 0.151150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.104815 restraints weight = 22976.605| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 3.12 r_work: 0.3195 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3218 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3218 r_free = 0.3218 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 = 0.3218 r_free = 0.3218 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3218 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.3842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 9083 Z= 0.310 Angle : 0.574 6.397 12294 Z= 0.309 Chirality : 0.043 0.152 1362 Planarity : 0.004 0.043 1572 Dihedral : 4.985 81.822 1235 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 2.24 % Allowed : 19.62 % Favored : 78.14 % 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: 0.90 (0.25), residues: 1115 helix: 2.30 (0.25), residues: 422 sheet: 0.18 (0.33), residues: 219 loop : -0.78 (0.27), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP R 256 HIS 0.011 0.002 HIS A 220 PHE 0.018 0.002 PHE N 108 TYR 0.024 0.002 TYR P 22 ARG 0.013 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 162 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 141 time to evaluate : 0.993 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 311 TYR cc_start: 0.7118 (m-80) cc_final: 0.6498 (m-80) REVERT: A 343 ASP cc_start: 0.8231 (m-30) cc_final: 0.7951 (m-30) REVERT: A 380 ARG cc_start: 0.7860 (ttm-80) cc_final: 0.7197 (ttp80) REVERT: G 17 GLU cc_start: 0.7832 (tt0) cc_final: 0.7490 (tm-30) REVERT: G 29 LYS cc_start: 0.8227 (mmmt) cc_final: 0.7861 (mmmt) REVERT: G 42 GLU cc_start: 0.7931 (mt-10) cc_final: 0.7422 (mm-30) REVERT: N 77 ASN cc_start: 0.8989 (m-40) cc_final: 0.8748 (m-40) REVERT: R 42 MET cc_start: 0.8183 (mpp) cc_final: 0.6607 (ppp) REVERT: R 134 GLN cc_start: 0.8285 (OUTLIER) cc_final: 0.8069 (pm20) REVERT: R 252 ARG cc_start: 0.7658 (tpt170) cc_final: 0.6420 (tpm170) REVERT: R 344 LEU cc_start: 0.8469 (tp) cc_final: 0.8211 (mm) REVERT: R 357 PHE cc_start: 0.8177 (m-10) cc_final: 0.7914 (m-80) REVERT: R 365 LYS cc_start: 0.8278 (pmmt) cc_final: 0.7529 (mtpp) REVERT: R 367 GLU cc_start: 0.6594 (mp0) cc_final: 0.5100 (mm-30) REVERT: R 398 GLU cc_start: 0.6703 (OUTLIER) cc_final: 0.6280 (tm-30) outliers start: 21 outliers final: 14 residues processed: 156 average time/residue: 1.4953 time to fit residues: 246.4809 Evaluate side-chains 153 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 137 time to evaluate : 1.017 ------------------------------------------------------------------------------- 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 R residue 134 GLN 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 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: 0.6980 chunk 74 optimal weight: 0.8980 chunk 17 optimal weight: 0.0980 chunk 32 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 chunk 52 optimal weight: 0.9980 chunk 91 optimal weight: 4.9990 chunk 43 optimal weight: 0.9990 chunk 58 optimal weight: 0.0270 chunk 35 optimal weight: 0.7980 chunk 61 optimal weight: 0.7980 overall best weight: 0.4838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 36 ASN N 84 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.154706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.108098 restraints weight = 16370.584| |-----------------------------------------------------------------------------| r_work (start): 0.3372 rms_B_bonded: 2.77 r_work: 0.3246 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3252 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3252 r_free = 0.3252 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 = 0.3252 r_free = 0.3252 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3252 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.3766 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= 0.169 Angle : 0.510 6.383 12294 Z= 0.276 Chirality : 0.041 0.157 1362 Planarity : 0.004 0.040 1572 Dihedral : 4.711 80.775 1235 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.60 % Allowed : 20.90 % 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: 1.14 (0.25), residues: 1115 helix: 2.58 (0.25), residues: 415 sheet: 0.55 (0.35), residues: 197 loop : -0.75 (0.27), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.001 TRP R 256 HIS 0.006 0.001 HIS A 220 PHE 0.017 0.001 PHE A 212 TYR 0.020 0.001 TYR R 254 ARG 0.011 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 155 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 140 time to evaluate : 0.992 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 311 TYR cc_start: 0.7013 (m-80) cc_final: 0.6441 (m-80) REVERT: A 343 ASP cc_start: 0.8195 (m-30) cc_final: 0.7872 (m-30) REVERT: A 380 ARG cc_start: 0.7776 (ttm-80) cc_final: 0.7121 (ttp80) REVERT: G 17 GLU cc_start: 0.7790 (tt0) cc_final: 0.7477 (tm-30) REVERT: G 42 GLU cc_start: 0.7849 (mt-10) cc_final: 0.7333 (mm-30) REVERT: N 82 GLN cc_start: 0.7922 (tp40) cc_final: 0.7701 (tp40) REVERT: N 96 CYS cc_start: 0.8318 (OUTLIER) cc_final: 0.7898 (p) REVERT: P 12 ARG cc_start: 0.8084 (mtt90) cc_final: 0.7833 (mtt-85) REVERT: R 42 MET cc_start: 0.8239 (mpp) cc_final: 0.6657 (ppp) REVERT: R 134 GLN cc_start: 0.8325 (OUTLIER) cc_final: 0.8123 (pm20) REVERT: R 253 LYS cc_start: 0.7478 (tmtm) cc_final: 0.6425 (mmpt) REVERT: R 344 LEU cc_start: 0.8429 (tp) cc_final: 0.8163 (mm) REVERT: R 357 PHE cc_start: 0.8151 (m-10) cc_final: 0.7912 (m-80) REVERT: R 367 GLU cc_start: 0.6527 (mp0) cc_final: 0.5100 (mm-30) REVERT: R 398 GLU cc_start: 0.6766 (OUTLIER) cc_final: 0.6447 (tm-30) outliers start: 15 outliers final: 12 residues processed: 151 average time/residue: 1.5266 time to fit residues: 243.7252 Evaluate side-chains 154 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 139 time to evaluate : 0.938 ------------------------------------------------------------------------------- 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 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 R residue 134 GLN 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 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 61 optimal weight: 0.8980 chunk 47 optimal weight: 0.9990 chunk 37 optimal weight: 0.0670 chunk 63 optimal weight: 2.9990 chunk 59 optimal weight: 0.6980 chunk 5 optimal weight: 1.9990 chunk 2 optimal weight: 0.7980 chunk 30 optimal weight: 0.4980 chunk 99 optimal weight: 2.9990 chunk 8 optimal weight: 3.9990 chunk 46 optimal weight: 0.0980 overall best weight: 0.4318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 390 GLN N 82 GLN N 84 ASN R 223 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.155581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.108131 restraints weight = 22086.867| |-----------------------------------------------------------------------------| r_work (start): 0.3365 rms_B_bonded: 3.19 r_work: 0.3229 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3238 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3238 r_free = 0.3238 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3238 r_free = 0.3238 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3238 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.3755 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= 0.165 Angle : 0.509 7.511 12294 Z= 0.275 Chirality : 0.041 0.154 1362 Planarity : 0.004 0.042 1572 Dihedral : 4.633 79.955 1235 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.03 % Allowed : 20.68 % Favored : 77.29 % 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: 1.16 (0.25), residues: 1115 helix: 2.56 (0.25), residues: 415 sheet: 0.54 (0.34), residues: 202 loop : -0.72 (0.27), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.001 TRP R 256 HIS 0.007 0.001 HIS A 220 PHE 0.016 0.001 PHE A 212 TYR 0.023 0.001 TYR P 22 ARG 0.011 0.001 ARG A 232 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8400.91 seconds wall clock time: 148 minutes 20.80 seconds (8900.80 seconds total)