Starting phenix.real_space_refine on Thu Feb 13 08:31:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xw9_33494/02_2025/7xw9_33494.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xw9_33494/02_2025/7xw9_33494.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7xw9_33494/02_2025/7xw9_33494.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xw9_33494/02_2025/7xw9_33494.map" model { file = "/net/cci-nas-00/data/ceres_data/7xw9_33494/02_2025/7xw9_33494.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xw9_33494/02_2025/7xw9_33494.cif" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.033 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 63 5.16 5 C 5729 2.51 5 N 1533 2.21 5 O 1663 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 8988 Number of models: 1 Model: "" Number of chains: 7 Chain: "R" Number of atoms: 2294 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2294 Classifications: {'peptide': 288} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 9, 'TRANS': 278} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "A" Number of atoms: 1862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1862 Classifications: {'peptide': 227} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 220} Chain breaks: 1 Chain: "B" Number of atoms: 2600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2600 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "G" Number of atoms: 429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 429 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 4, 'TRANS': 51} Chain: "S" Number of atoms: 1777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1777 Classifications: {'peptide': 231} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 220} Chain breaks: 1 Chain: "L" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 25 Classifications: {'peptide': 3} Link IDs: {'PTRANS': 1, 'TRANS': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'PCA:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.44, per 1000 atoms: 0.61 Number of scatterers: 8988 At special positions: 0 Unit cell: (116.61, 111.54, 123.708, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 63 16.00 O 1663 8.00 N 1533 7.00 C 5729 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS R 98 " - pdb=" SG CYS R 179 " distance=2.04 Simple disulfide: pdb=" SG CYS S 147 " - pdb=" SG CYS S 217 " 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.62 Conformation dependent library (CDL) restraints added in 1.1 seconds 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2140 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 13 sheets defined 37.9% alpha, 22.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.10 Creating SS restraints... Processing helix chain 'R' and resid 23 through 53 Processing helix chain 'R' and resid 58 through 79 Processing helix chain 'R' and resid 79 through 89 removed outlier: 3.782A pdb=" N ILE R 83 " --> pdb=" O GLY R 79 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N THR R 84 " --> pdb=" O LEU R 80 " (cutoff:3.500A) Processing helix chain 'R' and resid 94 through 129 removed outlier: 4.031A pdb=" N SER R 113 " --> pdb=" O ILE R 109 " (cutoff:3.500A) Processing helix chain 'R' and resid 129 through 137 Processing helix chain 'R' and resid 138 through 162 removed outlier: 3.837A pdb=" N TYR R 156 " --> pdb=" O PHE R 152 " (cutoff:3.500A) Processing helix chain 'R' and resid 184 through 187 Processing helix chain 'R' and resid 188 through 220 Proline residue: R 203 - end of helix removed outlier: 3.553A pdb=" N LEU R 220 " --> pdb=" O ARG R 216 " (cutoff:3.500A) Processing helix chain 'R' and resid 258 through 290 removed outlier: 4.051A pdb=" N GLN R 263 " --> pdb=" O SER R 259 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N VAL R 264 " --> pdb=" O SER R 260 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N THR R 265 " --> pdb=" O ARG R 261 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N LYS R 266 " --> pdb=" O LYS R 262 " (cutoff:3.500A) Proline residue: R 281 - end of helix removed outlier: 3.648A pdb=" N SER R 290 " --> pdb=" O VAL R 286 " (cutoff:3.500A) Processing helix chain 'R' and resid 300 through 321 Proline residue: R 317 - end of helix Processing helix chain 'R' and resid 325 through 335 Processing helix chain 'A' and resid 6 through 32 removed outlier: 4.143A pdb=" N ARG A 32 " --> pdb=" O GLU A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 41 through 45 removed outlier: 4.236A pdb=" N GLY A 45 " --> pdb=" O GLY A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 264 removed outlier: 3.733A pdb=" N GLN A 261 " --> pdb=" O LYS A 258 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ASN A 264 " --> pdb=" O GLN A 261 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 293 Processing helix chain 'A' and resid 308 through 319 removed outlier: 3.903A pdb=" N LEU A 312 " --> pdb=" O LYS A 308 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLY A 319 " --> pdb=" O LYS A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 327 removed outlier: 4.067A pdb=" N TYR A 326 " --> pdb=" O LYS A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 366 removed outlier: 3.542A pdb=" N THR A 350 " --> pdb=" O ASP A 346 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ALA A 352 " --> pdb=" O ARG A 348 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N PHE A 360 " --> pdb=" O ILE A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 406 removed outlier: 3.560A pdb=" N ARG A 404 " --> pdb=" O GLN A 400 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 25 Processing helix chain 'B' and resid 29 through 35 Processing helix chain 'G' and resid 8 through 24 removed outlier: 3.592A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'G' and resid 55 through 59 Processing helix chain 'S' and resid 28 through 32 Processing helix chain 'S' and resid 87 through 91 removed outlier: 3.550A pdb=" N THR S 91 " --> pdb=" O SER S 88 " (cutoff:3.500A) Processing helix chain 'S' and resid 208 through 212 removed outlier: 3.517A pdb=" N ASP S 211 " --> pdb=" O GLU S 208 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N VAL S 212 " --> pdb=" O ALA S 209 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 208 through 212' Processing sheet with id=AA1, first strand: chain 'R' and resid 164 through 168 Processing sheet with id=AA2, first strand: chain 'A' and resid 232 through 239 removed outlier: 4.631A pdb=" N VAL A 249 " --> pdb=" O LEU A 38 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N LYS A 35 " --> pdb=" O ALA A 268 " (cutoff:3.500A) removed outlier: 8.039A pdb=" N ILE A 270 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N LEU A 37 " --> pdb=" O ILE A 270 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N VAL A 272 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N LEU A 39 " --> pdb=" O VAL A 272 " (cutoff:3.500A) removed outlier: 8.253A pdb=" N ASP A 274 " --> pdb=" O LEU A 39 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.508A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.665A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.843A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.171A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.355A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 149 through 151 removed outlier: 3.552A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.729A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.414A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.890A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 5.875A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'S' and resid 3 through 7 removed outlier: 3.513A pdb=" N THR S 78 " --> pdb=" O ASP S 73 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'S' and resid 10 through 12 removed outlier: 6.978A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 128 through 129 removed outlier: 3.635A pdb=" N ALA S 199 " --> pdb=" O SER S 196 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'S' and resid 134 through 136 removed outlier: 6.482A pdb=" N LEU S 162 " --> pdb=" O TYR S 178 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N TYR S 178 " --> pdb=" O LEU S 162 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N TRP S 164 " --> pdb=" O LEU S 176 " (cutoff:3.500A) 453 hydrogen bonds defined for protein. 1272 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.64 Time building geometry restraints manager: 2.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.30: 1449 1.30 - 1.43: 2504 1.43 - 1.57: 5132 1.57 - 1.70: 0 1.70 - 1.83: 91 Bond restraints: 9176 Sorted by residual: bond pdb=" CG PCA L 1 " pdb=" CD PCA L 1 " ideal model delta sigma weight residual 1.517 1.420 0.097 2.00e-02 2.50e+03 2.37e+01 bond pdb=" CA HIS L 2 " pdb=" C HIS L 2 " ideal model delta sigma weight residual 1.525 1.424 0.101 2.10e-02 2.27e+03 2.29e+01 bond pdb=" N PCA L 1 " pdb=" CD PCA L 1 " ideal model delta sigma weight residual 1.345 1.253 0.092 2.00e-02 2.50e+03 2.10e+01 bond pdb=" N PCA L 1 " pdb=" CA PCA L 1 " ideal model delta sigma weight residual 1.458 1.379 0.079 1.90e-02 2.77e+03 1.73e+01 bond pdb=" CA PCA L 1 " pdb=" CB PCA L 1 " ideal model delta sigma weight residual 1.530 1.456 0.074 2.00e-02 2.50e+03 1.37e+01 ... (remaining 9171 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.96: 12332 2.96 - 5.92: 88 5.92 - 8.88: 12 8.88 - 11.84: 1 11.84 - 14.80: 1 Bond angle restraints: 12434 Sorted by residual: angle pdb=" N SER A 44 " pdb=" CA SER A 44 " pdb=" C SER A 44 " ideal model delta sigma weight residual 111.28 126.08 -14.80 1.09e+00 8.42e-01 1.84e+02 angle pdb=" C VAL R 201 " pdb=" N VAL R 202 " pdb=" CA VAL R 202 " ideal model delta sigma weight residual 122.13 113.55 8.58 1.85e+00 2.92e-01 2.15e+01 angle pdb=" C GLU A 43 " pdb=" N SER A 44 " pdb=" CA SER A 44 " ideal model delta sigma weight residual 120.28 126.31 -6.03 1.34e+00 5.57e-01 2.02e+01 angle pdb=" N TRP R 300 " pdb=" CA TRP R 300 " pdb=" C TRP R 300 " ideal model delta sigma weight residual 114.56 109.00 5.56 1.27e+00 6.20e-01 1.92e+01 angle pdb=" N PCA L 1 " pdb=" CA PCA L 1 " pdb=" CB PCA L 1 " ideal model delta sigma weight residual 110.50 103.75 6.75 1.70e+00 3.46e-01 1.58e+01 ... (remaining 12429 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.42: 4916 15.42 - 30.85: 426 30.85 - 46.27: 85 46.27 - 61.70: 18 61.70 - 77.12: 6 Dihedral angle restraints: 5451 sinusoidal: 2129 harmonic: 3322 Sorted by residual: dihedral pdb=" CA LEU R 22 " pdb=" C LEU R 22 " pdb=" N GLU R 23 " pdb=" CA GLU R 23 " ideal model delta harmonic sigma weight residual 180.00 156.11 23.89 0 5.00e+00 4.00e-02 2.28e+01 dihedral pdb=" CA TYR S 101 " pdb=" C TYR S 101 " pdb=" N TYR S 102 " pdb=" CA TYR S 102 " ideal model delta harmonic sigma weight residual 180.00 159.82 20.18 0 5.00e+00 4.00e-02 1.63e+01 dihedral pdb=" CA GLU R 298 " pdb=" C GLU R 298 " pdb=" N ASN R 299 " pdb=" CA ASN R 299 " ideal model delta harmonic sigma weight residual 180.00 161.53 18.47 0 5.00e+00 4.00e-02 1.36e+01 ... (remaining 5448 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.092: 1300 0.092 - 0.184: 102 0.184 - 0.276: 3 0.276 - 0.369: 1 0.369 - 0.461: 2 Chirality restraints: 1408 Sorted by residual: chirality pdb=" CA SER A 44 " pdb=" N SER A 44 " pdb=" C SER A 44 " pdb=" CB SER A 44 " both_signs ideal model delta sigma weight residual False 2.51 2.05 0.46 2.00e-01 2.50e+01 5.31e+00 chirality pdb=" CA PRO L 3 " pdb=" N PRO L 3 " pdb=" C PRO L 3 " pdb=" CB PRO L 3 " both_signs ideal model delta sigma weight residual False 2.72 2.30 0.42 2.00e-01 2.50e+01 4.38e+00 chirality pdb=" CB VAL R 202 " pdb=" CA VAL R 202 " pdb=" CG1 VAL R 202 " pdb=" CG2 VAL R 202 " both_signs ideal model delta sigma weight residual False -2.63 -2.32 -0.31 2.00e-01 2.50e+01 2.39e+00 ... (remaining 1405 not shown) Planarity restraints: 1573 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" N PCA L 1 " -0.064 2.00e-02 2.50e+03 4.54e-02 2.58e+01 pdb=" CA PCA L 1 " 0.057 2.00e-02 2.50e+03 pdb=" CG PCA L 1 " -0.023 2.00e-02 2.50e+03 pdb=" CD PCA L 1 " -0.016 2.00e-02 2.50e+03 pdb=" OE PCA L 1 " 0.046 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL R 198 " 0.015 2.00e-02 2.50e+03 2.95e-02 8.69e+00 pdb=" C VAL R 198 " -0.051 2.00e-02 2.50e+03 pdb=" O VAL R 198 " 0.019 2.00e-02 2.50e+03 pdb=" N PHE R 199 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 40 " 0.011 2.00e-02 2.50e+03 2.24e-02 5.01e+00 pdb=" C GLY A 40 " -0.039 2.00e-02 2.50e+03 pdb=" O GLY A 40 " 0.015 2.00e-02 2.50e+03 pdb=" N THR A 41 " 0.013 2.00e-02 2.50e+03 ... (remaining 1570 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 319 2.71 - 3.26: 8460 3.26 - 3.81: 14220 3.81 - 4.35: 18140 4.35 - 4.90: 31421 Nonbonded interactions: 72560 Sorted by model distance: nonbonded pdb=" OD1 ASP A 274 " pdb=" NZ LYS A 308 " model vdw 2.167 3.120 nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.214 3.040 nonbonded pdb=" OG SER B 281 " pdb=" OD2 ASP G 48 " model vdw 2.264 3.040 nonbonded pdb=" OG SER B 331 " pdb=" OD1 ASP B 333 " model vdw 2.266 3.040 nonbonded pdb=" OE1 GLU A 234 " pdb=" NE2 HIS A 245 " model vdw 2.326 3.120 ... (remaining 72555 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=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: 0.360 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.340 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 22.980 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.030 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:12.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7382 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 : 0.005 0.104 9176 Z= 0.329 Angle : 0.680 14.803 12434 Z= 0.390 Chirality : 0.050 0.461 1408 Planarity : 0.005 0.064 1573 Dihedral : 12.265 77.123 3305 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 0.37 (0.25), residues: 1124 helix: 0.43 (0.26), residues: 384 sheet: 1.23 (0.32), residues: 272 loop : -0.41 (0.29), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP R 91 HIS 0.011 0.001 HIS L 2 PHE 0.021 0.002 PHE R 161 TYR 0.021 0.002 TYR R 24 ARG 0.016 0.001 ARG B 22 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 242 time to evaluate : 0.955 Fit side-chains REVERT: R 139 PHE cc_start: 0.8130 (t80) cc_final: 0.7129 (t80) REVERT: R 147 ILE cc_start: 0.8123 (pt) cc_final: 0.7897 (mt) REVERT: A 32 ARG cc_start: 0.6777 (mmt90) cc_final: 0.6502 (mmt90) REVERT: A 314 GLU cc_start: 0.6772 (mp0) cc_final: 0.6408 (mp0) REVERT: A 329 GLU cc_start: 0.6658 (mp0) cc_final: 0.6429 (mp0) REVERT: A 396 ASP cc_start: 0.6708 (m-30) cc_final: 0.6473 (m-30) REVERT: B 175 GLN cc_start: 0.7519 (mm-40) cc_final: 0.7294 (mm-40) REVERT: B 258 ASP cc_start: 0.6670 (t70) cc_final: 0.6390 (t70) REVERT: S 57 THR cc_start: 0.8332 (p) cc_final: 0.8104 (t) outliers start: 0 outliers final: 1 residues processed: 242 average time/residue: 1.2268 time to fit residues: 316.5317 Evaluate side-chains 227 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 226 time to evaluate : 0.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 291 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 93 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 chunk 46 optimal weight: 3.9990 chunk 28 optimal weight: 7.9990 chunk 56 optimal weight: 1.9990 chunk 44 optimal weight: 0.8980 chunk 87 optimal weight: 3.9990 chunk 33 optimal weight: 0.0170 chunk 52 optimal weight: 0.0050 chunk 64 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 overall best weight: 0.9836 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 61 ASN A 400 GLN A 402 ASN B 176 GLN B 259 GLN B 293 ASN B 340 ASN S 167 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.131742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.114625 restraints weight = 11728.745| |-----------------------------------------------------------------------------| r_work (start): 0.3467 rms_B_bonded: 1.74 r_work: 0.3352 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3208 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.1175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 9176 Z= 0.235 Angle : 0.588 9.846 12434 Z= 0.313 Chirality : 0.044 0.204 1408 Planarity : 0.004 0.051 1573 Dihedral : 4.644 37.579 1254 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 2.14 % Allowed : 7.96 % Favored : 89.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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 (0.26), residues: 1124 helix: 1.43 (0.26), residues: 383 sheet: 1.22 (0.31), residues: 304 loop : -0.35 (0.31), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 82 HIS 0.005 0.001 HIS B 62 PHE 0.017 0.001 PHE R 161 TYR 0.014 0.002 TYR R 24 ARG 0.008 0.001 ARG B 22 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 221 time to evaluate : 1.100 Fit side-chains revert: symmetry clash REVERT: R 141 ARG cc_start: 0.8114 (ttt-90) cc_final: 0.7884 (ttt180) REVERT: R 146 ILE cc_start: 0.8390 (OUTLIER) cc_final: 0.8178 (mp) REVERT: R 147 ILE cc_start: 0.8272 (pt) cc_final: 0.8025 (mt) REVERT: R 202 VAL cc_start: 0.8245 (OUTLIER) cc_final: 0.8003 (t) REVERT: R 315 ILE cc_start: 0.8408 (mt) cc_final: 0.8190 (mp) REVERT: A 243 ASN cc_start: 0.8829 (m-40) cc_final: 0.8420 (m110) REVERT: A 329 GLU cc_start: 0.7170 (mp0) cc_final: 0.6679 (mp0) REVERT: A 375 TYR cc_start: 0.8593 (m-80) cc_final: 0.8306 (m-80) REVERT: A 396 ASP cc_start: 0.7530 (m-30) cc_final: 0.7253 (m-30) REVERT: B 22 ARG cc_start: 0.7386 (mtt90) cc_final: 0.6855 (mpt180) REVERT: B 175 GLN cc_start: 0.8096 (mm-40) cc_final: 0.7861 (mm-40) REVERT: B 258 ASP cc_start: 0.7358 (t70) cc_final: 0.6313 (t70) outliers start: 21 outliers final: 6 residues processed: 230 average time/residue: 1.3935 time to fit residues: 339.0067 Evaluate side-chains 222 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 214 time to evaluate : 1.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 146 ILE Chi-restraints excluded: chain R residue 202 VAL Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain S residue 192 SER Chi-restraints excluded: chain S residue 201 THR Chi-restraints excluded: chain S residue 214 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 10 optimal weight: 2.9990 chunk 21 optimal weight: 0.8980 chunk 106 optimal weight: 4.9990 chunk 19 optimal weight: 0.8980 chunk 7 optimal weight: 0.9980 chunk 43 optimal weight: 0.3980 chunk 81 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 chunk 9 optimal weight: 0.2980 chunk 87 optimal weight: 3.9990 chunk 74 optimal weight: 4.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 293 ASN A 400 GLN B 259 GLN B 340 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.132374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.115278 restraints weight = 11988.424| |-----------------------------------------------------------------------------| r_work (start): 0.3475 rms_B_bonded: 1.77 r_work: 0.3359 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3214 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.1470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9176 Z= 0.182 Angle : 0.557 10.671 12434 Z= 0.293 Chirality : 0.043 0.196 1408 Planarity : 0.004 0.046 1573 Dihedral : 4.550 45.250 1254 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 2.76 % Allowed : 11.12 % Favored : 86.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.26), residues: 1124 helix: 1.81 (0.27), residues: 383 sheet: 1.15 (0.31), residues: 299 loop : -0.35 (0.31), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.004 0.001 HIS L 2 PHE 0.018 0.001 PHE R 139 TYR 0.013 0.001 TYR S 178 ARG 0.007 0.000 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 219 time to evaluate : 0.988 Fit side-chains revert: symmetry clash REVERT: R 146 ILE cc_start: 0.8354 (OUTLIER) cc_final: 0.8153 (mp) REVERT: R 147 ILE cc_start: 0.8267 (pt) cc_final: 0.8004 (mt) REVERT: R 202 VAL cc_start: 0.8223 (OUTLIER) cc_final: 0.7998 (t) REVERT: R 315 ILE cc_start: 0.8402 (mt) cc_final: 0.8187 (mp) REVERT: A 243 ASN cc_start: 0.8777 (m-40) cc_final: 0.8373 (m-40) REVERT: A 273 VAL cc_start: 0.8833 (t) cc_final: 0.8626 (p) REVERT: A 329 GLU cc_start: 0.7167 (mp0) cc_final: 0.6834 (mp0) REVERT: A 375 TYR cc_start: 0.8611 (m-80) cc_final: 0.8320 (m-80) REVERT: A 389 ARG cc_start: 0.8219 (mtm180) cc_final: 0.8002 (mtm180) REVERT: A 396 ASP cc_start: 0.7552 (m-30) cc_final: 0.7253 (m-30) REVERT: B 45 MET cc_start: 0.8519 (OUTLIER) cc_final: 0.7943 (mtm) REVERT: B 175 GLN cc_start: 0.8080 (mm-40) cc_final: 0.7872 (mm-40) REVERT: B 212 ASP cc_start: 0.8147 (p0) cc_final: 0.7837 (p0) REVERT: B 258 ASP cc_start: 0.7383 (t70) cc_final: 0.6979 (t70) REVERT: S 18 ARG cc_start: 0.8127 (ttm-80) cc_final: 0.7837 (ttt180) REVERT: S 218 MET cc_start: 0.8267 (ttp) cc_final: 0.8037 (ttp) outliers start: 27 outliers final: 13 residues processed: 230 average time/residue: 1.3709 time to fit residues: 334.2455 Evaluate side-chains 229 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 213 time to evaluate : 0.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 90 SER Chi-restraints excluded: chain R residue 146 ILE Chi-restraints excluded: chain R residue 177 ILE Chi-restraints excluded: chain R residue 179 CYS Chi-restraints excluded: chain R residue 202 VAL Chi-restraints excluded: chain R residue 220 LEU Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 48 ARG Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain S residue 201 THR Chi-restraints excluded: chain S residue 214 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 54 optimal weight: 0.9980 chunk 56 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 chunk 1 optimal weight: 4.9990 chunk 99 optimal weight: 6.9990 chunk 53 optimal weight: 0.6980 chunk 31 optimal weight: 0.9980 chunk 104 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 400 GLN A 402 ASN B 293 ASN B 340 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.129983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.112815 restraints weight = 11872.061| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 1.76 r_work: 0.3318 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3173 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 moved from start: 0.1682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 9176 Z= 0.358 Angle : 0.622 11.881 12434 Z= 0.330 Chirality : 0.046 0.211 1408 Planarity : 0.005 0.052 1573 Dihedral : 4.931 47.257 1254 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 2.76 % Allowed : 12.65 % Favored : 84.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.26), residues: 1124 helix: 1.70 (0.27), residues: 384 sheet: 1.09 (0.30), residues: 308 loop : -0.47 (0.31), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 82 HIS 0.007 0.001 HIS B 62 PHE 0.015 0.002 PHE R 296 TYR 0.021 0.002 TYR B 105 ARG 0.009 0.001 ARG B 22 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 216 time to evaluate : 1.030 Fit side-chains revert: symmetry clash REVERT: R 146 ILE cc_start: 0.8433 (OUTLIER) cc_final: 0.8216 (mp) REVERT: R 147 ILE cc_start: 0.8314 (pt) cc_final: 0.8070 (mt) REVERT: R 202 VAL cc_start: 0.8279 (OUTLIER) cc_final: 0.8021 (t) REVERT: A 243 ASN cc_start: 0.8797 (m-40) cc_final: 0.8362 (m110) REVERT: A 329 GLU cc_start: 0.7208 (mp0) cc_final: 0.6663 (mp0) REVERT: A 375 TYR cc_start: 0.8637 (m-80) cc_final: 0.8346 (m-80) REVERT: A 389 ARG cc_start: 0.8203 (mtm180) cc_final: 0.7745 (mtt180) REVERT: A 396 ASP cc_start: 0.7616 (m-30) cc_final: 0.7306 (m-30) REVERT: B 175 GLN cc_start: 0.8133 (mm-40) cc_final: 0.7929 (mm-40) REVERT: B 258 ASP cc_start: 0.7493 (t70) cc_final: 0.6810 (t0) outliers start: 27 outliers final: 16 residues processed: 228 average time/residue: 1.4250 time to fit residues: 343.5078 Evaluate side-chains 228 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 210 time to evaluate : 0.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 90 SER Chi-restraints excluded: chain R residue 146 ILE Chi-restraints excluded: chain R residue 177 ILE Chi-restraints excluded: chain R residue 179 CYS Chi-restraints excluded: chain R residue 198 VAL Chi-restraints excluded: chain R residue 202 VAL Chi-restraints excluded: chain R residue 220 LEU Chi-restraints excluded: chain A residue 32 ARG Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 48 ARG Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain S residue 192 SER Chi-restraints excluded: chain S residue 214 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 88 optimal weight: 5.9990 chunk 68 optimal weight: 0.0870 chunk 82 optimal weight: 0.8980 chunk 87 optimal weight: 1.9990 chunk 103 optimal weight: 0.9980 chunk 98 optimal weight: 0.7980 chunk 71 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 59 optimal weight: 0.3980 chunk 26 optimal weight: 0.6980 chunk 22 optimal weight: 0.6980 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 400 GLN B 293 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.132734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.115711 restraints weight = 11864.127| |-----------------------------------------------------------------------------| r_work (start): 0.3475 rms_B_bonded: 1.76 r_work: 0.3361 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3220 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.1782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9176 Z= 0.160 Angle : 0.540 11.125 12434 Z= 0.285 Chirality : 0.042 0.198 1408 Planarity : 0.004 0.044 1573 Dihedral : 4.489 41.160 1254 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 2.96 % Allowed : 14.59 % Favored : 82.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 1.22 (0.26), residues: 1124 helix: 1.97 (0.27), residues: 384 sheet: 1.10 (0.31), residues: 296 loop : -0.40 (0.31), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.003 0.001 HIS B 62 PHE 0.013 0.001 PHE R 139 TYR 0.013 0.001 TYR S 178 ARG 0.008 0.000 ARG B 22 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 222 time to evaluate : 0.987 Fit side-chains revert: symmetry clash REVERT: R 122 GLU cc_start: 0.7787 (mt-10) cc_final: 0.7535 (mt-10) REVERT: R 146 ILE cc_start: 0.8388 (OUTLIER) cc_final: 0.8180 (mp) REVERT: R 147 ILE cc_start: 0.8278 (pt) cc_final: 0.8012 (mt) REVERT: R 202 VAL cc_start: 0.8202 (OUTLIER) cc_final: 0.7979 (t) REVERT: A 243 ASN cc_start: 0.8777 (m-40) cc_final: 0.8405 (m-40) REVERT: A 329 GLU cc_start: 0.7168 (mp0) cc_final: 0.6824 (mp0) REVERT: A 375 TYR cc_start: 0.8640 (m-80) cc_final: 0.8337 (m-80) REVERT: A 396 ASP cc_start: 0.7594 (m-30) cc_final: 0.7278 (m-30) REVERT: B 175 GLN cc_start: 0.8158 (mm-40) cc_final: 0.7945 (mm-40) REVERT: B 258 ASP cc_start: 0.7500 (t70) cc_final: 0.7057 (t0) REVERT: S 18 ARG cc_start: 0.8034 (ttm-80) cc_final: 0.7740 (ttt180) REVERT: S 167 GLN cc_start: 0.8570 (tt0) cc_final: 0.8338 (tt0) outliers start: 29 outliers final: 18 residues processed: 237 average time/residue: 1.3388 time to fit residues: 337.9984 Evaluate side-chains 231 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 211 time to evaluate : 0.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 90 SER Chi-restraints excluded: chain R residue 146 ILE Chi-restraints excluded: chain R residue 149 VAL Chi-restraints excluded: chain R residue 177 ILE Chi-restraints excluded: chain R residue 179 CYS Chi-restraints excluded: chain R residue 202 VAL Chi-restraints excluded: chain R residue 220 LEU Chi-restraints excluded: chain A residue 32 ARG Chi-restraints excluded: chain A residue 245 HIS Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain S residue 192 SER Chi-restraints excluded: chain S residue 214 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 62 optimal weight: 0.9990 chunk 59 optimal weight: 0.0470 chunk 15 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 110 optimal weight: 0.7980 chunk 101 optimal weight: 6.9990 chunk 43 optimal weight: 0.3980 chunk 90 optimal weight: 3.9990 chunk 26 optimal weight: 0.7980 chunk 66 optimal weight: 0.7980 chunk 78 optimal weight: 0.7980 overall best weight: 0.5678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 297 GLN A 400 GLN B 293 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.133263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.115970 restraints weight = 11915.548| |-----------------------------------------------------------------------------| r_work (start): 0.3483 rms_B_bonded: 1.78 r_work: 0.3367 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3223 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7708 moved from start: 0.1871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9176 Z= 0.160 Angle : 0.533 11.047 12434 Z= 0.280 Chirality : 0.042 0.194 1408 Planarity : 0.004 0.041 1573 Dihedral : 4.379 41.366 1252 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 2.76 % Allowed : 16.22 % Favored : 81.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 1.32 (0.26), residues: 1124 helix: 2.16 (0.27), residues: 378 sheet: 1.12 (0.31), residues: 290 loop : -0.37 (0.30), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.003 0.001 HIS L 2 PHE 0.011 0.001 PHE R 296 TYR 0.012 0.001 TYR S 178 ARG 0.007 0.000 ARG B 22 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 215 time to evaluate : 1.133 Fit side-chains revert: symmetry clash REVERT: R 30 LEU cc_start: 0.7593 (mt) cc_final: 0.7325 (mm) REVERT: R 122 GLU cc_start: 0.7805 (mt-10) cc_final: 0.7554 (mt-10) REVERT: R 147 ILE cc_start: 0.8276 (pt) cc_final: 0.7970 (mt) REVERT: R 202 VAL cc_start: 0.8193 (OUTLIER) cc_final: 0.7979 (t) REVERT: A 243 ASN cc_start: 0.8754 (m-40) cc_final: 0.8386 (m-40) REVERT: A 329 GLU cc_start: 0.7175 (mp0) cc_final: 0.6831 (mp0) REVERT: A 375 TYR cc_start: 0.8635 (m-80) cc_final: 0.8339 (m-80) REVERT: A 379 THR cc_start: 0.8278 (p) cc_final: 0.8053 (m) REVERT: A 396 ASP cc_start: 0.7567 (m-30) cc_final: 0.7260 (m-30) REVERT: B 175 GLN cc_start: 0.8179 (mm-40) cc_final: 0.7958 (mm-40) REVERT: B 184 THR cc_start: 0.8341 (p) cc_final: 0.8008 (m) REVERT: B 212 ASP cc_start: 0.8245 (p0) cc_final: 0.7880 (p0) REVERT: B 258 ASP cc_start: 0.7466 (t70) cc_final: 0.7006 (t0) REVERT: S 18 ARG cc_start: 0.8036 (ttm170) cc_final: 0.7736 (ttt180) REVERT: S 167 GLN cc_start: 0.8578 (tt0) cc_final: 0.8344 (tt0) outliers start: 27 outliers final: 17 residues processed: 227 average time/residue: 1.3020 time to fit residues: 314.1448 Evaluate side-chains 227 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 209 time to evaluate : 0.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 149 VAL Chi-restraints excluded: chain R residue 177 ILE Chi-restraints excluded: chain R residue 179 CYS Chi-restraints excluded: chain R residue 198 VAL Chi-restraints excluded: chain R residue 202 VAL Chi-restraints excluded: chain R residue 220 LEU Chi-restraints excluded: chain A residue 32 ARG Chi-restraints excluded: chain A residue 245 HIS Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 48 ARG Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain S residue 192 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 45 optimal weight: 0.8980 chunk 55 optimal weight: 4.9990 chunk 101 optimal weight: 9.9990 chunk 35 optimal weight: 0.9990 chunk 79 optimal weight: 0.8980 chunk 89 optimal weight: 5.9990 chunk 9 optimal weight: 2.9990 chunk 16 optimal weight: 5.9990 chunk 69 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 38 optimal weight: 0.7980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 25 GLN B 259 GLN B 293 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.131274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.113871 restraints weight = 11976.946| |-----------------------------------------------------------------------------| r_work (start): 0.3453 rms_B_bonded: 1.78 r_work: 0.3337 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3195 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.1928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 9176 Z= 0.250 Angle : 0.574 11.099 12434 Z= 0.304 Chirality : 0.044 0.210 1408 Planarity : 0.004 0.048 1573 Dihedral : 4.595 42.899 1252 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 2.96 % Allowed : 16.53 % Favored : 80.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 1.20 (0.26), residues: 1124 helix: 1.97 (0.27), residues: 385 sheet: 1.03 (0.30), residues: 302 loop : -0.42 (0.31), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.005 0.001 HIS B 62 PHE 0.012 0.001 PHE R 296 TYR 0.012 0.002 TYR S 178 ARG 0.006 0.000 ARG B 22 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 212 time to evaluate : 1.077 Fit side-chains revert: symmetry clash REVERT: R 30 LEU cc_start: 0.7597 (mt) cc_final: 0.7363 (mm) REVERT: R 122 GLU cc_start: 0.7790 (mt-10) cc_final: 0.7521 (mt-10) REVERT: R 147 ILE cc_start: 0.8301 (pt) cc_final: 0.8002 (mp) REVERT: R 202 VAL cc_start: 0.8240 (OUTLIER) cc_final: 0.8036 (t) REVERT: A 329 GLU cc_start: 0.7202 (mp0) cc_final: 0.6862 (mp0) REVERT: A 375 TYR cc_start: 0.8641 (m-80) cc_final: 0.8335 (m-80) REVERT: A 396 ASP cc_start: 0.7624 (m-30) cc_final: 0.7300 (m-30) REVERT: B 175 GLN cc_start: 0.8168 (mm-40) cc_final: 0.7947 (mm-40) REVERT: B 212 ASP cc_start: 0.8197 (p0) cc_final: 0.7820 (p0) REVERT: B 258 ASP cc_start: 0.7468 (t70) cc_final: 0.6968 (t0) REVERT: S 18 ARG cc_start: 0.8068 (ttm170) cc_final: 0.7712 (ttt180) REVERT: S 167 GLN cc_start: 0.8584 (tt0) cc_final: 0.8331 (tt0) outliers start: 29 outliers final: 19 residues processed: 228 average time/residue: 1.3293 time to fit residues: 321.0813 Evaluate side-chains 228 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 208 time to evaluate : 0.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 149 VAL Chi-restraints excluded: chain R residue 177 ILE Chi-restraints excluded: chain R residue 179 CYS Chi-restraints excluded: chain R residue 198 VAL Chi-restraints excluded: chain R residue 202 VAL Chi-restraints excluded: chain R residue 220 LEU Chi-restraints excluded: chain A residue 32 ARG Chi-restraints excluded: chain A residue 245 HIS Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 48 ARG Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain S residue 177 ILE Chi-restraints excluded: chain S residue 192 SER Chi-restraints excluded: chain S residue 198 THR Chi-restraints excluded: chain S residue 214 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 90 optimal weight: 0.8980 chunk 9 optimal weight: 0.5980 chunk 39 optimal weight: 0.9980 chunk 6 optimal weight: 0.9990 chunk 36 optimal weight: 0.9980 chunk 42 optimal weight: 0.8980 chunk 82 optimal weight: 0.9980 chunk 62 optimal weight: 0.6980 chunk 28 optimal weight: 6.9990 chunk 48 optimal weight: 0.6980 chunk 60 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 400 GLN B 259 GLN B 293 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.132373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.114945 restraints weight = 12153.137| |-----------------------------------------------------------------------------| r_work (start): 0.3477 rms_B_bonded: 1.80 r_work: 0.3357 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3208 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.1981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 9176 Z= 0.190 Angle : 0.551 11.230 12434 Z= 0.292 Chirality : 0.043 0.206 1408 Planarity : 0.004 0.040 1573 Dihedral : 4.466 40.326 1252 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 2.86 % Allowed : 16.53 % Favored : 80.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 1.27 (0.26), residues: 1124 helix: 2.16 (0.27), residues: 378 sheet: 1.02 (0.30), residues: 300 loop : -0.42 (0.31), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.003 0.001 HIS B 62 PHE 0.014 0.001 PHE R 304 TYR 0.012 0.001 TYR S 178 ARG 0.006 0.000 ARG B 314 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 209 time to evaluate : 1.050 Fit side-chains revert: symmetry clash REVERT: R 30 LEU cc_start: 0.7604 (mt) cc_final: 0.7380 (mm) REVERT: R 122 GLU cc_start: 0.7803 (OUTLIER) cc_final: 0.7551 (mt-10) REVERT: R 147 ILE cc_start: 0.8291 (pt) cc_final: 0.8013 (mp) REVERT: A 329 GLU cc_start: 0.7205 (mp0) cc_final: 0.6856 (mp0) REVERT: A 375 TYR cc_start: 0.8647 (m-80) cc_final: 0.8315 (m-80) REVERT: A 396 ASP cc_start: 0.7629 (m-30) cc_final: 0.7316 (m-30) REVERT: B 175 GLN cc_start: 0.8196 (mm-40) cc_final: 0.7973 (mm-40) REVERT: B 184 THR cc_start: 0.8325 (p) cc_final: 0.8033 (m) REVERT: B 212 ASP cc_start: 0.8199 (p0) cc_final: 0.7825 (p0) REVERT: B 258 ASP cc_start: 0.7478 (t70) cc_final: 0.7021 (t0) REVERT: S 18 ARG cc_start: 0.8066 (ttm170) cc_final: 0.7714 (ttt180) REVERT: S 167 GLN cc_start: 0.8581 (tt0) cc_final: 0.8330 (tt0) outliers start: 28 outliers final: 20 residues processed: 225 average time/residue: 1.3102 time to fit residues: 312.9505 Evaluate side-chains 232 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 211 time to evaluate : 0.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 122 GLU Chi-restraints excluded: chain R residue 138 THR Chi-restraints excluded: chain R residue 149 VAL Chi-restraints excluded: chain R residue 177 ILE Chi-restraints excluded: chain R residue 179 CYS Chi-restraints excluded: chain R residue 198 VAL Chi-restraints excluded: chain R residue 220 LEU Chi-restraints excluded: chain A residue 32 ARG Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain S residue 177 ILE Chi-restraints excluded: chain S residue 192 SER Chi-restraints excluded: chain S residue 198 THR Chi-restraints excluded: chain S residue 214 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 71 optimal weight: 4.9990 chunk 61 optimal weight: 3.9990 chunk 92 optimal weight: 0.5980 chunk 80 optimal weight: 8.9990 chunk 93 optimal weight: 0.9980 chunk 25 optimal weight: 0.7980 chunk 87 optimal weight: 2.9990 chunk 104 optimal weight: 0.0970 chunk 50 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 2 optimal weight: 0.6980 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 400 GLN B 259 GLN B 293 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.132959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.115563 restraints weight = 11999.928| |-----------------------------------------------------------------------------| r_work (start): 0.3487 rms_B_bonded: 1.79 r_work: 0.3367 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3220 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.2031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 9176 Z= 0.173 Angle : 0.543 11.425 12434 Z= 0.285 Chirality : 0.042 0.148 1408 Planarity : 0.004 0.040 1573 Dihedral : 4.374 39.682 1252 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 2.55 % Allowed : 16.94 % Favored : 80.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 1.33 (0.26), residues: 1124 helix: 2.24 (0.27), residues: 378 sheet: 1.02 (0.30), residues: 301 loop : -0.39 (0.31), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 82 HIS 0.002 0.001 HIS S 35 PHE 0.016 0.001 PHE R 304 TYR 0.013 0.001 TYR S 178 ARG 0.006 0.000 ARG B 314 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 202 time to evaluate : 1.042 Fit side-chains revert: symmetry clash REVERT: R 30 LEU cc_start: 0.7559 (mt) cc_final: 0.7334 (mm) REVERT: R 122 GLU cc_start: 0.7816 (OUTLIER) cc_final: 0.7566 (mt-10) REVERT: R 147 ILE cc_start: 0.8271 (pt) cc_final: 0.8000 (mp) REVERT: R 315 ILE cc_start: 0.8380 (mt) cc_final: 0.8163 (mp) REVERT: A 329 GLU cc_start: 0.7197 (mp0) cc_final: 0.6861 (mp0) REVERT: A 375 TYR cc_start: 0.8649 (m-80) cc_final: 0.8327 (m-80) REVERT: A 396 ASP cc_start: 0.7596 (m-30) cc_final: 0.7282 (m-30) REVERT: B 175 GLN cc_start: 0.8195 (mm-40) cc_final: 0.7974 (mm-40) REVERT: B 184 THR cc_start: 0.8313 (p) cc_final: 0.8021 (m) REVERT: B 212 ASP cc_start: 0.8199 (p0) cc_final: 0.7822 (p0) REVERT: B 258 ASP cc_start: 0.7439 (t70) cc_final: 0.6997 (t0) REVERT: S 18 ARG cc_start: 0.8058 (ttm170) cc_final: 0.7689 (ttt180) REVERT: S 167 GLN cc_start: 0.8594 (tt0) cc_final: 0.8322 (tt0) outliers start: 25 outliers final: 20 residues processed: 215 average time/residue: 1.3169 time to fit residues: 300.4912 Evaluate side-chains 221 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 200 time to evaluate : 1.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 122 GLU Chi-restraints excluded: chain R residue 138 THR Chi-restraints excluded: chain R residue 149 VAL Chi-restraints excluded: chain R residue 177 ILE Chi-restraints excluded: chain R residue 179 CYS Chi-restraints excluded: chain R residue 220 LEU Chi-restraints excluded: chain A residue 32 ARG Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain S residue 177 ILE Chi-restraints excluded: chain S residue 192 SER Chi-restraints excluded: chain S residue 198 THR Chi-restraints excluded: chain S residue 214 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 59 optimal weight: 0.9990 chunk 60 optimal weight: 0.0370 chunk 21 optimal weight: 1.9990 chunk 80 optimal weight: 8.9990 chunk 108 optimal weight: 2.9990 chunk 13 optimal weight: 0.6980 chunk 87 optimal weight: 0.4980 chunk 12 optimal weight: 0.8980 chunk 66 optimal weight: 0.5980 chunk 92 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 overall best weight: 0.5458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 25 GLN A 400 GLN B 259 GLN B 293 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.133574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.116205 restraints weight = 12049.795| |-----------------------------------------------------------------------------| r_work (start): 0.3495 rms_B_bonded: 1.79 r_work: 0.3375 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3229 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.2090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 9176 Z= 0.159 Angle : 0.537 11.480 12434 Z= 0.282 Chirality : 0.042 0.136 1408 Planarity : 0.004 0.040 1573 Dihedral : 4.288 38.071 1252 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 2.14 % Allowed : 17.76 % Favored : 80.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 1.35 (0.26), residues: 1124 helix: 2.30 (0.27), residues: 378 sheet: 0.90 (0.30), residues: 304 loop : -0.33 (0.31), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 82 HIS 0.003 0.001 HIS B 62 PHE 0.015 0.001 PHE R 304 TYR 0.012 0.001 TYR S 178 ARG 0.006 0.000 ARG B 314 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 204 time to evaluate : 0.991 Fit side-chains revert: symmetry clash REVERT: R 122 GLU cc_start: 0.7829 (OUTLIER) cc_final: 0.7584 (mt-10) REVERT: R 147 ILE cc_start: 0.8277 (pt) cc_final: 0.8049 (mt) REVERT: R 176 VAL cc_start: 0.7536 (t) cc_final: 0.7096 (p) REVERT: R 315 ILE cc_start: 0.8388 (mt) cc_final: 0.8175 (mp) REVERT: A 329 GLU cc_start: 0.7182 (mp0) cc_final: 0.6848 (mp0) REVERT: A 375 TYR cc_start: 0.8648 (m-80) cc_final: 0.8343 (m-80) REVERT: A 396 ASP cc_start: 0.7597 (m-30) cc_final: 0.7278 (m-30) REVERT: B 173 THR cc_start: 0.8309 (p) cc_final: 0.8106 (p) REVERT: B 175 GLN cc_start: 0.8184 (mm-40) cc_final: 0.7954 (mm-40) REVERT: B 184 THR cc_start: 0.8302 (p) cc_final: 0.8019 (m) REVERT: B 212 ASP cc_start: 0.8228 (p0) cc_final: 0.7861 (p0) REVERT: B 258 ASP cc_start: 0.7424 (t70) cc_final: 0.7007 (t70) REVERT: S 18 ARG cc_start: 0.8026 (ttm170) cc_final: 0.7729 (ttt180) REVERT: S 43 LYS cc_start: 0.7708 (mppt) cc_final: 0.7361 (mppt) REVERT: S 72 ARG cc_start: 0.8091 (ttm-80) cc_final: 0.7886 (ttm-80) REVERT: S 167 GLN cc_start: 0.8578 (tt0) cc_final: 0.8287 (tt0) outliers start: 21 outliers final: 16 residues processed: 214 average time/residue: 1.3262 time to fit residues: 301.5261 Evaluate side-chains 222 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 205 time to evaluate : 0.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 122 GLU Chi-restraints excluded: chain R residue 138 THR Chi-restraints excluded: chain R residue 149 VAL Chi-restraints excluded: chain R residue 177 ILE Chi-restraints excluded: chain R residue 179 CYS Chi-restraints excluded: chain A residue 32 ARG Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain S residue 177 ILE Chi-restraints excluded: chain S residue 192 SER Chi-restraints excluded: chain S residue 214 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 4 optimal weight: 0.5980 chunk 35 optimal weight: 0.9980 chunk 79 optimal weight: 2.9990 chunk 78 optimal weight: 0.9990 chunk 49 optimal weight: 0.7980 chunk 91 optimal weight: 3.9990 chunk 74 optimal weight: 0.7980 chunk 7 optimal weight: 0.5980 chunk 89 optimal weight: 2.9990 chunk 105 optimal weight: 0.1980 chunk 75 optimal weight: 0.7980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 293 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.133525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.116151 restraints weight = 12020.278| |-----------------------------------------------------------------------------| r_work (start): 0.3494 rms_B_bonded: 1.79 r_work: 0.3375 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3229 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.2115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 9176 Z= 0.168 Angle : 0.550 12.510 12434 Z= 0.288 Chirality : 0.042 0.145 1408 Planarity : 0.004 0.039 1573 Dihedral : 4.295 38.442 1252 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 2.14 % Allowed : 17.76 % Favored : 80.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 1.33 (0.26), residues: 1124 helix: 2.28 (0.27), residues: 378 sheet: 0.89 (0.30), residues: 304 loop : -0.34 (0.31), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.002 0.001 HIS B 62 PHE 0.014 0.001 PHE R 304 TYR 0.013 0.001 TYR S 178 ARG 0.005 0.000 ARG B 314 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8185.32 seconds wall clock time: 144 minutes 39.50 seconds (8679.50 seconds total)