Starting phenix.real_space_refine on Tue Jul 29 06:46:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8j7w_36051/07_2025/8j7w_36051.cif Found real_map, /net/cci-nas-00/data/ceres_data/8j7w_36051/07_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_36051/07_2025/8j7w_36051.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8j7w_36051/07_2025/8j7w_36051.map" model { file = "/net/cci-nas-00/data/ceres_data/8j7w_36051/07_2025/8j7w_36051.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8j7w_36051/07_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-5711/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: 7.43, per 1000 atoms: 0.67 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: 2.54 Conformation dependent library (CDL) restraints added in 1.5 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: 1.54 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: 3.88 Time building geometry restraints manager: 2.95 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: 0.700 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: 0.490 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 30.680 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.730 ------------------------------------------------------------------------------- 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 : 1.201 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: 1.1743 time to fit residues: 202.4373 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 : 1.228 ------------------------------------------------------------------------------- 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: 0.4141 rms_B_bonded: 1.58 restraints_weight: 0.2500 r_work (final): 0.4141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6912 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 : 1.230 Fit side-chains revert: symmetry clash REVERT: A 123 PHE cc_start: 0.5573 (t80) cc_final: 0.5254 (t80) REVERT: A 307 GLN cc_start: 0.8101 (OUTLIER) cc_final: 0.7635 (tm-30) REVERT: A 365 ARG cc_start: 0.7433 (OUTLIER) cc_final: 0.7154 (mmt-90) REVERT: B 322 GLN cc_start: 0.8356 (OUTLIER) cc_final: 0.7955 (mt0) REVERT: E 1 GLU cc_start: 0.6631 (OUTLIER) cc_final: 0.6346 (tm-30) REVERT: F 43 LYS cc_start: 0.7631 (OUTLIER) cc_final: 0.7217 (mtmp) outliers start: 55 outliers final: 18 residues processed: 167 average time/residue: 1.2130 time to fit residues: 220.0174 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 : 1.203 ------------------------------------------------------------------------------- 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: 0.0010 chunk 134 optimal weight: 40.0000 chunk 115 optimal weight: 40.0000 chunk 83 optimal weight: 4.9990 chunk 121 optimal weight: 3.9990 chunk 93 optimal weight: 4.9990 chunk 76 optimal weight: 8.9990 chunk 70 optimal weight: 0.9990 chunk 44 optimal weight: 2.9990 chunk 105 optimal weight: 8.9990 chunk 62 optimal weight: 5.9990 overall best weight: 2.5994 ------------------------------------------------------------------------------- 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 = 0.4395 r_free = 0.4395 target = 0.227403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.209729 restraints weight = 11205.966| |-----------------------------------------------------------------------------| r_work (start): 0.4247 rms_B_bonded: 0.70 r_work: 0.4126 rms_B_bonded: 1.31 restraints_weight: 0.5000 r_work: 0.4076 rms_B_bonded: 2.11 restraints_weight: 0.2500 r_work (final): 0.4076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7023 moved from start: 0.1418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 11299 Z= 0.187 Angle : 0.633 7.816 15383 Z= 0.325 Chirality : 0.045 0.197 1764 Planarity : 0.005 0.049 1943 Dihedral : 5.270 43.738 1533 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % 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: 0.55 (0.22), residues: 1407 helix: 1.13 (0.25), residues: 406 sheet: 0.85 (0.23), residues: 485 loop : -0.66 (0.26), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP F 52 HIS 0.007 0.001 HIS A 240 PHE 0.020 0.002 PHE D 36 TYR 0.017 0.002 TYR E 94 ARG 0.005 0.001 ARG F 56 Details of bonding type rmsd hydrogen bonds : bond 0.04203 ( 589) hydrogen bonds : angle 5.09709 ( 1731) metal coordination : bond 0.00275 ( 3) SS BOND : bond 0.00453 ( 8) SS BOND : angle 0.89313 ( 16) covalent geometry : bond 0.00414 (11288) covalent geometry : angle 0.63257 (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 184 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 128 time to evaluate : 1.118 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 307 GLN cc_start: 0.8107 (OUTLIER) cc_final: 0.7651 (tm-30) REVERT: B 322 GLN cc_start: 0.8312 (OUTLIER) cc_final: 0.7911 (mt0) REVERT: E 1 GLU cc_start: 0.6683 (OUTLIER) cc_final: 0.6351 (tm-30) outliers start: 56 outliers final: 25 residues processed: 173 average time/residue: 1.1680 time to fit residues: 219.0871 Evaluate side-chains 151 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 123 time to evaluate : 1.060 ------------------------------------------------------------------------------- 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 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 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 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: 1.9990 chunk 77 optimal weight: 20.0000 chunk 43 optimal weight: 30.0000 chunk 69 optimal weight: 10.0000 chunk 81 optimal weight: 2.9990 chunk 113 optimal weight: 30.0000 chunk 74 optimal weight: 8.9990 chunk 85 optimal weight: 0.8980 chunk 50 optimal weight: 4.9990 chunk 72 optimal weight: 4.9990 chunk 125 optimal weight: 2.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- 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 F 169 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4395 r_free = 0.4395 target = 0.227214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.208635 restraints weight = 11078.308| |-----------------------------------------------------------------------------| r_work (start): 0.4221 rms_B_bonded: 0.75 r_work: 0.4096 rms_B_bonded: 1.38 restraints_weight: 0.5000 r_work: 0.4058 rms_B_bonded: 1.88 restraints_weight: 0.2500 r_work (final): 0.4058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7037 moved from start: 0.1611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 11299 Z= 0.194 Angle : 0.653 8.822 15383 Z= 0.329 Chirality : 0.046 0.210 1764 Planarity : 0.005 0.049 1943 Dihedral : 5.289 45.776 1532 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 3.90 % Allowed : 25.04 % Favored : 71.06 % 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: 0.62 (0.22), residues: 1407 helix: 1.25 (0.25), residues: 405 sheet: 0.90 (0.23), residues: 487 loop : -0.70 (0.26), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP F 52 HIS 0.007 0.001 HIS A 240 PHE 0.028 0.002 PHE B 72 TYR 0.018 0.002 TYR E 150 ARG 0.007 0.001 ARG C 18 Details of bonding type rmsd hydrogen bonds : bond 0.04069 ( 589) hydrogen bonds : angle 4.96202 ( 1731) metal coordination : bond 0.00288 ( 3) SS BOND : bond 0.00464 ( 8) SS BOND : angle 0.94684 ( 16) covalent geometry : bond 0.00434 (11288) covalent geometry : angle 0.65230 (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 171 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 123 time to evaluate : 1.173 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 278 ILE cc_start: 0.7403 (OUTLIER) cc_final: 0.7115 (mt) REVERT: A 307 GLN cc_start: 0.8097 (OUTLIER) cc_final: 0.7641 (tm-30) REVERT: B 322 GLN cc_start: 0.8335 (OUTLIER) cc_final: 0.7928 (mt0) REVERT: E 1 GLU cc_start: 0.6778 (OUTLIER) cc_final: 0.6350 (tm-30) outliers start: 48 outliers final: 28 residues processed: 164 average time/residue: 1.2081 time to fit residues: 215.1336 Evaluate side-chains 153 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 121 time to evaluate : 1.171 ------------------------------------------------------------------------------- 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 92 ASP 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 10 SER 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 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 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 99 optimal weight: 2.9990 chunk 106 optimal weight: 8.9990 chunk 71 optimal weight: 10.0000 chunk 69 optimal weight: 40.0000 chunk 94 optimal weight: 50.0000 chunk 26 optimal weight: 1.9990 chunk 119 optimal weight: 20.0000 chunk 116 optimal weight: 7.9990 chunk 58 optimal weight: 4.9990 chunk 43 optimal weight: 20.0000 chunk 13 optimal weight: 7.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 310 GLN ** B 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4388 r_free = 0.4388 target = 0.226270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4277 r_free = 0.4277 target = 0.214546 restraints weight = 11003.506| |-----------------------------------------------------------------------------| r_work (start): 0.4289 rms_B_bonded: 0.54 r_work: 0.4183 rms_B_bonded: 0.96 restraints_weight: 0.5000 r_work: 0.4142 rms_B_bonded: 1.48 restraints_weight: 0.2500 r_work (final): 0.4142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6917 moved from start: 0.1853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.076 11299 Z= 0.308 Angle : 0.725 11.625 15383 Z= 0.368 Chirality : 0.049 0.229 1764 Planarity : 0.005 0.070 1943 Dihedral : 5.589 48.400 1532 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 4.80 % Allowed : 24.72 % Favored : 70.49 % 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: 0.46 (0.22), residues: 1407 helix: 1.15 (0.25), residues: 405 sheet: 0.77 (0.22), residues: 485 loop : -0.78 (0.26), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP F 52 HIS 0.006 0.002 HIS A 240 PHE 0.027 0.002 PHE D 36 TYR 0.022 0.003 TYR E 94 ARG 0.008 0.001 ARG C 18 Details of bonding type rmsd hydrogen bonds : bond 0.04509 ( 589) hydrogen bonds : angle 4.99065 ( 1731) metal coordination : bond 0.00324 ( 3) SS BOND : bond 0.00672 ( 8) SS BOND : angle 1.28938 ( 16) covalent geometry : bond 0.00712 (11288) covalent geometry : angle 0.72452 (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 179 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 120 time to evaluate : 1.091 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 278 ILE cc_start: 0.7411 (OUTLIER) cc_final: 0.7095 (mt) REVERT: A 307 GLN cc_start: 0.8109 (OUTLIER) cc_final: 0.7684 (tm-30) REVERT: A 365 ARG cc_start: 0.7432 (OUTLIER) cc_final: 0.7136 (mmt-90) REVERT: B 322 GLN cc_start: 0.8356 (OUTLIER) cc_final: 0.7907 (mt0) REVERT: C 59 GLU cc_start: 0.8273 (OUTLIER) cc_final: 0.7258 (tp30) REVERT: E 1 GLU cc_start: 0.6810 (OUTLIER) cc_final: 0.6378 (tm-30) outliers start: 59 outliers final: 33 residues processed: 172 average time/residue: 1.1792 time to fit residues: 219.6068 Evaluate side-chains 151 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 112 time to evaluate : 1.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ILE Chi-restraints excluded: chain A residue 36 ARG Chi-restraints excluded: chain A residue 41 PHE Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 307 GLN Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 365 ARG Chi-restraints excluded: chain B residue 52 GLU Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 92 ASP Chi-restraints excluded: chain B residue 104 GLU 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 10 SER Chi-restraints excluded: chain C residue 58 LEU 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 E residue 1 GLU Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 53 SER Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain E residue 215 ILE 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 110 optimal weight: 50.0000 chunk 38 optimal weight: 5.9990 chunk 58 optimal weight: 4.9990 chunk 69 optimal weight: 0.8980 chunk 42 optimal weight: 20.0000 chunk 78 optimal weight: 6.9990 chunk 112 optimal weight: 7.9990 chunk 115 optimal weight: 10.0000 chunk 45 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 53 optimal weight: 0.7980 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 152 ASN 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 = 0.4411 r_free = 0.4411 target = 0.228809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4301 r_free = 0.4301 target = 0.217097 restraints weight = 11106.986| |-----------------------------------------------------------------------------| r_work (start): 0.4303 rms_B_bonded: 0.55 r_work: 0.4192 rms_B_bonded: 0.94 restraints_weight: 0.5000 r_work: 0.4154 rms_B_bonded: 1.45 restraints_weight: 0.2500 r_work (final): 0.4154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6885 moved from start: 0.1893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 11299 Z= 0.169 Angle : 0.663 11.588 15383 Z= 0.330 Chirality : 0.046 0.248 1764 Planarity : 0.004 0.050 1943 Dihedral : 5.331 46.237 1532 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 4.31 % Allowed : 25.53 % 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: 0.67 (0.22), residues: 1407 helix: 1.44 (0.25), residues: 407 sheet: 0.85 (0.23), residues: 485 loop : -0.72 (0.26), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP F 52 HIS 0.005 0.001 HIS A 240 PHE 0.031 0.002 PHE B 72 TYR 0.020 0.002 TYR E 150 ARG 0.005 0.000 ARG B 91 Details of bonding type rmsd hydrogen bonds : bond 0.03933 ( 589) hydrogen bonds : angle 4.84719 ( 1731) metal coordination : bond 0.00166 ( 3) SS BOND : bond 0.00372 ( 8) SS BOND : angle 0.77543 ( 16) covalent geometry : bond 0.00378 (11288) covalent geometry : angle 0.66303 (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 172 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 119 time to evaluate : 1.220 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 307 GLN cc_start: 0.8083 (OUTLIER) cc_final: 0.7614 (tm-30) REVERT: B 273 LEU cc_start: 0.7087 (OUTLIER) cc_final: 0.6813 (tm) REVERT: B 322 GLN cc_start: 0.8308 (OUTLIER) cc_final: 0.7910 (mt0) REVERT: E 1 GLU cc_start: 0.6736 (OUTLIER) cc_final: 0.6337 (tm-30) outliers start: 53 outliers final: 28 residues processed: 160 average time/residue: 1.1787 time to fit residues: 204.2651 Evaluate side-chains 143 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 111 time to evaluate : 1.232 ------------------------------------------------------------------------------- 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 92 ASP 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 15 LEU 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 14 SER Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 168 THR Chi-restraints excluded: chain D residue 180 SER Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain E residue 1 GLU Chi-restraints excluded: chain E residue 53 SER Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain F residue 53 SER Chi-restraints excluded: chain F residue 68 SER Chi-restraints excluded: chain F residue 143 LEU Chi-restraints excluded: chain F residue 156 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 58 optimal weight: 5.9990 chunk 131 optimal weight: 40.0000 chunk 0 optimal weight: 50.0000 chunk 60 optimal weight: 0.9990 chunk 8 optimal weight: 2.9990 chunk 125 optimal weight: 2.9990 chunk 134 optimal weight: 4.9990 chunk 81 optimal weight: 0.9990 chunk 69 optimal weight: 0.3980 chunk 29 optimal weight: 6.9990 chunk 94 optimal weight: 50.0000 overall best weight: 1.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 128 GLN D 161 ASN ** 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 = 0.229917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4286 r_free = 0.4286 target = 0.215591 restraints weight = 11155.271| |-----------------------------------------------------------------------------| r_work (start): 0.4286 rms_B_bonded: 0.69 r_work: 0.4157 rms_B_bonded: 1.31 restraints_weight: 0.5000 r_work: 0.4118 rms_B_bonded: 1.86 restraints_weight: 0.2500 r_work (final): 0.4118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6944 moved from start: 0.1934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 11299 Z= 0.149 Angle : 0.658 12.363 15383 Z= 0.324 Chirality : 0.045 0.267 1764 Planarity : 0.004 0.048 1943 Dihedral : 5.110 45.893 1532 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 3.74 % Allowed : 26.02 % Favored : 70.24 % 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: 0.82 (0.22), residues: 1407 helix: 1.63 (0.25), residues: 407 sheet: 0.92 (0.23), residues: 486 loop : -0.68 (0.27), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP F 159 HIS 0.005 0.001 HIS A 240 PHE 0.022 0.002 PHE B 123 TYR 0.022 0.001 TYR E 150 ARG 0.005 0.000 ARG C 18 Details of bonding type rmsd hydrogen bonds : bond 0.03771 ( 589) hydrogen bonds : angle 4.76836 ( 1731) metal coordination : bond 0.00302 ( 3) SS BOND : bond 0.00340 ( 8) SS BOND : angle 0.75235 ( 16) covalent geometry : bond 0.00330 (11288) covalent geometry : angle 0.65779 (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: 46 poor density : 110 time to evaluate : 1.075 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 307 GLN cc_start: 0.8058 (OUTLIER) cc_final: 0.7577 (tm-30) REVERT: A 365 ARG cc_start: 0.7439 (OUTLIER) cc_final: 0.7153 (mmt-90) REVERT: B 273 LEU cc_start: 0.7089 (OUTLIER) cc_final: 0.6825 (tm) REVERT: B 322 GLN cc_start: 0.8305 (OUTLIER) cc_final: 0.7890 (mt0) REVERT: E 1 GLU cc_start: 0.6740 (OUTLIER) cc_final: 0.6311 (tm-30) outliers start: 46 outliers final: 25 residues processed: 147 average time/residue: 1.3701 time to fit residues: 218.4164 Evaluate side-chains 139 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 109 time to evaluate : 1.587 ------------------------------------------------------------------------------- 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 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 92 ASP Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 270 CYS Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 322 GLN Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 104 SER Chi-restraints excluded: chain C residue 154 ILE 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 185 LEU Chi-restraints excluded: chain E residue 1 GLU Chi-restraints excluded: chain E residue 53 SER Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain F residue 53 SER Chi-restraints excluded: chain F residue 57 THR Chi-restraints excluded: chain F residue 165 SER Chi-restraints excluded: chain F residue 208 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 40 optimal weight: 7.9990 chunk 11 optimal weight: 0.7980 chunk 21 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 4.9990 chunk 68 optimal weight: 6.9990 chunk 97 optimal weight: 10.0000 chunk 113 optimal weight: 50.0000 chunk 132 optimal weight: 10.0000 chunk 109 optimal weight: 0.4980 chunk 137 optimal weight: 0.0370 overall best weight: 1.8662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 128 GLN ** E 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4411 r_free = 0.4411 target = 0.229029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4272 r_free = 0.4272 target = 0.214183 restraints weight = 11127.594| |-----------------------------------------------------------------------------| r_work (start): 0.4251 rms_B_bonded: 0.71 r_work: 0.4127 rms_B_bonded: 1.19 restraints_weight: 0.5000 r_work: 0.4090 rms_B_bonded: 1.67 restraints_weight: 0.2500 r_work (final): 0.4090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6947 moved from start: 0.2081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 11299 Z= 0.155 Angle : 0.672 12.662 15383 Z= 0.330 Chirality : 0.045 0.262 1764 Planarity : 0.004 0.048 1943 Dihedral : 5.092 51.244 1531 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 3.25 % Allowed : 26.75 % 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: 0.87 (0.22), residues: 1407 helix: 1.70 (0.25), residues: 407 sheet: 0.96 (0.23), residues: 485 loop : -0.69 (0.27), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP E 159 HIS 0.005 0.001 HIS A 240 PHE 0.030 0.002 PHE B 72 TYR 0.022 0.001 TYR E 150 ARG 0.011 0.001 ARG B 91 Details of bonding type rmsd hydrogen bonds : bond 0.03707 ( 589) hydrogen bonds : angle 4.73445 ( 1731) metal coordination : bond 0.00158 ( 3) SS BOND : bond 0.00377 ( 8) SS BOND : angle 0.78144 ( 16) covalent geometry : bond 0.00346 (11288) covalent geometry : angle 0.67165 (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 149 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 109 time to evaluate : 1.229 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 PHE cc_start: 0.7410 (OUTLIER) cc_final: 0.6894 (m-80) REVERT: A 307 GLN cc_start: 0.8050 (OUTLIER) cc_final: 0.7567 (tm-30) REVERT: A 365 ARG cc_start: 0.7442 (OUTLIER) cc_final: 0.7152 (mmt-90) REVERT: B 273 LEU cc_start: 0.7015 (OUTLIER) cc_final: 0.6707 (tm) REVERT: B 322 GLN cc_start: 0.8295 (OUTLIER) cc_final: 0.7916 (mt0) REVERT: E 1 GLU cc_start: 0.6734 (OUTLIER) cc_final: 0.6267 (tm-30) outliers start: 40 outliers final: 23 residues processed: 140 average time/residue: 1.6780 time to fit residues: 251.7610 Evaluate side-chains 136 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 107 time to evaluate : 1.268 ------------------------------------------------------------------------------- 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 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 92 ASP Chi-restraints excluded: chain B residue 270 CYS Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 322 GLN Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 104 SER Chi-restraints excluded: chain 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 56 SER Chi-restraints excluded: chain D residue 180 SER 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 53 SER Chi-restraints excluded: chain F residue 57 THR Chi-restraints excluded: chain F residue 68 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 68 optimal weight: 9.9990 chunk 128 optimal weight: 3.9990 chunk 42 optimal weight: 9.9990 chunk 41 optimal weight: 0.7980 chunk 130 optimal weight: 7.9990 chunk 2 optimal weight: 6.9990 chunk 52 optimal weight: 0.9990 chunk 72 optimal weight: 20.0000 chunk 36 optimal weight: 0.5980 chunk 20 optimal weight: 2.9990 chunk 110 optimal weight: 0.4980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 128 GLN ** E 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4429 r_free = 0.4429 target = 0.230960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4298 r_free = 0.4298 target = 0.216970 restraints weight = 11222.723| |-----------------------------------------------------------------------------| r_work (start): 0.4290 rms_B_bonded: 0.67 r_work: 0.4169 rms_B_bonded: 1.25 restraints_weight: 0.5000 r_work: 0.4117 rms_B_bonded: 2.12 restraints_weight: 0.2500 r_work (final): 0.4117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6920 moved from start: 0.2139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 11299 Z= 0.130 Angle : 0.669 15.234 15383 Z= 0.325 Chirality : 0.045 0.249 1764 Planarity : 0.004 0.048 1943 Dihedral : 4.939 56.262 1529 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 3.09 % Allowed : 26.59 % Favored : 70.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.22), residues: 1407 helix: 1.87 (0.26), residues: 408 sheet: 1.02 (0.23), residues: 486 loop : -0.63 (0.27), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP E 159 HIS 0.005 0.001 HIS A 240 PHE 0.021 0.001 PHE B 123 TYR 0.024 0.001 TYR E 150 ARG 0.009 0.000 ARG B 91 Details of bonding type rmsd hydrogen bonds : bond 0.03546 ( 589) hydrogen bonds : angle 4.68534 ( 1731) metal coordination : bond 0.00186 ( 3) SS BOND : bond 0.00304 ( 8) SS BOND : angle 0.63447 ( 16) covalent geometry : bond 0.00285 (11288) covalent geometry : angle 0.66857 (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: 38 poor density : 112 time to evaluate : 1.177 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 PHE cc_start: 0.7421 (OUTLIER) cc_final: 0.6906 (m-80) REVERT: A 307 GLN cc_start: 0.7999 (OUTLIER) cc_final: 0.7492 (tm-30) REVERT: A 365 ARG cc_start: 0.7465 (OUTLIER) cc_final: 0.7177 (mmt-90) REVERT: B 273 LEU cc_start: 0.6878 (OUTLIER) cc_final: 0.6581 (tm) REVERT: B 322 GLN cc_start: 0.8250 (OUTLIER) cc_final: 0.7892 (mt0) REVERT: D 71 SER cc_start: 0.9200 (p) cc_final: 0.8995 (t) REVERT: E 1 GLU cc_start: 0.6707 (OUTLIER) cc_final: 0.6263 (tm-30) outliers start: 38 outliers final: 24 residues processed: 140 average time/residue: 1.4712 time to fit residues: 222.4751 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 : 2.089 ------------------------------------------------------------------------------- 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 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 92 ASP 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 24 ARG Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 180 SER 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 57 THR 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: 7.9990 chunk 41 optimal weight: 8.9990 chunk 27 optimal weight: 3.9990 chunk 23 optimal weight: 6.9990 chunk 51 optimal weight: 3.9990 chunk 91 optimal weight: 9.9990 chunk 55 optimal weight: 5.9990 chunk 83 optimal weight: 2.9990 chunk 124 optimal weight: 0.9990 chunk 137 optimal weight: 9.9990 chunk 59 optimal weight: 1.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 128 GLN ** E 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 16 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4416 r_free = 0.4416 target = 0.229406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4306 r_free = 0.4306 target = 0.217657 restraints weight = 11049.157| |-----------------------------------------------------------------------------| r_work (start): 0.4300 rms_B_bonded: 0.55 r_work: 0.4194 rms_B_bonded: 0.95 restraints_weight: 0.5000 r_work: 0.4155 rms_B_bonded: 1.48 restraints_weight: 0.2500 r_work (final): 0.4155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6872 moved from start: 0.2170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 11299 Z= 0.194 Angle : 0.686 13.086 15383 Z= 0.337 Chirality : 0.046 0.249 1764 Planarity : 0.005 0.047 1943 Dihedral : 5.187 56.444 1529 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 3.01 % Allowed : 26.99 % 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: 1.75 (0.25), residues: 407 sheet: 0.99 (0.23), residues: 485 loop : -0.72 (0.27), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP E 159 HIS 0.004 0.001 HIS A 240 PHE 0.033 0.002 PHE B 72 TYR 0.026 0.002 TYR E 150 ARG 0.004 0.000 ARG F 56 Details of bonding type rmsd hydrogen bonds : bond 0.03898 ( 589) hydrogen bonds : angle 4.74969 ( 1731) metal coordination : bond 0.00125 ( 3) SS BOND : bond 0.00471 ( 8) SS BOND : angle 0.98323 ( 16) covalent geometry : bond 0.00445 (11288) covalent geometry : angle 0.68606 (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 147 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 110 time to evaluate : 1.090 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 PHE cc_start: 0.7409 (OUTLIER) cc_final: 0.6882 (m-80) REVERT: A 307 GLN cc_start: 0.8070 (OUTLIER) cc_final: 0.7588 (tm-30) REVERT: A 365 ARG cc_start: 0.7443 (OUTLIER) cc_final: 0.7140 (mmt-90) REVERT: B 91 ARG cc_start: 0.6686 (OUTLIER) cc_final: 0.6272 (mtt90) REVERT: B 273 LEU cc_start: 0.6836 (OUTLIER) cc_final: 0.6556 (tm) REVERT: B 322 GLN cc_start: 0.8354 (OUTLIER) cc_final: 0.7922 (mt0) REVERT: E 1 GLU cc_start: 0.6783 (OUTLIER) cc_final: 0.6290 (tm-30) outliers start: 37 outliers final: 25 residues processed: 139 average time/residue: 1.3111 time to fit residues: 195.8255 Evaluate side-chains 143 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 111 time to evaluate : 1.088 ------------------------------------------------------------------------------- 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 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 91 ARG Chi-restraints excluded: chain B residue 92 ASP 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 24 ARG Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 180 SER 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 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: 0.7980 chunk 138 optimal weight: 10.0000 chunk 49 optimal weight: 0.7980 chunk 97 optimal weight: 9.9990 chunk 41 optimal weight: 10.0000 chunk 96 optimal weight: 7.9990 chunk 15 optimal weight: 8.9990 chunk 105 optimal weight: 8.9990 chunk 92 optimal weight: 2.9990 chunk 137 optimal weight: 20.0000 overall best weight: 4.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 128 GLN ** E 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 16 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4405 r_free = 0.4405 target = 0.228172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4295 r_free = 0.4295 target = 0.216465 restraints weight = 10948.208| |-----------------------------------------------------------------------------| r_work (start): 0.4280 rms_B_bonded: 0.54 r_work: 0.4164 rms_B_bonded: 0.91 restraints_weight: 0.5000 r_work: 0.4126 rms_B_bonded: 1.43 restraints_weight: 0.2500 r_work (final): 0.4126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6921 moved from start: 0.2247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 11299 Z= 0.265 Angle : 0.731 13.107 15383 Z= 0.362 Chirality : 0.048 0.242 1764 Planarity : 0.005 0.064 1943 Dihedral : 5.412 49.182 1529 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 2.93 % Allowed : 26.99 % 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: 0.71 (0.22), residues: 1407 helix: 1.57 (0.25), residues: 407 sheet: 0.84 (0.23), residues: 486 loop : -0.75 (0.27), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP E 159 HIS 0.004 0.001 HIS B 325 PHE 0.026 0.002 PHE D 36 TYR 0.027 0.002 TYR E 150 ARG 0.004 0.001 ARG C 18 Details of bonding type rmsd hydrogen bonds : bond 0.04227 ( 589) hydrogen bonds : angle 4.85042 ( 1731) metal coordination : bond 0.00340 ( 3) SS BOND : bond 0.00578 ( 8) SS BOND : angle 1.20781 ( 16) covalent geometry : bond 0.00610 (11288) covalent geometry : angle 0.73010 (15367) =============================================================================== Job complete usr+sys time: 7635.29 seconds wall clock time: 134 minutes 51.36 seconds (8091.36 seconds total)