Starting phenix.real_space_refine on Sat Aug 23 09:18:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8j7w_36051/08_2025/8j7w_36051.cif Found real_map, /net/cci-nas-00/data/ceres_data/8j7w_36051/08_2025/8j7w_36051.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.92 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8j7w_36051/08_2025/8j7w_36051.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8j7w_36051/08_2025/8j7w_36051.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8j7w_36051/08_2025/8j7w_36051.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8j7w_36051/08_2025/8j7w_36051.map" } resolution = 2.92 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= 0.013 sd= 0.076 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: 5 Type Number sf(0) Gaussians Zn 2 6.06 5 S 48 5.16 5 C 7056 2.51 5 N 1831 2.21 5 O 2089 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11026 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 2213 Classifications: {'peptide': 282} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 274} Chain breaks: 2 Chain: "B" Number of atoms: 2183 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 2183 Classifications: {'peptide': 277} Link IDs: {'PTRANS': 8, 'TRANS': 268} Chain breaks: 1 Chain: "C" Number of atoms: 1672 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1672 Classifications: {'peptide': 215} Link IDs: {'PCIS': 4, 'PTRANS': 7, 'TRANS': 203} Chain: "D" Number of atoms: 1672 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1672 Classifications: {'peptide': 215} Link IDs: {'PCIS': 4, 'PTRANS': 7, 'TRANS': 203} Chain: "E" Number of atoms: 1642 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1642 Classifications: {'peptide': 218} Link IDs: {'PCIS': 3, 'PTRANS': 11, 'TRANS': 203} Chain: "F" Number of atoms: 1642 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1642 Classifications: {'peptide': 218} Link IDs: {'PCIS': 3, 'PTRANS': 11, 'TRANS': 203} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.52, per 1000 atoms: 0.23 Number of scatterers: 11026 At special positions: 0 Unit cell: (88.256, 112.684, 159.964, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 2 29.99 S 48 16.00 O 2089 8.00 N 1831 7.00 C 7056 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS C 23 " - pdb=" SG CYS C 92 " distance=2.03 Simple disulfide: pdb=" SG CYS C 138 " - pdb=" SG CYS C 198 " distance=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 92 " distance=2.03 Simple disulfide: pdb=" SG CYS D 138 " - pdb=" SG CYS D 198 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 95 " distance=2.03 Simple disulfide: pdb=" SG CYS E 145 " - pdb=" SG CYS E 200 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 95 " distance=2.03 Simple disulfide: pdb=" SG CYS F 145 " - pdb=" SG CYS F 200 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.94 Conformation dependent library (CDL) restraints added in 377.8 milliseconds Enol-peptide restraints added in 715.3 nanoseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 401 " pdb="ZN ZN A 401 " - pdb=" NE2 HIS A 240 " pdb=" ZN B 401 " pdb="ZN ZN B 401 " - pdb=" NE2 HIS B 240 " pdb="ZN ZN B 401 " - pdb=" NE2 HIS B 70 " 2814 Ramachandran restraints generated. 1407 Oldfield, 0 Emsley, 1407 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2668 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 26 sheets defined 32.1% alpha, 36.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.40 Creating SS restraints... Processing helix chain 'A' and resid 22 through 32 removed outlier: 3.530A pdb=" N PHE A 26 " --> pdb=" O ILE A 22 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ARG A 27 " --> pdb=" O SER A 23 " (cutoff:3.500A) Processing helix chain 'A' and resid 32 through 58 Processing helix chain 'A' and resid 63 through 89 Processing helix chain 'A' and resid 102 through 128 Processing helix chain 'A' and resid 143 through 159 removed outlier: 3.638A pdb=" N LEU A 147 " --> pdb=" O LEU A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 163 removed outlier: 3.834A pdb=" N GLY A 163 " --> pdb=" O LYS A 160 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 160 through 163' Processing helix chain 'A' and resid 230 through 261 removed outlier: 4.068A pdb=" N GLN A 235 " --> pdb=" O ARG A 231 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLN A 259 " --> pdb=" O ALA A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 294 removed outlier: 3.672A pdb=" N ILE A 269 " --> pdb=" O ILE A 265 " (cutoff:3.500A) Proline residue: A 284 - end of helix Processing helix chain 'A' and resid 298 through 303 removed outlier: 4.342A pdb=" N ASN A 303 " --> pdb=" O PRO A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 314 Processing helix chain 'A' and resid 347 through 362 removed outlier: 3.521A pdb=" N ALA A 362 " --> pdb=" O ILE A 358 " (cutoff:3.500A) Processing helix chain 'B' and resid 23 through 32 Processing helix chain 'B' and resid 33 through 59 Processing helix chain 'B' and resid 61 through 89 Processing helix chain 'B' and resid 102 through 132 Processing helix chain 'B' and resid 143 through 158 removed outlier: 3.722A pdb=" N LEU B 147 " --> pdb=" O LEU B 143 " (cutoff:3.500A) Processing helix chain 'B' and resid 240 through 258 removed outlier: 4.187A pdb=" N ASP B 244 " --> pdb=" O HIS B 240 " (cutoff:3.500A) removed outlier: 5.628A pdb=" N THR B 245 " --> pdb=" O ILE B 241 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU B 246 " --> pdb=" O LEU B 242 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N SER B 248 " --> pdb=" O ASP B 244 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ILE B 249 " --> pdb=" O THR B 245 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLY B 250 " --> pdb=" O LEU B 246 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N VAL B 251 " --> pdb=" O GLY B 247 " (cutoff:3.500A) Processing helix chain 'B' and resid 265 through 294 Proline residue: B 284 - end of helix Processing helix chain 'B' and resid 298 through 303 removed outlier: 4.433A pdb=" N ASN B 303 " --> pdb=" O PRO B 299 " (cutoff:3.500A) Processing helix chain 'B' and resid 304 through 314 Processing helix chain 'B' and resid 347 through 362 Processing helix chain 'C' and resid 125 through 132 Processing helix chain 'C' and resid 187 through 192 Processing helix chain 'D' and resid 83 through 87 removed outlier: 3.731A pdb=" N ALA D 87 " --> pdb=" O ALA D 84 " (cutoff:3.500A) Processing helix chain 'D' and resid 125 through 132 Processing helix chain 'D' and resid 186 through 193 removed outlier: 3.524A pdb=" N HIS D 193 " --> pdb=" O GLU D 189 " (cutoff:3.500A) Processing helix chain 'E' and resid 86 through 90 removed outlier: 3.962A pdb=" N THR E 90 " --> pdb=" O ALA E 87 " (cutoff:3.500A) Processing helix chain 'F' and resid 61 through 64 removed outlier: 3.565A pdb=" N ILE F 64 " --> pdb=" O ALA F 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 61 through 64' Processing helix chain 'F' and resid 86 through 90 Processing helix chain 'F' and resid 161 through 163 No H-bonds generated for 'chain 'F' and resid 161 through 163' Processing helix chain 'F' and resid 191 through 193 No H-bonds generated for 'chain 'F' and resid 191 through 193' Processing sheet with id=AA1, first strand: chain 'A' and resid 318 through 330 removed outlier: 6.703A pdb=" N ILE A 341 " --> pdb=" O TYR A 319 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N LEU A 321 " --> pdb=" O LYS A 339 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N LYS A 339 " --> pdb=" O LEU A 321 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N GLU A 323 " --> pdb=" O THR A 337 " (cutoff:3.500A) removed outlier: 5.918A pdb=" N THR A 337 " --> pdb=" O GLU A 323 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N HIS A 325 " --> pdb=" O VAL A 335 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N VAL A 335 " --> pdb=" O HIS A 325 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N TRP A 327 " --> pdb=" O VAL A 333 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N VAL A 333 " --> pdb=" O TRP A 327 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N TYR A 334 " --> pdb=" O GLN A 366 " (cutoff:3.500A) removed outlier: 8.165A pdb=" N TYR A 368 " --> pdb=" O TYR A 334 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N GLY A 336 " --> pdb=" O TYR A 368 " (cutoff:3.500A) removed outlier: 7.996A pdb=" N GLN A 370 " --> pdb=" O GLY A 336 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N LEU A 338 " --> pdb=" O GLN A 370 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N ASP A 372 " --> pdb=" O LEU A 338 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N LEU A 340 " --> pdb=" O ASP A 372 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 318 through 330 removed outlier: 6.725A pdb=" N ILE B 341 " --> pdb=" O TYR B 319 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N LEU B 321 " --> pdb=" O LYS B 339 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N LYS B 339 " --> pdb=" O LEU B 321 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N GLU B 323 " --> pdb=" O THR B 337 " (cutoff:3.500A) removed outlier: 5.921A pdb=" N THR B 337 " --> pdb=" O GLU B 323 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N HIS B 325 " --> pdb=" O VAL B 335 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N VAL B 335 " --> pdb=" O HIS B 325 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N TRP B 327 " --> pdb=" O VAL B 333 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N VAL B 333 " --> pdb=" O TRP B 327 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 4 through 7 Processing sheet with id=AA4, first strand: chain 'C' and resid 10 through 14 removed outlier: 6.284A pdb=" N LEU C 11 " --> pdb=" O GLU C 109 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N LYS C 111 " --> pdb=" O LEU C 11 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N VAL C 13 " --> pdb=" O LYS C 111 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N GLN C 41 " --> pdb=" O LEU C 50 " (cutoff:3.500A) removed outlier: 5.187A pdb=" N LEU C 50 " --> pdb=" O GLN C 41 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 10 through 14 removed outlier: 6.284A pdb=" N LEU C 11 " --> pdb=" O GLU C 109 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N LYS C 111 " --> pdb=" O LEU C 11 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N VAL C 13 " --> pdb=" O LYS C 111 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N THR C 101 " --> pdb=" O GLN C 94 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 30 through 31 Processing sheet with id=AA7, first strand: chain 'C' and resid 118 through 122 removed outlier: 5.839A pdb=" N TYR C 177 " --> pdb=" O ASN C 142 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 157 through 159 removed outlier: 4.150A pdb=" N TRP C 152 " --> pdb=" O ARG C 159 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 4 through 7 Processing sheet with id=AB1, first strand: chain 'D' and resid 10 through 14 removed outlier: 6.432A pdb=" N LEU D 11 " --> pdb=" O GLU D 109 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N LYS D 111 " --> pdb=" O LEU D 11 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N VAL D 13 " --> pdb=" O LYS D 111 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N MET D 37 " --> pdb=" O TYR D 53 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N TYR D 53 " --> pdb=" O MET D 37 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N TRP D 39 " --> pdb=" O LEU D 51 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 10 through 14 removed outlier: 6.432A pdb=" N LEU D 11 " --> pdb=" O GLU D 109 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N LYS D 111 " --> pdb=" O LEU D 11 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N VAL D 13 " --> pdb=" O LYS D 111 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N THR D 101 " --> pdb=" O GLN D 94 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 30 through 31 Processing sheet with id=AB4, first strand: chain 'D' and resid 118 through 122 removed outlier: 5.675A pdb=" N TYR D 177 " --> pdb=" O ASN D 142 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N SER D 178 " --> pdb=" O THR D 168 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 157 through 159 removed outlier: 4.319A pdb=" N TRP D 152 " --> pdb=" O ARG D 159 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LYS D 153 " --> pdb=" O THR D 197 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AB7, first strand: chain 'E' and resid 11 through 12 removed outlier: 6.586A pdb=" N VAL E 34 " --> pdb=" O VAL E 50 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N VAL E 50 " --> pdb=" O VAL E 34 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N TRP E 36 " --> pdb=" O LEU E 48 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 11 through 12 removed outlier: 3.639A pdb=" N TYR E 107 " --> pdb=" O ARG E 97 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 125 through 129 removed outlier: 6.079A pdb=" N TYR E 180 " --> pdb=" O GLY E 149 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 125 through 129 removed outlier: 6.079A pdb=" N TYR E 180 " --> pdb=" O GLY E 149 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 156 through 159 removed outlier: 3.603A pdb=" N LYS E 213 " --> pdb=" O CYS E 200 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 3 through 7 Processing sheet with id=AC4, first strand: chain 'F' and resid 11 through 12 removed outlier: 6.775A pdb=" N VAL F 34 " --> pdb=" O VAL F 50 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N VAL F 50 " --> pdb=" O VAL F 34 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N TRP F 36 " --> pdb=" O LEU F 48 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 11 through 12 removed outlier: 3.750A pdb=" N TYR F 107 " --> pdb=" O ARG F 97 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 125 through 129 removed outlier: 6.338A pdb=" N TYR F 180 " --> pdb=" O GLY F 149 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 125 through 129 removed outlier: 6.338A pdb=" N TYR F 180 " --> pdb=" O GLY F 149 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 156 through 159 633 hydrogen bonds defined for protein. 1731 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.99 Time building geometry restraints manager: 1.21 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: 3125 1.33 - 1.45: 2135 1.45 - 1.57: 5958 1.57 - 1.69: 0 1.69 - 1.82: 70 Bond restraints: 11288 Sorted by residual: bond pdb=" CG1 ILE A 274 " pdb=" CD1 ILE A 274 " ideal model delta sigma weight residual 1.513 1.378 0.135 3.90e-02 6.57e+02 1.19e+01 bond pdb=" N VAL B 136 " pdb=" CA VAL B 136 " ideal model delta sigma weight residual 1.459 1.496 -0.037 1.25e-02 6.40e+03 8.76e+00 bond pdb=" N MET B 258 " pdb=" CA MET B 258 " ideal model delta sigma weight residual 1.456 1.492 -0.036 1.32e-02 5.74e+03 7.58e+00 bond pdb=" CA SER F 53 " pdb=" CB SER F 53 " ideal model delta sigma weight residual 1.530 1.483 0.047 1.69e-02 3.50e+03 7.57e+00 bond pdb=" N HIS B 138 " pdb=" CA HIS B 138 " ideal model delta sigma weight residual 1.456 1.489 -0.033 1.22e-02 6.72e+03 7.50e+00 ... (remaining 11283 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.38: 15102 2.38 - 4.77: 217 4.77 - 7.15: 38 7.15 - 9.54: 8 9.54 - 11.92: 2 Bond angle restraints: 15367 Sorted by residual: angle pdb=" N LEU A 53 " pdb=" CA LEU A 53 " pdb=" C LEU A 53 " ideal model delta sigma weight residual 111.36 107.20 4.16 1.09e+00 8.42e-01 1.46e+01 angle pdb=" N SER E 139 " pdb=" CA SER E 139 " pdb=" C SER E 139 " ideal model delta sigma weight residual 113.43 108.67 4.76 1.26e+00 6.30e-01 1.43e+01 angle pdb=" N ASN F 54 " pdb=" CA ASN F 54 " pdb=" C ASN F 54 " ideal model delta sigma weight residual 113.20 108.87 4.33 1.21e+00 6.83e-01 1.28e+01 angle pdb=" CA ASP B 135 " pdb=" CB ASP B 135 " pdb=" CG ASP B 135 " ideal model delta sigma weight residual 112.60 116.17 -3.57 1.00e+00 1.00e+00 1.27e+01 angle pdb=" CA CYS B 61 " pdb=" C CYS B 61 " pdb=" O CYS B 61 " ideal model delta sigma weight residual 122.64 118.19 4.45 1.25e+00 6.40e-01 1.27e+01 ... (remaining 15362 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 5771 17.93 - 35.86: 671 35.86 - 53.79: 179 53.79 - 71.72: 40 71.72 - 89.65: 11 Dihedral angle restraints: 6672 sinusoidal: 2536 harmonic: 4136 Sorted by residual: dihedral pdb=" CB CYS D 138 " pdb=" SG CYS D 138 " pdb=" SG CYS D 198 " pdb=" CB CYS D 198 " ideal model delta sinusoidal sigma weight residual -86.00 -149.61 63.61 1 1.00e+01 1.00e-02 5.33e+01 dihedral pdb=" CB CYS E 145 " pdb=" SG CYS E 145 " pdb=" SG CYS E 200 " pdb=" CB CYS E 200 " ideal model delta sinusoidal sigma weight residual 93.00 58.70 34.30 1 1.00e+01 1.00e-02 1.67e+01 dihedral pdb=" CA MET A 71 " pdb=" C MET A 71 " pdb=" N PHE A 72 " pdb=" CA PHE A 72 " ideal model delta harmonic sigma weight residual 180.00 160.43 19.57 0 5.00e+00 4.00e-02 1.53e+01 ... (remaining 6669 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 1464 0.062 - 0.123: 261 0.123 - 0.185: 32 0.185 - 0.247: 6 0.247 - 0.309: 1 Chirality restraints: 1764 Sorted by residual: chirality pdb=" CG LEU B 42 " pdb=" CB LEU B 42 " pdb=" CD1 LEU B 42 " pdb=" CD2 LEU B 42 " both_signs ideal model delta sigma weight residual False -2.59 -2.28 -0.31 2.00e-01 2.50e+01 2.38e+00 chirality pdb=" CA ASN E 138 " pdb=" N ASN E 138 " pdb=" C ASN E 138 " pdb=" CB ASN E 138 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.08e+00 chirality pdb=" CA LEU A 62 " pdb=" N LEU A 62 " pdb=" C LEU A 62 " pdb=" CB LEU A 62 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.07e+00 ... (remaining 1761 not shown) Planarity restraints: 1943 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 129 " 0.446 9.50e-02 1.11e+02 2.00e-01 2.45e+01 pdb=" NE ARG B 129 " -0.027 2.00e-02 2.50e+03 pdb=" CZ ARG B 129 " -0.002 2.00e-02 2.50e+03 pdb=" NH1 ARG B 129 " -0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG B 129 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 238 " 0.015 2.00e-02 2.50e+03 2.16e-02 8.19e+00 pdb=" CG PHE A 238 " -0.049 2.00e-02 2.50e+03 pdb=" CD1 PHE A 238 " 0.017 2.00e-02 2.50e+03 pdb=" CD2 PHE A 238 " 0.018 2.00e-02 2.50e+03 pdb=" CE1 PHE A 238 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE A 238 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE A 238 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG F 56 " -0.257 9.50e-02 1.11e+02 1.15e-01 8.13e+00 pdb=" NE ARG F 56 " 0.016 2.00e-02 2.50e+03 pdb=" CZ ARG F 56 " 0.001 2.00e-02 2.50e+03 pdb=" NH1 ARG F 56 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG F 56 " -0.009 2.00e-02 2.50e+03 ... (remaining 1940 not shown) Histogram of nonbonded interaction distances: 1.83 - 2.44: 44 2.44 - 3.06: 6945 3.06 - 3.67: 17207 3.67 - 4.29: 26282 4.29 - 4.90: 42925 Nonbonded interactions: 93403 Sorted by model distance: nonbonded pdb=" OD2 ASP A 74 " pdb=" OD2 ASP A 244 " model vdw 1.831 3.040 nonbonded pdb=" OD1 ASP B 244 " pdb="ZN ZN B 401 " model vdw 1.886 2.230 nonbonded pdb=" OD2 ASP A 74 " pdb="ZN ZN A 401 " model vdw 1.989 2.230 nonbonded pdb=" OD2 ASP A 244 " pdb="ZN ZN A 401 " model vdw 1.990 2.230 nonbonded pdb=" OD2 ASP B 74 " pdb=" OD2 ASP B 244 " model vdw 1.994 3.040 ... (remaining 93398 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 22 through 160 or resid 239 through 375 or (resid 376 and \ (name N or name CA or name C or name O or name CB or name CG or name SD or name \ CE )) or resid 401)) selection = (chain 'B' and (resid 22 through 132 or resid 141 through 401)) } ncs_group { reference = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.650 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.210 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 11.960 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6388 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 : 0.006 0.269 11299 Z= 0.251 Angle : 0.737 11.923 15383 Z= 0.404 Chirality : 0.049 0.309 1764 Planarity : 0.007 0.200 1943 Dihedral : 16.932 89.646 3980 Min Nonbonded Distance : 1.831 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 2.60 % Allowed : 26.67 % Favored : 70.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.30 (0.22), residues: 1407 helix: 0.43 (0.25), residues: 404 sheet: 0.86 (0.23), residues: 480 loop : -0.49 (0.26), residues: 523 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 16 TYR 0.025 0.001 TYR E 150 PHE 0.049 0.002 PHE A 238 TRP 0.035 0.002 TRP F 159 HIS 0.013 0.002 HIS A 240 Details of bonding type rmsd covalent geometry : bond 0.00400 (11288) covalent geometry : angle 0.73680 (15367) SS BOND : bond 0.00232 ( 8) SS BOND : angle 0.64016 ( 16) hydrogen bonds : bond 0.17336 ( 589) hydrogen bonds : angle 7.34479 ( 1731) metal coordination : bond 0.23224 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2814 Ramachandran restraints generated. 1407 Oldfield, 0 Emsley, 1407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2814 Ramachandran restraints generated. 1407 Oldfield, 0 Emsley, 1407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 131 time to evaluate : 0.432 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 287 ARG cc_start: 0.5791 (ttp-170) cc_final: 0.4379 (mmp-170) REVERT: B 71 MET cc_start: 0.7230 (pmt) cc_final: 0.6980 (pmm) REVERT: B 91 ARG cc_start: 0.6148 (mpt180) cc_final: 0.5845 (ttp80) REVERT: C 18 ARG cc_start: 0.7668 (ttm170) cc_final: 0.7279 (ttm170) REVERT: D 71 SER cc_start: 0.8119 (p) cc_final: 0.7493 (t) REVERT: D 173 LYS cc_start: 0.8528 (mtmt) cc_final: 0.8126 (mppt) outliers start: 32 outliers final: 24 residues processed: 159 average time/residue: 0.5218 time to fit residues: 89.6696 Evaluate side-chains 152 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 128 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 270 CYS Chi-restraints excluded: chain C residue 10 SER Chi-restraints excluded: chain C residue 114 ASP Chi-restraints excluded: chain C residue 154 ILE Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 69 SER Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain D residue 138 CYS Chi-restraints excluded: chain D residue 148 ILE Chi-restraints excluded: chain D residue 149 ASN Chi-restraints excluded: chain D residue 168 THR Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain E residue 15 SER Chi-restraints excluded: chain E residue 17 SER Chi-restraints excluded: chain E residue 53 SER Chi-restraints excluded: chain E residue 68 SER Chi-restraints excluded: chain E residue 70 SER Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain F residue 53 SER Chi-restraints excluded: chain F residue 122 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 98 optimal weight: 0.0970 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 10.0000 chunk 130 optimal weight: 0.0870 chunk 124 optimal weight: 9.9990 chunk 103 optimal weight: 6.9990 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 20.0000 chunk 55 optimal weight: 8.9990 overall best weight: 2.4362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 ASN A 232 GLN A 325 HIS A 356 HIS A 361 GLN B 37 ASN B 313 GLN B 325 HIS B 356 HIS B 357 ASN C 57 ASN C 128 GLN D 128 GLN D 141 ASN ** E 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 73 ASN E 138 ASN E 204 HIS F 60 ASN F 73 ASN F 160 ASN F 204 HIS Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4416 r_free = 0.4416 target = 0.229530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4306 r_free = 0.4306 target = 0.217692 restraints weight = 11146.842| |-----------------------------------------------------------------------------| r_work (start): 0.4297 rms_B_bonded: 0.57 r_work: 0.4171 rms_B_bonded: 0.99 restraints_weight: 0.5000 r_work: 0.4133 rms_B_bonded: 1.52 restraints_weight: 0.2500 r_work (final): 0.4133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6906 moved from start: 0.1027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 11299 Z= 0.184 Angle : 0.633 8.606 15383 Z= 0.327 Chirality : 0.046 0.189 1764 Planarity : 0.005 0.049 1943 Dihedral : 5.786 44.088 1552 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 3.98 % Allowed : 23.41 % Favored : 72.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.59 (0.22), residues: 1407 helix: 1.01 (0.25), residues: 410 sheet: 0.95 (0.23), residues: 485 loop : -0.58 (0.26), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 56 TYR 0.015 0.002 TYR F 94 PHE 0.026 0.002 PHE B 72 TRP 0.016 0.002 TRP F 52 HIS 0.009 0.001 HIS A 240 Details of bonding type rmsd covalent geometry : bond 0.00408 (11288) covalent geometry : angle 0.63286 (15367) SS BOND : bond 0.00489 ( 8) SS BOND : angle 0.93690 ( 16) hydrogen bonds : bond 0.04451 ( 589) hydrogen bonds : angle 5.39091 ( 1731) metal coordination : bond 0.00388 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2814 Ramachandran restraints generated. 1407 Oldfield, 0 Emsley, 1407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2814 Ramachandran restraints generated. 1407 Oldfield, 0 Emsley, 1407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 133 time to evaluate : 0.326 Fit side-chains revert: symmetry clash REVERT: A 123 PHE cc_start: 0.5609 (t80) cc_final: 0.5187 (t80) REVERT: A 307 GLN cc_start: 0.8037 (OUTLIER) cc_final: 0.7571 (tm-30) REVERT: B 92 ASP cc_start: 0.7175 (OUTLIER) cc_final: 0.6972 (p0) REVERT: B 322 GLN cc_start: 0.8293 (OUTLIER) cc_final: 0.7905 (mt0) REVERT: E 1 GLU cc_start: 0.6485 (OUTLIER) cc_final: 0.6269 (tm-30) REVERT: F 43 LYS cc_start: 0.7635 (OUTLIER) cc_final: 0.7240 (mtmp) outliers start: 49 outliers final: 18 residues processed: 168 average time/residue: 0.4883 time to fit residues: 88.4769 Evaluate side-chains 141 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 118 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 PHE Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 307 GLN Chi-restraints excluded: chain A residue 310 GLN Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 92 ASP Chi-restraints excluded: chain B residue 270 CYS Chi-restraints excluded: chain B residue 322 GLN Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain D residue 168 THR Chi-restraints excluded: chain D residue 180 SER Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain E residue 1 GLU Chi-restraints excluded: chain E residue 53 SER Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain F residue 25 SER Chi-restraints excluded: chain F residue 43 LYS Chi-restraints excluded: chain F residue 53 SER Chi-restraints excluded: chain F residue 68 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 67 optimal weight: 10.0000 chunk 95 optimal weight: 30.0000 chunk 53 optimal weight: 1.9990 chunk 110 optimal weight: 40.0000 chunk 88 optimal weight: 7.9990 chunk 23 optimal weight: 0.8980 chunk 0 optimal weight: 50.0000 chunk 122 optimal weight: 0.7980 chunk 6 optimal weight: 0.0980 chunk 62 optimal weight: 0.9980 chunk 18 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 111 ASN ** B 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 128 GLN ** E 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4431 r_free = 0.4431 target = 0.231127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4293 r_free = 0.4293 target = 0.216333 restraints weight = 11227.391| |-----------------------------------------------------------------------------| r_work (start): 0.4295 rms_B_bonded: 0.71 r_work: 0.4172 rms_B_bonded: 1.37 restraints_weight: 0.5000 r_work: 0.4129 rms_B_bonded: 2.02 restraints_weight: 0.2500 r_work (final): 0.4129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6913 moved from start: 0.1363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 11299 Z= 0.121 Angle : 0.595 7.777 15383 Z= 0.301 Chirality : 0.044 0.226 1764 Planarity : 0.004 0.046 1943 Dihedral : 4.847 41.400 1534 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 3.58 % Allowed : 23.90 % Favored : 72.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.80 (0.22), residues: 1407 helix: 1.34 (0.26), residues: 407 sheet: 1.06 (0.23), residues: 483 loop : -0.61 (0.26), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 91 TYR 0.015 0.001 TYR C 196 PHE 0.017 0.001 PHE F 80 TRP 0.012 0.001 TRP F 47 HIS 0.011 0.001 HIS B 137 Details of bonding type rmsd covalent geometry : bond 0.00250 (11288) covalent geometry : angle 0.59466 (15367) SS BOND : bond 0.00334 ( 8) SS BOND : angle 0.60487 ( 16) hydrogen bonds : bond 0.03771 ( 589) hydrogen bonds : angle 5.02203 ( 1731) metal coordination : bond 0.00144 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2814 Ramachandran restraints generated. 1407 Oldfield, 0 Emsley, 1407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2814 Ramachandran restraints generated. 1407 Oldfield, 0 Emsley, 1407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 125 time to evaluate : 0.436 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 307 GLN cc_start: 0.7957 (OUTLIER) cc_final: 0.7463 (tm-30) REVERT: E 1 GLU cc_start: 0.6463 (OUTLIER) cc_final: 0.6232 (tm-30) outliers start: 44 outliers final: 16 residues processed: 158 average time/residue: 0.5383 time to fit residues: 91.0835 Evaluate side-chains 142 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 124 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 PHE Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 307 GLN Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain B residue 52 GLU Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 270 CYS Chi-restraints excluded: chain C residue 10 SER Chi-restraints excluded: chain C residue 104 SER Chi-restraints excluded: chain D residue 168 THR Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain E residue 1 GLU Chi-restraints excluded: chain E residue 105 MET Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain F residue 25 SER Chi-restraints excluded: chain F residue 156 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 54 optimal weight: 3.9990 chunk 135 optimal weight: 30.0000 chunk 13 optimal weight: 9.9990 chunk 98 optimal weight: 10.0000 chunk 108 optimal weight: 20.0000 chunk 83 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 97 optimal weight: 0.9990 chunk 128 optimal weight: 0.8980 chunk 2 optimal weight: 5.9990 chunk 0 optimal weight: 50.0000 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 310 GLN B 322 GLN D 128 GLN ** E 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4402 r_free = 0.4402 target = 0.227995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.210269 restraints weight = 11177.233| |-----------------------------------------------------------------------------| r_work (start): 0.4238 rms_B_bonded: 0.74 r_work: 0.4112 rms_B_bonded: 1.38 restraints_weight: 0.5000 r_work: 0.4071 rms_B_bonded: 1.96 restraints_weight: 0.2500 r_work (final): 0.4071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7007 moved from start: 0.1591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 11299 Z= 0.174 Angle : 0.625 9.142 15383 Z= 0.315 Chirality : 0.045 0.216 1764 Planarity : 0.005 0.046 1943 Dihedral : 4.858 44.214 1530 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 3.58 % Allowed : 24.07 % Favored : 72.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.81 (0.22), residues: 1407 helix: 1.37 (0.25), residues: 407 sheet: 1.10 (0.23), residues: 485 loop : -0.67 (0.26), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 18 TYR 0.018 0.002 TYR E 150 PHE 0.028 0.002 PHE B 72 TRP 0.015 0.002 TRP F 52 HIS 0.006 0.001 HIS B 137 Details of bonding type rmsd covalent geometry : bond 0.00392 (11288) covalent geometry : angle 0.62434 (15367) SS BOND : bond 0.00460 ( 8) SS BOND : angle 0.91054 ( 16) hydrogen bonds : bond 0.03947 ( 589) hydrogen bonds : angle 4.91665 ( 1731) metal coordination : bond 0.00387 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2814 Ramachandran restraints generated. 1407 Oldfield, 0 Emsley, 1407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2814 Ramachandran restraints generated. 1407 Oldfield, 0 Emsley, 1407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 126 time to evaluate : 0.424 Fit side-chains revert: symmetry clash REVERT: A 307 GLN cc_start: 0.8057 (OUTLIER) cc_final: 0.7597 (tm-30) REVERT: A 365 ARG cc_start: 0.7504 (OUTLIER) cc_final: 0.7221 (mmt-90) REVERT: B 322 GLN cc_start: 0.8328 (OUTLIER) cc_final: 0.7822 (mm110) REVERT: E 1 GLU cc_start: 0.6636 (OUTLIER) cc_final: 0.6340 (tm-30) outliers start: 44 outliers final: 20 residues processed: 159 average time/residue: 0.5226 time to fit residues: 89.6263 Evaluate side-chains 142 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 118 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 PHE Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 307 GLN Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 365 ARG Chi-restraints excluded: chain B residue 52 GLU Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 270 CYS Chi-restraints excluded: chain B residue 322 GLN Chi-restraints excluded: chain C residue 10 SER Chi-restraints excluded: chain C residue 104 SER Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 168 THR Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain E residue 1 GLU Chi-restraints excluded: chain E residue 53 SER Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain F residue 25 SER Chi-restraints excluded: chain F residue 68 SER Chi-restraints excluded: chain F residue 156 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 127 optimal weight: 6.9990 chunk 137 optimal weight: 9.9990 chunk 93 optimal weight: 30.0000 chunk 132 optimal weight: 40.0000 chunk 115 optimal weight: 7.9990 chunk 10 optimal weight: 9.9990 chunk 80 optimal weight: 2.9990 chunk 117 optimal weight: 6.9990 chunk 116 optimal weight: 40.0000 chunk 60 optimal weight: 0.0470 chunk 136 optimal weight: 10.0000 overall best weight: 5.0086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 310 GLN B 152 ASN D 128 GLN ** E 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 16 GLN F 169 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4391 r_free = 0.4391 target = 0.226738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4243 r_free = 0.4243 target = 0.211171 restraints weight = 11138.874| |-----------------------------------------------------------------------------| r_work (start): 0.4238 rms_B_bonded: 0.67 r_work: 0.4124 rms_B_bonded: 1.23 restraints_weight: 0.5000 r_work: 0.4085 rms_B_bonded: 1.77 restraints_weight: 0.2500 r_work (final): 0.4085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6987 moved from start: 0.1784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.074 11299 Z= 0.298 Angle : 0.710 9.718 15383 Z= 0.360 Chirality : 0.049 0.217 1764 Planarity : 0.005 0.073 1943 Dihedral : 5.182 48.578 1530 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 4.15 % Allowed : 24.31 % Favored : 71.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.57 (0.22), residues: 1407 helix: 1.15 (0.25), residues: 407 sheet: 0.92 (0.23), residues: 485 loop : -0.72 (0.26), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 91 TYR 0.022 0.002 TYR E 94 PHE 0.026 0.002 PHE D 36 TRP 0.023 0.002 TRP F 52 HIS 0.006 0.002 HIS A 240 Details of bonding type rmsd covalent geometry : bond 0.00687 (11288) covalent geometry : angle 0.70876 (15367) SS BOND : bond 0.00677 ( 8) SS BOND : angle 1.30038 ( 16) hydrogen bonds : bond 0.04425 ( 589) hydrogen bonds : angle 5.02318 ( 1731) metal coordination : bond 0.00365 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2814 Ramachandran restraints generated. 1407 Oldfield, 0 Emsley, 1407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2814 Ramachandran restraints generated. 1407 Oldfield, 0 Emsley, 1407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 121 time to evaluate : 0.287 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 278 ILE cc_start: 0.7401 (OUTLIER) cc_final: 0.7183 (mt) REVERT: A 307 GLN cc_start: 0.8121 (OUTLIER) cc_final: 0.7691 (tm-30) REVERT: A 365 ARG cc_start: 0.7459 (OUTLIER) cc_final: 0.7169 (mmt-90) REVERT: B 322 GLN cc_start: 0.8397 (OUTLIER) cc_final: 0.7840 (mt0) REVERT: E 1 GLU cc_start: 0.6780 (OUTLIER) cc_final: 0.6372 (tm-30) outliers start: 51 outliers final: 27 residues processed: 165 average time/residue: 0.5074 time to fit residues: 90.1878 Evaluate side-chains 145 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 113 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ARG Chi-restraints excluded: chain A residue 41 PHE Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 307 GLN Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 365 ARG Chi-restraints excluded: chain B residue 52 GLU Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 104 GLU Chi-restraints excluded: chain B residue 270 CYS Chi-restraints excluded: chain B residue 322 GLN Chi-restraints excluded: chain C residue 10 SER Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 104 SER Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 14 SER Chi-restraints excluded: chain D residue 168 THR Chi-restraints excluded: chain D residue 180 SER Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain E residue 1 GLU Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 53 SER Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain E residue 183 SER Chi-restraints excluded: chain F residue 57 THR Chi-restraints excluded: chain F residue 68 SER Chi-restraints excluded: chain F residue 156 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 51 optimal weight: 2.9990 chunk 16 optimal weight: 40.0000 chunk 47 optimal weight: 2.9990 chunk 5 optimal weight: 7.9990 chunk 40 optimal weight: 6.9990 chunk 95 optimal weight: 40.0000 chunk 106 optimal weight: 2.9990 chunk 18 optimal weight: 6.9990 chunk 59 optimal weight: 6.9990 chunk 36 optimal weight: 0.7980 chunk 108 optimal weight: 9.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 322 GLN D 128 GLN ** E 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4396 r_free = 0.4396 target = 0.227260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4249 r_free = 0.4249 target = 0.211664 restraints weight = 11146.408| |-----------------------------------------------------------------------------| r_work (start): 0.4260 rms_B_bonded: 0.67 r_work: 0.4141 rms_B_bonded: 1.26 restraints_weight: 0.5000 r_work: 0.4100 rms_B_bonded: 1.83 restraints_weight: 0.2500 r_work (final): 0.4100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6981 moved from start: 0.1867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 11299 Z= 0.220 Angle : 0.682 11.101 15383 Z= 0.342 Chirality : 0.047 0.250 1764 Planarity : 0.005 0.048 1943 Dihedral : 5.118 49.562 1530 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 3.90 % Allowed : 25.20 % Favored : 70.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.64 (0.22), residues: 1407 helix: 1.30 (0.25), residues: 407 sheet: 0.90 (0.23), residues: 485 loop : -0.71 (0.26), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 56 TYR 0.020 0.002 TYR E 150 PHE 0.030 0.002 PHE B 72 TRP 0.020 0.002 TRP F 52 HIS 0.006 0.001 HIS A 240 Details of bonding type rmsd covalent geometry : bond 0.00501 (11288) covalent geometry : angle 0.68166 (15367) SS BOND : bond 0.00477 ( 8) SS BOND : angle 1.00398 ( 16) hydrogen bonds : bond 0.04123 ( 589) hydrogen bonds : angle 4.90966 ( 1731) metal coordination : bond 0.00227 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2814 Ramachandran restraints generated. 1407 Oldfield, 0 Emsley, 1407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2814 Ramachandran restraints generated. 1407 Oldfield, 0 Emsley, 1407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 116 time to evaluate : 0.273 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 278 ILE cc_start: 0.7384 (OUTLIER) cc_final: 0.7095 (mt) REVERT: A 307 GLN cc_start: 0.8097 (OUTLIER) cc_final: 0.7641 (tm-30) REVERT: A 365 ARG cc_start: 0.7454 (OUTLIER) cc_final: 0.7159 (mmt-90) REVERT: B 273 LEU cc_start: 0.7209 (OUTLIER) cc_final: 0.6930 (tm) REVERT: B 322 GLN cc_start: 0.8345 (OUTLIER) cc_final: 0.7654 (mm110) REVERT: E 1 GLU cc_start: 0.6776 (OUTLIER) cc_final: 0.6419 (tm-30) outliers start: 48 outliers final: 30 residues processed: 157 average time/residue: 0.5026 time to fit residues: 85.2026 Evaluate side-chains 145 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 109 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ILE Chi-restraints excluded: chain A residue 36 ARG Chi-restraints excluded: chain A residue 41 PHE Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 307 GLN Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 365 ARG Chi-restraints excluded: chain B residue 52 GLU Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 104 GLU Chi-restraints excluded: chain B residue 270 CYS Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 322 GLN Chi-restraints excluded: chain C residue 10 SER Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 104 SER Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 14 SER Chi-restraints excluded: chain D residue 24 ARG Chi-restraints excluded: chain D residue 168 THR Chi-restraints excluded: chain D residue 180 SER Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain E residue 1 GLU Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 53 SER Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain E residue 183 SER Chi-restraints excluded: chain F residue 53 SER Chi-restraints excluded: chain F residue 57 THR Chi-restraints excluded: chain F residue 68 SER Chi-restraints excluded: chain F residue 143 LEU Chi-restraints excluded: chain F residue 156 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 93 optimal weight: 4.9990 chunk 125 optimal weight: 0.6980 chunk 72 optimal weight: 6.9990 chunk 127 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 24 optimal weight: 0.8980 chunk 8 optimal weight: 0.9990 chunk 71 optimal weight: 30.0000 chunk 75 optimal weight: 20.0000 chunk 11 optimal weight: 6.9990 chunk 96 optimal weight: 20.0000 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 361 GLN D 128 GLN D 161 ASN ** E 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 16 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4421 r_free = 0.4421 target = 0.229824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4289 r_free = 0.4289 target = 0.215740 restraints weight = 11079.477| |-----------------------------------------------------------------------------| r_work (start): 0.4290 rms_B_bonded: 0.69 r_work: 0.4164 rms_B_bonded: 1.29 restraints_weight: 0.5000 r_work: 0.4125 rms_B_bonded: 1.85 restraints_weight: 0.2500 r_work (final): 0.4125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6930 moved from start: 0.1897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 11299 Z= 0.143 Angle : 0.648 11.753 15383 Z= 0.319 Chirality : 0.045 0.280 1764 Planarity : 0.004 0.047 1943 Dihedral : 4.955 50.284 1530 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 3.41 % Allowed : 25.85 % Favored : 70.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.85 (0.22), residues: 1407 helix: 1.59 (0.25), residues: 407 sheet: 0.98 (0.23), residues: 486 loop : -0.65 (0.26), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 18 TYR 0.021 0.001 TYR E 150 PHE 0.017 0.001 PHE D 36 TRP 0.013 0.001 TRP F 47 HIS 0.006 0.001 HIS A 240 Details of bonding type rmsd covalent geometry : bond 0.00316 (11288) covalent geometry : angle 0.64805 (15367) SS BOND : bond 0.00326 ( 8) SS BOND : angle 0.69233 ( 16) hydrogen bonds : bond 0.03740 ( 589) hydrogen bonds : angle 4.78269 ( 1731) metal coordination : bond 0.00126 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2814 Ramachandran restraints generated. 1407 Oldfield, 0 Emsley, 1407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2814 Ramachandran restraints generated. 1407 Oldfield, 0 Emsley, 1407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 111 time to evaluate : 0.414 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 278 ILE cc_start: 0.7303 (OUTLIER) cc_final: 0.7063 (mt) REVERT: A 307 GLN cc_start: 0.8068 (OUTLIER) cc_final: 0.7600 (tm-30) REVERT: B 273 LEU cc_start: 0.7086 (OUTLIER) cc_final: 0.6816 (tm) REVERT: B 322 GLN cc_start: 0.8403 (OUTLIER) cc_final: 0.7826 (mt0) REVERT: E 1 GLU cc_start: 0.6679 (OUTLIER) cc_final: 0.6316 (tm-30) outliers start: 42 outliers final: 23 residues processed: 150 average time/residue: 0.5875 time to fit residues: 94.4934 Evaluate side-chains 136 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 108 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ARG Chi-restraints excluded: chain A residue 41 PHE Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 307 GLN Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain B residue 52 GLU Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 104 GLU Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 270 CYS Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 322 GLN Chi-restraints excluded: chain C residue 104 SER Chi-restraints excluded: chain D residue 14 SER Chi-restraints excluded: chain D residue 180 SER Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain E residue 1 GLU Chi-restraints excluded: chain E residue 53 SER Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain E residue 183 SER Chi-restraints excluded: chain F residue 53 SER Chi-restraints excluded: chain F residue 68 SER Chi-restraints excluded: chain F residue 143 LEU Chi-restraints excluded: chain F residue 208 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 121 optimal weight: 8.9990 chunk 88 optimal weight: 4.9990 chunk 10 optimal weight: 4.9990 chunk 138 optimal weight: 1.9990 chunk 44 optimal weight: 5.9990 chunk 82 optimal weight: 10.0000 chunk 71 optimal weight: 30.0000 chunk 20 optimal weight: 0.9990 chunk 106 optimal weight: 3.9990 chunk 55 optimal weight: 6.9990 chunk 127 optimal weight: 4.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 322 GLN D 128 GLN ** E 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4407 r_free = 0.4407 target = 0.228486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4294 r_free = 0.4294 target = 0.216403 restraints weight = 11031.347| |-----------------------------------------------------------------------------| r_work (start): 0.4287 rms_B_bonded: 0.57 r_work: 0.4175 rms_B_bonded: 0.98 restraints_weight: 0.5000 r_work: 0.4135 rms_B_bonded: 1.49 restraints_weight: 0.2500 r_work (final): 0.4135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6907 moved from start: 0.2015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 11299 Z= 0.220 Angle : 0.691 12.368 15383 Z= 0.342 Chirality : 0.047 0.271 1764 Planarity : 0.005 0.051 1943 Dihedral : 5.058 52.330 1529 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 3.01 % Allowed : 26.67 % Favored : 70.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.78 (0.22), residues: 1407 helix: 1.53 (0.25), residues: 405 sheet: 0.93 (0.23), residues: 485 loop : -0.66 (0.26), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 56 TYR 0.022 0.002 TYR E 150 PHE 0.031 0.002 PHE B 72 TRP 0.019 0.002 TRP F 159 HIS 0.005 0.001 HIS A 240 Details of bonding type rmsd covalent geometry : bond 0.00504 (11288) covalent geometry : angle 0.69093 (15367) SS BOND : bond 0.00509 ( 8) SS BOND : angle 1.06429 ( 16) hydrogen bonds : bond 0.04052 ( 589) hydrogen bonds : angle 4.85139 ( 1731) metal coordination : bond 0.00288 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2814 Ramachandran restraints generated. 1407 Oldfield, 0 Emsley, 1407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2814 Ramachandran restraints generated. 1407 Oldfield, 0 Emsley, 1407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 114 time to evaluate : 0.355 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 117 PHE cc_start: 0.7359 (OUTLIER) cc_final: 0.6829 (m-80) REVERT: A 278 ILE cc_start: 0.7356 (OUTLIER) cc_final: 0.7106 (mt) REVERT: A 307 GLN cc_start: 0.8117 (OUTLIER) cc_final: 0.7654 (tm-30) REVERT: B 273 LEU cc_start: 0.7043 (OUTLIER) cc_final: 0.6779 (tm) REVERT: B 322 GLN cc_start: 0.8359 (OUTLIER) cc_final: 0.7639 (mm110) REVERT: E 1 GLU cc_start: 0.6741 (OUTLIER) cc_final: 0.6292 (tm-30) outliers start: 37 outliers final: 25 residues processed: 145 average time/residue: 0.6022 time to fit residues: 93.4732 Evaluate side-chains 143 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 112 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ARG Chi-restraints excluded: chain A residue 41 PHE Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 117 PHE Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 307 GLN Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain B residue 52 GLU Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 104 GLU Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 270 CYS Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 322 GLN Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 104 SER Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 14 SER Chi-restraints excluded: chain D residue 24 ARG Chi-restraints excluded: chain D residue 180 SER Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain E residue 1 GLU Chi-restraints excluded: chain E residue 53 SER Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain E residue 183 SER Chi-restraints excluded: chain F residue 53 SER Chi-restraints excluded: chain F residue 68 SER Chi-restraints excluded: chain F residue 143 LEU Chi-restraints excluded: chain F residue 208 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 125 optimal weight: 0.0170 chunk 46 optimal weight: 7.9990 chunk 116 optimal weight: 8.9990 chunk 41 optimal weight: 6.9990 chunk 23 optimal weight: 4.9990 chunk 78 optimal weight: 3.9990 chunk 105 optimal weight: 10.0000 chunk 57 optimal weight: 4.9990 chunk 67 optimal weight: 8.9990 chunk 25 optimal weight: 3.9990 chunk 120 optimal weight: 2.9990 overall best weight: 3.2026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 322 GLN D 128 GLN ** E 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 16 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4391 r_free = 0.4391 target = 0.227031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4218 r_free = 0.4218 target = 0.208800 restraints weight = 11075.484| |-----------------------------------------------------------------------------| r_work (start): 0.4220 rms_B_bonded: 0.76 r_work: 0.4093 rms_B_bonded: 1.36 restraints_weight: 0.5000 r_work: 0.4054 rms_B_bonded: 1.89 restraints_weight: 0.2500 r_work (final): 0.4054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7038 moved from start: 0.2035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 11299 Z= 0.215 Angle : 0.706 13.783 15383 Z= 0.349 Chirality : 0.047 0.256 1764 Planarity : 0.005 0.055 1943 Dihedral : 5.069 54.194 1527 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 3.50 % Allowed : 26.50 % Favored : 70.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.73 (0.22), residues: 1407 helix: 1.48 (0.25), residues: 407 sheet: 0.91 (0.23), residues: 485 loop : -0.69 (0.26), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 91 TYR 0.024 0.002 TYR E 150 PHE 0.023 0.002 PHE D 36 TRP 0.022 0.002 TRP E 159 HIS 0.005 0.001 HIS A 240 Details of bonding type rmsd covalent geometry : bond 0.00494 (11288) covalent geometry : angle 0.70517 (15367) SS BOND : bond 0.00478 ( 8) SS BOND : angle 1.02096 ( 16) hydrogen bonds : bond 0.04024 ( 589) hydrogen bonds : angle 4.84187 ( 1731) metal coordination : bond 0.00261 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2814 Ramachandran restraints generated. 1407 Oldfield, 0 Emsley, 1407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2814 Ramachandran restraints generated. 1407 Oldfield, 0 Emsley, 1407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 111 time to evaluate : 0.322 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 PHE cc_start: 0.7483 (OUTLIER) cc_final: 0.6963 (m-80) REVERT: A 307 GLN cc_start: 0.8125 (OUTLIER) cc_final: 0.7661 (tm-30) REVERT: A 365 ARG cc_start: 0.7495 (OUTLIER) cc_final: 0.7207 (mmt-90) REVERT: B 322 GLN cc_start: 0.8419 (OUTLIER) cc_final: 0.7791 (mm110) REVERT: E 1 GLU cc_start: 0.6796 (OUTLIER) cc_final: 0.6327 (tm-30) outliers start: 43 outliers final: 28 residues processed: 146 average time/residue: 0.5502 time to fit residues: 86.1823 Evaluate side-chains 142 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 109 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ARG Chi-restraints excluded: chain A residue 41 PHE Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 117 PHE Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 307 GLN Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 365 ARG Chi-restraints excluded: chain B residue 52 GLU Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 104 GLU Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 270 CYS Chi-restraints excluded: chain B residue 322 GLN Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 104 SER Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 14 SER Chi-restraints excluded: chain D residue 24 ARG Chi-restraints excluded: chain D residue 168 THR Chi-restraints excluded: chain D residue 180 SER Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain E residue 1 GLU Chi-restraints excluded: chain E residue 53 SER Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain E residue 183 SER Chi-restraints excluded: chain F residue 53 SER Chi-restraints excluded: chain F residue 57 THR Chi-restraints excluded: chain F residue 68 SER Chi-restraints excluded: chain F residue 143 LEU Chi-restraints excluded: chain F residue 156 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 35 optimal weight: 4.9990 chunk 18 optimal weight: 1.9990 chunk 108 optimal weight: 20.0000 chunk 6 optimal weight: 10.0000 chunk 79 optimal weight: 3.9990 chunk 125 optimal weight: 2.9990 chunk 3 optimal weight: 20.0000 chunk 78 optimal weight: 4.9990 chunk 33 optimal weight: 3.9990 chunk 86 optimal weight: 7.9990 chunk 37 optimal weight: 0.9980 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 322 GLN D 128 GLN ** E 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 16 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4413 r_free = 0.4413 target = 0.229062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4280 r_free = 0.4280 target = 0.214934 restraints weight = 11103.686| |-----------------------------------------------------------------------------| r_work (start): 0.4265 rms_B_bonded: 0.69 r_work: 0.4138 rms_B_bonded: 1.23 restraints_weight: 0.5000 r_work: 0.4096 rms_B_bonded: 1.84 restraints_weight: 0.2500 r_work (final): 0.4096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6961 moved from start: 0.2119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 11299 Z= 0.195 Angle : 0.692 13.158 15383 Z= 0.340 Chirality : 0.046 0.252 1764 Planarity : 0.005 0.051 1943 Dihedral : 5.072 56.484 1527 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 2.85 % Allowed : 27.32 % Favored : 69.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.79 (0.22), residues: 1407 helix: 1.60 (0.25), residues: 406 sheet: 0.90 (0.23), residues: 486 loop : -0.68 (0.26), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 91 TYR 0.023 0.002 TYR E 150 PHE 0.033 0.002 PHE B 72 TRP 0.025 0.002 TRP E 159 HIS 0.005 0.001 HIS A 240 Details of bonding type rmsd covalent geometry : bond 0.00446 (11288) covalent geometry : angle 0.69196 (15367) SS BOND : bond 0.00444 ( 8) SS BOND : angle 0.94706 ( 16) hydrogen bonds : bond 0.03929 ( 589) hydrogen bonds : angle 4.80380 ( 1731) metal coordination : bond 0.00125 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2814 Ramachandran restraints generated. 1407 Oldfield, 0 Emsley, 1407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2814 Ramachandran restraints generated. 1407 Oldfield, 0 Emsley, 1407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 111 time to evaluate : 0.413 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 307 GLN cc_start: 0.8075 (OUTLIER) cc_final: 0.7615 (tm-30) REVERT: A 310 GLN cc_start: 0.8444 (mt0) cc_final: 0.8205 (mt0) REVERT: A 365 ARG cc_start: 0.7467 (OUTLIER) cc_final: 0.7185 (mmt-90) REVERT: B 322 GLN cc_start: 0.8420 (OUTLIER) cc_final: 0.7823 (mm110) REVERT: E 1 GLU cc_start: 0.6786 (OUTLIER) cc_final: 0.6290 (tm-30) outliers start: 35 outliers final: 28 residues processed: 141 average time/residue: 0.6287 time to fit residues: 94.7711 Evaluate side-chains 141 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 109 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ARG Chi-restraints excluded: chain A residue 41 PHE Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 307 GLN Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 365 ARG Chi-restraints excluded: chain B residue 52 GLU Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 104 GLU Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 270 CYS Chi-restraints excluded: chain B residue 322 GLN Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 104 SER Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 24 ARG Chi-restraints excluded: chain D residue 168 THR Chi-restraints excluded: chain D residue 180 SER Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain E residue 1 GLU Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 53 SER Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain E residue 183 SER Chi-restraints excluded: chain F residue 53 SER Chi-restraints excluded: chain F residue 57 THR Chi-restraints excluded: chain F residue 68 SER Chi-restraints excluded: chain F residue 143 LEU Chi-restraints excluded: chain F residue 156 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 64 optimal weight: 0.9980 chunk 67 optimal weight: 8.9990 chunk 20 optimal weight: 0.7980 chunk 62 optimal weight: 2.9990 chunk 127 optimal weight: 1.9990 chunk 68 optimal weight: 6.9990 chunk 36 optimal weight: 0.9980 chunk 118 optimal weight: 1.9990 chunk 112 optimal weight: 6.9990 chunk 111 optimal weight: 30.0000 chunk 61 optimal weight: 6.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 128 GLN ** E 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 16 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4413 r_free = 0.4413 target = 0.229330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4275 r_free = 0.4275 target = 0.214610 restraints weight = 11108.067| |-----------------------------------------------------------------------------| r_work (start): 0.4262 rms_B_bonded: 0.71 r_work: 0.4133 rms_B_bonded: 1.31 restraints_weight: 0.5000 r_work: 0.4095 rms_B_bonded: 1.83 restraints_weight: 0.2500 r_work (final): 0.4095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6942 moved from start: 0.2120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 11299 Z= 0.138 Angle : 0.674 13.048 15383 Z= 0.328 Chirality : 0.045 0.261 1764 Planarity : 0.004 0.047 1943 Dihedral : 4.945 59.210 1527 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 2.44 % Allowed : 27.56 % Favored : 70.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.86 (0.22), residues: 1407 helix: 1.72 (0.25), residues: 406 sheet: 0.96 (0.23), residues: 486 loop : -0.72 (0.27), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 91 TYR 0.024 0.001 TYR E 150 PHE 0.017 0.001 PHE B 123 TRP 0.032 0.001 TRP E 159 HIS 0.005 0.001 HIS A 240 Details of bonding type rmsd covalent geometry : bond 0.00307 (11288) covalent geometry : angle 0.67371 (15367) SS BOND : bond 0.00328 ( 8) SS BOND : angle 0.70737 ( 16) hydrogen bonds : bond 0.03656 ( 589) hydrogen bonds : angle 4.72898 ( 1731) metal coordination : bond 0.00133 ( 3) =============================================================================== Job complete usr+sys time: 3153.82 seconds wall clock time: 54 minutes 33.85 seconds (3273.85 seconds total)