Starting phenix.real_space_refine on Tue May 13 23:18:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8j7w_36051/05_2025/8j7w_36051.cif Found real_map, /net/cci-nas-00/data/ceres_data/8j7w_36051/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8j7w_36051/05_2025/8j7w_36051.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8j7w_36051/05_2025/8j7w_36051.map" model { file = "/net/cci-nas-00/data/ceres_data/8j7w_36051/05_2025/8j7w_36051.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8j7w_36051/05_2025/8j7w_36051.cif" } resolution = 2.92 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 6.94, per 1000 atoms: 0.63 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: 3.45 Conformation dependent library (CDL) restraints added in 1.4 seconds 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: 1.48 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: 3.68 Time building geometry restraints manager: 2.88 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 376 or resid 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: 0.450 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.400 Check model and map are aligned: 0.080 Set scattering table: 0.090 Process input model: 29.100 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.010 Total: 42.170 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (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 TRP 0.035 0.002 TRP F 159 HIS 0.013 0.002 HIS A 240 PHE 0.049 0.002 PHE A 238 TYR 0.025 0.001 TYR E 150 ARG 0.004 0.000 ARG C 16 Details of bonding type rmsd hydrogen bonds : bond 0.17336 ( 589) hydrogen bonds : angle 7.34479 ( 1731) metal coordination : bond 0.23224 ( 3) SS BOND : bond 0.00232 ( 8) SS BOND : angle 0.64016 ( 16) covalent geometry : bond 0.00400 (11288) covalent geometry : angle 0.73680 (15367) *********************** 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 : 1.232 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: 1.1737 time to fit residues: 202.1668 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 : 1.214 ------------------------------------------------------------------------------- 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 117 optimal weight: 1.9990 chunk 105 optimal weight: 7.9990 chunk 58 optimal weight: 8.9990 chunk 35 optimal weight: 1.9990 chunk 71 optimal weight: 6.9990 chunk 56 optimal weight: 20.0000 chunk 108 optimal weight: 10.0000 chunk 42 optimal weight: 8.9990 chunk 66 optimal weight: 8.9990 chunk 81 optimal weight: 3.9990 chunk 126 optimal weight: 10.0000 overall best weight: 4.5990 ------------------------------------------------------------------------------- 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 310 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 ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4402 r_free = 0.4402 target = 0.227940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4292 r_free = 0.4292 target = 0.216256 restraints weight = 10949.422| |-----------------------------------------------------------------------------| r_work (start): 0.4294 rms_B_bonded: 0.55 r_work: 0.4184 rms_B_bonded: 0.96 restraints_weight: 0.5000 r_work: 0.4146 rms_B_bonded: 1.46 restraints_weight: 0.2500 r_work (final): 0.4146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6906 moved from start: 0.1125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 11299 Z= 0.280 Angle : 0.686 9.062 15383 Z= 0.356 Chirality : 0.048 0.188 1764 Planarity : 0.005 0.060 1943 Dihedral : 6.092 46.178 1552 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 4.47 % Allowed : 23.82 % Favored : 71.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.22), residues: 1407 helix: 0.80 (0.25), residues: 410 sheet: 0.81 (0.23), residues: 485 loop : -0.62 (0.26), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP F 52 HIS 0.007 0.002 HIS A 240 PHE 0.026 0.002 PHE B 72 TYR 0.019 0.002 TYR E 94 ARG 0.004 0.001 ARG A 296 Details of bonding type rmsd hydrogen bonds : bond 0.05003 ( 589) hydrogen bonds : angle 5.49186 ( 1731) metal coordination : bond 0.00474 ( 3) SS BOND : bond 0.00640 ( 8) SS BOND : angle 1.19439 ( 16) covalent geometry : bond 0.00642 (11288) covalent geometry : angle 0.68563 (15367) *********************** 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: 55 poor density : 127 time to evaluate : 1.149 Fit side-chains revert: symmetry clash REVERT: A 123 PHE cc_start: 0.5564 (t80) cc_final: 0.5244 (t80) REVERT: A 307 GLN cc_start: 0.8099 (OUTLIER) cc_final: 0.7634 (tm-30) REVERT: A 365 ARG cc_start: 0.7431 (OUTLIER) cc_final: 0.7152 (mmt-90) REVERT: B 322 GLN cc_start: 0.8348 (OUTLIER) cc_final: 0.7949 (mt0) REVERT: E 1 GLU cc_start: 0.6630 (OUTLIER) cc_final: 0.6343 (tm-30) REVERT: F 43 LYS cc_start: 0.7635 (OUTLIER) cc_final: 0.7220 (mtmp) outliers start: 55 outliers final: 18 residues processed: 167 average time/residue: 1.1579 time to fit residues: 210.0560 Evaluate side-chains 140 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 117 time to evaluate : 1.108 ------------------------------------------------------------------------------- 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 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 86 VAL Chi-restraints excluded: chain B residue 270 CYS Chi-restraints excluded: chain B residue 282 VAL Chi-restraints excluded: chain B residue 322 GLN Chi-restraints excluded: chain D residue 62 VAL 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 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 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 61 optimal weight: 0.3980 chunk 134 optimal weight: 30.0000 chunk 115 optimal weight: 40.0000 chunk 83 optimal weight: 4.9990 chunk 121 optimal weight: 3.9990 chunk 93 optimal weight: 2.9990 chunk 76 optimal weight: 8.9990 chunk 70 optimal weight: 20.0000 chunk 44 optimal weight: 1.9990 chunk 105 optimal weight: 8.9990 chunk 62 optimal weight: 5.9990 overall best weight: 2.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 310 GLN B 111 ASN ** B 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 128 GLN D 128 GLN ** E 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 16 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4392 r_free = 0.4392 target = 0.227128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.209287 restraints weight = 11196.536| |-----------------------------------------------------------------------------| r_work (start): 0.4242 rms_B_bonded: 0.70 r_work: 0.4122 rms_B_bonded: 1.33 restraints_weight: 0.5000 r_work: 0.4080 rms_B_bonded: 1.93 restraints_weight: 0.2500 r_work (final): 0.4080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7021 moved from start: 0.1422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 11299 Z= 0.199 Angle : 0.639 7.745 15383 Z= 0.329 Chirality : 0.046 0.183 1764 Planarity : 0.005 0.050 1943 Dihedral : 5.322 44.961 1533 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 4.55 % Allowed : 23.98 % Favored : 71.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.22), residues: 1407 helix: 1.09 (0.25), residues: 406 sheet: 0.83 (0.23), residues: 485 loop : -0.66 (0.26), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP F 52 HIS 0.007 0.001 HIS A 240 PHE 0.021 0.002 PHE D 36 TYR 0.018 0.002 TYR E 94 ARG 0.005 0.001 ARG B 91 Details of bonding type rmsd hydrogen bonds : bond 0.04269 ( 589) hydrogen bonds : angle 5.12009 ( 1731) metal coordination : bond 0.00328 ( 3) SS BOND : bond 0.00531 ( 8) SS BOND : angle 0.93773 ( 16) covalent geometry : bond 0.00445 (11288) covalent geometry : angle 0.63890 (15367) *********************** 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 181 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 125 time to evaluate : 1.126 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 307 GLN cc_start: 0.8110 (OUTLIER) cc_final: 0.7653 (tm-30) REVERT: B 322 GLN cc_start: 0.8337 (OUTLIER) cc_final: 0.7925 (mt0) REVERT: E 1 GLU cc_start: 0.6681 (OUTLIER) cc_final: 0.6345 (tm-30) outliers start: 56 outliers final: 28 residues processed: 171 average time/residue: 1.1282 time to fit residues: 209.4503 Evaluate side-chains 155 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 124 time to evaluate : 1.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ILE 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 B residue 282 VAL Chi-restraints excluded: chain B residue 322 GLN Chi-restraints excluded: chain C residue 154 ILE 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 141 VAL Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain E residue 174 VAL Chi-restraints excluded: chain F residue 25 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 45 optimal weight: 5.9990 chunk 77 optimal weight: 20.0000 chunk 43 optimal weight: 40.0000 chunk 69 optimal weight: 10.0000 chunk 81 optimal weight: 0.2980 chunk 113 optimal weight: 20.0000 chunk 74 optimal weight: 0.0870 chunk 85 optimal weight: 0.8980 chunk 50 optimal weight: 4.9990 chunk 72 optimal weight: 9.9990 chunk 125 optimal weight: 0.9980 overall best weight: 1.4560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 310 GLN A 361 GLN ** B 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 128 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4414 r_free = 0.4414 target = 0.229236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4276 r_free = 0.4276 target = 0.214547 restraints weight = 11091.390| |-----------------------------------------------------------------------------| r_work (start): 0.4268 rms_B_bonded: 0.69 r_work: 0.4147 rms_B_bonded: 1.20 restraints_weight: 0.5000 r_work: 0.4102 rms_B_bonded: 1.82 restraints_weight: 0.2500 r_work (final): 0.4102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6940 moved from start: 0.1596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 11299 Z= 0.139 Angle : 0.623 9.007 15383 Z= 0.313 Chirality : 0.045 0.214 1764 Planarity : 0.004 0.047 1943 Dihedral : 5.052 43.343 1532 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 3.33 % Allowed : 24.80 % Favored : 71.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.22), residues: 1407 helix: 1.42 (0.25), residues: 405 sheet: 0.98 (0.23), residues: 487 loop : -0.68 (0.26), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 47 HIS 0.007 0.001 HIS A 240 PHE 0.029 0.002 PHE B 72 TYR 0.018 0.001 TYR E 150 ARG 0.007 0.000 ARG C 18 Details of bonding type rmsd hydrogen bonds : bond 0.03788 ( 589) hydrogen bonds : angle 4.89282 ( 1731) metal coordination : bond 0.00128 ( 3) SS BOND : bond 0.00344 ( 8) SS BOND : angle 0.69611 ( 16) covalent geometry : bond 0.00302 (11288) covalent geometry : angle 0.62329 (15367) *********************** 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 167 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 126 time to evaluate : 1.104 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 278 ILE cc_start: 0.7300 (OUTLIER) cc_final: 0.7045 (mt) REVERT: A 307 GLN cc_start: 0.8011 (OUTLIER) cc_final: 0.7527 (tm-30) REVERT: B 322 GLN cc_start: 0.8298 (OUTLIER) cc_final: 0.7910 (mt0) REVERT: E 1 GLU cc_start: 0.6657 (OUTLIER) cc_final: 0.6269 (tm-30) outliers start: 41 outliers final: 20 residues processed: 160 average time/residue: 1.1728 time to fit residues: 203.2233 Evaluate side-chains 143 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 119 time to evaluate : 1.201 ------------------------------------------------------------------------------- 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 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 154 ILE 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 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 53 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 99 optimal weight: 7.9990 chunk 106 optimal weight: 2.9990 chunk 71 optimal weight: 20.0000 chunk 69 optimal weight: 7.9990 chunk 94 optimal weight: 50.0000 chunk 26 optimal weight: 2.9990 chunk 119 optimal weight: 20.0000 chunk 116 optimal weight: 2.9990 chunk 58 optimal weight: 0.3980 chunk 43 optimal weight: 20.0000 chunk 13 optimal weight: 20.0000 overall best weight: 3.4788 ------------------------------------------------------------------------------- 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 = 0.4390 r_free = 0.4390 target = 0.226669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.207703 restraints weight = 11067.295| |-----------------------------------------------------------------------------| r_work (start): 0.4221 rms_B_bonded: 0.76 r_work: 0.4098 rms_B_bonded: 1.39 restraints_weight: 0.5000 r_work: 0.4060 rms_B_bonded: 1.89 restraints_weight: 0.2500 r_work (final): 0.4060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7046 moved from start: 0.1762 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= 0.226 Angle : 0.675 12.247 15383 Z= 0.340 Chirality : 0.046 0.236 1764 Planarity : 0.005 0.049 1943 Dihedral : 5.325 45.871 1532 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 4.31 % Allowed : 24.47 % Favored : 71.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.22), residues: 1407 helix: 1.39 (0.25), residues: 405 sheet: 0.94 (0.23), residues: 485 loop : -0.74 (0.26), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP F 52 HIS 0.006 0.001 HIS A 240 PHE 0.023 0.002 PHE D 36 TYR 0.020 0.002 TYR E 94 ARG 0.011 0.001 ARG C 18 Details of bonding type rmsd hydrogen bonds : bond 0.04126 ( 589) hydrogen bonds : angle 4.87931 ( 1731) metal coordination : bond 0.00281 ( 3) SS BOND : bond 0.00534 ( 8) SS BOND : angle 1.06832 ( 16) covalent geometry : bond 0.00514 (11288) covalent geometry : angle 0.67471 (15367) *********************** 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 171 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 118 time to evaluate : 1.222 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 278 ILE cc_start: 0.7422 (OUTLIER) cc_final: 0.7100 (mt) REVERT: A 307 GLN cc_start: 0.8119 (OUTLIER) cc_final: 0.7663 (tm-30) REVERT: A 365 ARG cc_start: 0.7483 (OUTLIER) cc_final: 0.7185 (mmt-90) REVERT: B 322 GLN cc_start: 0.8326 (OUTLIER) cc_final: 0.7897 (mt0) REVERT: E 1 GLU cc_start: 0.6771 (OUTLIER) cc_final: 0.6369 (tm-30) outliers start: 53 outliers final: 28 residues processed: 162 average time/residue: 1.1487 time to fit residues: 201.5839 Evaluate side-chains 144 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 111 time to evaluate : 1.096 ------------------------------------------------------------------------------- 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 277 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 58 LEU Chi-restraints excluded: chain C residue 104 SER Chi-restraints excluded: chain C residue 154 ILE 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 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 25 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 110 optimal weight: 0.0030 chunk 38 optimal weight: 5.9990 chunk 58 optimal weight: 4.9990 chunk 69 optimal weight: 30.0000 chunk 42 optimal weight: 30.0000 chunk 78 optimal weight: 3.9990 chunk 112 optimal weight: 5.9990 chunk 115 optimal weight: 6.9990 chunk 45 optimal weight: 5.9990 chunk 47 optimal weight: 2.9990 chunk 53 optimal weight: 0.6980 overall best weight: 2.5396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 310 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 = 0.4405 r_free = 0.4405 target = 0.228178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.212113 restraints weight = 11091.047| |-----------------------------------------------------------------------------| r_work (start): 0.4264 rms_B_bonded: 0.67 r_work: 0.4147 rms_B_bonded: 1.30 restraints_weight: 0.5000 r_work: 0.4108 rms_B_bonded: 1.82 restraints_weight: 0.2500 r_work (final): 0.4108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6967 moved from start: 0.1825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 11299 Z= 0.183 Angle : 0.666 10.975 15383 Z= 0.331 Chirality : 0.046 0.264 1764 Planarity : 0.004 0.048 1943 Dihedral : 5.277 46.330 1532 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 3.98 % Allowed : 25.61 % Favored : 70.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.22), residues: 1407 helix: 1.40 (0.25), residues: 407 sheet: 0.96 (0.23), residues: 485 loop : -0.69 (0.26), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP F 52 HIS 0.006 0.001 HIS A 240 PHE 0.031 0.002 PHE B 72 TYR 0.020 0.002 TYR E 150 ARG 0.008 0.001 ARG C 18 Details of bonding type rmsd hydrogen bonds : bond 0.03941 ( 589) hydrogen bonds : angle 4.82156 ( 1731) metal coordination : bond 0.00122 ( 3) SS BOND : bond 0.00419 ( 8) SS BOND : angle 0.87388 ( 16) covalent geometry : bond 0.00414 (11288) covalent geometry : angle 0.66551 (15367) *********************** 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: 49 poor density : 115 time to evaluate : 1.125 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 307 GLN cc_start: 0.8062 (OUTLIER) cc_final: 0.7603 (tm-30) REVERT: B 273 LEU cc_start: 0.7177 (OUTLIER) cc_final: 0.6893 (tm) REVERT: B 322 GLN cc_start: 0.8319 (OUTLIER) cc_final: 0.7914 (mt0) REVERT: C 59 GLU cc_start: 0.8214 (OUTLIER) cc_final: 0.7193 (tp30) REVERT: E 1 GLU cc_start: 0.6696 (OUTLIER) cc_final: 0.6327 (tm-30) outliers start: 49 outliers final: 27 residues processed: 156 average time/residue: 1.1484 time to fit residues: 193.8125 Evaluate side-chains 142 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 110 time to evaluate : 1.095 ------------------------------------------------------------------------------- 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 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 270 CYS Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 322 GLN Chi-restraints excluded: chain C residue 59 GLU Chi-restraints excluded: chain C residue 104 SER Chi-restraints excluded: chain C residue 154 ILE 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 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 25 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 156 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 58 optimal weight: 6.9990 chunk 131 optimal weight: 0.1980 chunk 0 optimal weight: 50.0000 chunk 60 optimal weight: 0.2980 chunk 8 optimal weight: 2.9990 chunk 125 optimal weight: 2.9990 chunk 134 optimal weight: 0.7980 chunk 81 optimal weight: 0.9980 chunk 69 optimal weight: 3.9990 chunk 29 optimal weight: 9.9990 chunk 94 optimal weight: 7.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 310 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 = 0.4428 r_free = 0.4428 target = 0.230634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4321 r_free = 0.4321 target = 0.219155 restraints weight = 11157.542| |-----------------------------------------------------------------------------| r_work (start): 0.4307 rms_B_bonded: 0.56 r_work: 0.4184 rms_B_bonded: 0.94 restraints_weight: 0.5000 r_work: 0.4146 rms_B_bonded: 1.46 restraints_weight: 0.2500 r_work (final): 0.4146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6869 moved from start: 0.1928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 11299 Z= 0.127 Angle : 0.646 13.122 15383 Z= 0.316 Chirality : 0.044 0.246 1764 Planarity : 0.004 0.047 1943 Dihedral : 4.948 45.726 1532 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 3.33 % Allowed : 26.50 % Favored : 70.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.22), residues: 1407 helix: 1.71 (0.25), residues: 405 sheet: 1.02 (0.23), residues: 486 loop : -0.66 (0.27), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 47 HIS 0.005 0.001 HIS A 240 PHE 0.021 0.001 PHE B 123 TYR 0.019 0.001 TYR E 150 ARG 0.011 0.000 ARG B 91 Details of bonding type rmsd hydrogen bonds : bond 0.03595 ( 589) hydrogen bonds : angle 4.71321 ( 1731) metal coordination : bond 0.00188 ( 3) SS BOND : bond 0.00273 ( 8) SS BOND : angle 0.56723 ( 16) covalent geometry : bond 0.00276 (11288) covalent geometry : angle 0.64640 (15367) *********************** 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 156 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 115 time to evaluate : 1.251 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 307 GLN cc_start: 0.7995 (OUTLIER) cc_final: 0.7499 (tm-30) REVERT: B 273 LEU cc_start: 0.6990 (OUTLIER) cc_final: 0.6713 (tm) REVERT: B 322 GLN cc_start: 0.8265 (OUTLIER) cc_final: 0.7883 (mt0) REVERT: E 1 GLU cc_start: 0.6670 (OUTLIER) cc_final: 0.6309 (tm-30) REVERT: E 186 VAL cc_start: 0.6858 (p) cc_final: 0.6650 (p) outliers start: 41 outliers final: 26 residues processed: 149 average time/residue: 1.2511 time to fit residues: 202.8806 Evaluate side-chains 142 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 112 time to evaluate : 1.169 ------------------------------------------------------------------------------- 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 277 LEU 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 C residue 154 ILE 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 25 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 40 optimal weight: 5.9990 chunk 11 optimal weight: 0.7980 chunk 21 optimal weight: 0.6980 chunk 77 optimal weight: 20.0000 chunk 122 optimal weight: 0.0270 chunk 68 optimal weight: 7.9990 chunk 97 optimal weight: 9.9990 chunk 113 optimal weight: 40.0000 chunk 132 optimal weight: 8.9990 chunk 109 optimal weight: 2.9990 chunk 137 optimal weight: 40.0000 overall best weight: 2.1042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 310 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 = 0.4421 r_free = 0.4421 target = 0.229975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4279 r_free = 0.4279 target = 0.214858 restraints weight = 11108.001| |-----------------------------------------------------------------------------| r_work (start): 0.4272 rms_B_bonded: 0.69 r_work: 0.4150 rms_B_bonded: 1.35 restraints_weight: 0.5000 r_work: 0.4106 rms_B_bonded: 2.01 restraints_weight: 0.2500 r_work (final): 0.4106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6952 moved from start: 0.1992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 11299 Z= 0.163 Angle : 0.667 13.218 15383 Z= 0.326 Chirality : 0.045 0.270 1764 Planarity : 0.004 0.046 1943 Dihedral : 5.021 46.464 1529 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 3.33 % Allowed : 26.91 % Favored : 69.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.22), residues: 1407 helix: 1.70 (0.25), residues: 406 sheet: 1.05 (0.23), residues: 485 loop : -0.63 (0.27), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP F 159 HIS 0.004 0.001 HIS A 240 PHE 0.032 0.002 PHE B 72 TYR 0.023 0.002 TYR E 150 ARG 0.006 0.000 ARG C 18 Details of bonding type rmsd hydrogen bonds : bond 0.03752 ( 589) hydrogen bonds : angle 4.72758 ( 1731) metal coordination : bond 0.00275 ( 3) SS BOND : bond 0.00401 ( 8) SS BOND : angle 0.83966 ( 16) covalent geometry : bond 0.00367 (11288) covalent geometry : angle 0.66683 (15367) *********************** 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 150 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 109 time to evaluate : 1.100 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 307 GLN cc_start: 0.8028 (OUTLIER) cc_final: 0.7549 (tm-30) REVERT: B 322 GLN cc_start: 0.8260 (OUTLIER) cc_final: 0.7842 (mt0) REVERT: E 1 GLU cc_start: 0.6701 (OUTLIER) cc_final: 0.6284 (tm-30) outliers start: 41 outliers final: 27 residues processed: 144 average time/residue: 1.2336 time to fit residues: 191.5401 Evaluate side-chains 138 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 108 time to evaluate : 1.163 ------------------------------------------------------------------------------- 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 277 LEU Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 283 ILE 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 145 SER Chi-restraints excluded: chain B residue 270 CYS Chi-restraints excluded: chain B residue 322 GLN Chi-restraints excluded: chain C residue 104 SER Chi-restraints excluded: chain C residue 154 ILE 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 25 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 68 optimal weight: 7.9990 chunk 128 optimal weight: 3.9990 chunk 42 optimal weight: 7.9990 chunk 41 optimal weight: 30.0000 chunk 130 optimal weight: 7.9990 chunk 2 optimal weight: 5.9990 chunk 52 optimal weight: 0.7980 chunk 72 optimal weight: 6.9990 chunk 36 optimal weight: 0.7980 chunk 20 optimal weight: 2.9990 chunk 110 optimal weight: 40.0000 overall best weight: 2.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 310 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 = 0.4413 r_free = 0.4413 target = 0.229088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4303 r_free = 0.4303 target = 0.217341 restraints weight = 11181.011| |-----------------------------------------------------------------------------| r_work (start): 0.4306 rms_B_bonded: 0.55 r_work: 0.4198 rms_B_bonded: 0.97 restraints_weight: 0.5000 r_work: 0.4158 rms_B_bonded: 1.48 restraints_weight: 0.2500 r_work (final): 0.4158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6882 moved from start: 0.2082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 11299 Z= 0.199 Angle : 0.703 14.793 15383 Z= 0.344 Chirality : 0.046 0.254 1764 Planarity : 0.005 0.047 1943 Dihedral : 5.192 48.516 1529 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 3.25 % Allowed : 26.67 % Favored : 70.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.22), residues: 1407 helix: 1.64 (0.25), residues: 407 sheet: 0.99 (0.23), residues: 485 loop : -0.66 (0.27), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP E 159 HIS 0.005 0.001 HIS A 240 PHE 0.022 0.002 PHE D 36 TYR 0.024 0.002 TYR E 150 ARG 0.010 0.001 ARG B 91 Details of bonding type rmsd hydrogen bonds : bond 0.03910 ( 589) hydrogen bonds : angle 4.77026 ( 1731) metal coordination : bond 0.00291 ( 3) SS BOND : bond 0.00460 ( 8) SS BOND : angle 0.96665 ( 16) covalent geometry : bond 0.00454 (11288) covalent geometry : angle 0.70225 (15367) *********************** 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 150 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 110 time to evaluate : 1.156 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 307 GLN cc_start: 0.8080 (OUTLIER) cc_final: 0.7624 (tm-30) REVERT: A 365 ARG cc_start: 0.7457 (OUTLIER) cc_final: 0.7158 (mmt-90) REVERT: B 322 GLN cc_start: 0.8321 (OUTLIER) cc_final: 0.7896 (mt0) REVERT: E 1 GLU cc_start: 0.6752 (OUTLIER) cc_final: 0.6313 (tm-30) outliers start: 40 outliers final: 28 residues processed: 143 average time/residue: 1.2999 time to fit residues: 200.1793 Evaluate side-chains 140 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 108 time to evaluate : 1.094 ------------------------------------------------------------------------------- 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 277 LEU Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 283 ILE 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 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 56 SER 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 25 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 156 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 38 optimal weight: 8.9990 chunk 41 optimal weight: 6.9990 chunk 27 optimal weight: 0.9980 chunk 23 optimal weight: 6.9990 chunk 51 optimal weight: 2.9990 chunk 91 optimal weight: 4.9990 chunk 55 optimal weight: 5.9990 chunk 83 optimal weight: 4.9990 chunk 124 optimal weight: 0.0670 chunk 137 optimal weight: 20.0000 chunk 59 optimal weight: 0.0370 overall best weight: 1.8200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 310 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 = 0.4422 r_free = 0.4422 target = 0.230061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4313 r_free = 0.4313 target = 0.218408 restraints weight = 11081.607| |-----------------------------------------------------------------------------| r_work (start): 0.4315 rms_B_bonded: 0.55 r_work: 0.4207 rms_B_bonded: 0.95 restraints_weight: 0.5000 r_work: 0.4169 rms_B_bonded: 1.45 restraints_weight: 0.2500 r_work (final): 0.4169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6860 moved from start: 0.2117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 11299 Z= 0.152 Angle : 0.666 12.968 15383 Z= 0.325 Chirality : 0.045 0.251 1764 Planarity : 0.004 0.047 1943 Dihedral : 5.069 48.266 1529 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 2.76 % Allowed : 27.24 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.22), residues: 1407 helix: 1.69 (0.25), residues: 408 sheet: 0.99 (0.23), residues: 486 loop : -0.66 (0.27), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP E 159 HIS 0.011 0.001 HIS C 193 PHE 0.035 0.002 PHE A 238 TYR 0.025 0.002 TYR E 150 ARG 0.007 0.000 ARG D 17 Details of bonding type rmsd hydrogen bonds : bond 0.03712 ( 589) hydrogen bonds : angle 4.70505 ( 1731) metal coordination : bond 0.00120 ( 3) SS BOND : bond 0.00357 ( 8) SS BOND : angle 0.76553 ( 16) covalent geometry : bond 0.00343 (11288) covalent geometry : angle 0.66539 (15367) ********************** 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 143 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 109 time to evaluate : 1.221 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 PHE cc_start: 0.7395 (OUTLIER) cc_final: 0.6876 (m-80) REVERT: A 307 GLN cc_start: 0.8020 (OUTLIER) cc_final: 0.7545 (tm-30) REVERT: A 365 ARG cc_start: 0.7443 (OUTLIER) cc_final: 0.7151 (mmt-90) REVERT: B 322 GLN cc_start: 0.8278 (OUTLIER) cc_final: 0.7865 (mt0) REVERT: E 1 GLU cc_start: 0.6728 (OUTLIER) cc_final: 0.6305 (tm-30) outliers start: 34 outliers final: 26 residues processed: 136 average time/residue: 1.3339 time to fit residues: 195.0845 Evaluate side-chains 139 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 108 time to evaluate : 1.251 ------------------------------------------------------------------------------- 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 277 LEU Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 283 ILE 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 145 SER Chi-restraints excluded: chain B residue 270 CYS Chi-restraints excluded: chain B residue 322 GLN 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 56 SER 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 25 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 156 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 34 optimal weight: 9.9990 chunk 128 optimal weight: 0.6980 chunk 138 optimal weight: 3.9990 chunk 49 optimal weight: 0.9980 chunk 97 optimal weight: 10.0000 chunk 41 optimal weight: 10.0000 chunk 96 optimal weight: 1.9990 chunk 15 optimal weight: 8.9990 chunk 105 optimal weight: 5.9990 chunk 92 optimal weight: 0.8980 chunk 137 optimal weight: 30.0000 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 310 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 = 0.4422 r_free = 0.4422 target = 0.230133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4313 r_free = 0.4313 target = 0.218432 restraints weight = 10987.625| |-----------------------------------------------------------------------------| r_work (start): 0.4316 rms_B_bonded: 0.55 r_work: 0.4210 rms_B_bonded: 0.95 restraints_weight: 0.5000 r_work: 0.4173 rms_B_bonded: 1.42 restraints_weight: 0.2500 r_work (final): 0.4173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6849 moved from start: 0.2155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 11299 Z= 0.147 Angle : 0.670 12.979 15383 Z= 0.327 Chirality : 0.045 0.244 1764 Planarity : 0.004 0.047 1943 Dihedral : 5.012 48.108 1529 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 3.01 % Allowed : 26.83 % Favored : 70.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.22), residues: 1407 helix: 1.78 (0.25), residues: 406 sheet: 1.02 (0.23), residues: 485 loop : -0.69 (0.27), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP E 159 HIS 0.010 0.001 HIS C 193 PHE 0.017 0.001 PHE D 36 TYR 0.024 0.002 TYR E 150 ARG 0.005 0.000 ARG C 18 Details of bonding type rmsd hydrogen bonds : bond 0.03659 ( 589) hydrogen bonds : angle 4.67262 ( 1731) metal coordination : bond 0.00155 ( 3) SS BOND : bond 0.00362 ( 8) SS BOND : angle 0.77219 ( 16) covalent geometry : bond 0.00331 (11288) covalent geometry : angle 0.67011 (15367) =============================================================================== Job complete usr+sys time: 7163.53 seconds wall clock time: 124 minutes 26.31 seconds (7466.31 seconds total)