Starting phenix.real_space_refine on Wed Mar 4 00:47:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7duq_30866/03_2026/7duq_30866_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7duq_30866/03_2026/7duq_30866.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7duq_30866/03_2026/7duq_30866.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7duq_30866/03_2026/7duq_30866.map" model { file = "/net/cci-nas-00/data/ceres_data/7duq_30866/03_2026/7duq_30866_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7duq_30866/03_2026/7duq_30866_trim.cif" } resolution = 2.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.008 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 S 55 5.16 5 Cl 2 4.86 5 C 6175 2.51 5 N 1632 2.21 5 O 1738 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9602 Number of models: 1 Model: "" Number of chains: 7 Chain: "P" Number of atoms: 233 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 233 Classifications: {'peptide': 30} Link IDs: {'TRANS': 29} Chain: "R" Number of atoms: 3176 Number of conformers: 1 Conformer: "" Number of residues, atoms: 384, 3176 Classifications: {'peptide': 384} Link IDs: {'PTRANS': 14, 'TRANS': 369} Chain breaks: 2 Chain: "A" Number of atoms: 1990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1990 Classifications: {'peptide': 240} Link IDs: {'PTRANS': 6, 'TRANS': 233} Chain breaks: 2 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: "N" Number of atoms: 961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 961 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 5, 'TRANS': 120} Chain: "R" Number of atoms: 213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 213 Unusual residues: {'CLR': 7, 'HNO': 1} Classifications: {'undetermined': 8} Link IDs: {None: 7} Time building chain proxies: 2.22, per 1000 atoms: 0.23 Number of scatterers: 9602 At special positions: 0 Unit cell: (164.065, 105.545, 97.185, 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) Cl 2 17.00 S 55 16.00 O 1738 8.00 N 1632 7.00 C 6175 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS R 46 " - pdb=" SG CYS R 71 " distance=2.03 Simple disulfide: pdb=" SG CYS R 62 " - pdb=" SG CYS R 104 " distance=2.03 Simple disulfide: pdb=" SG CYS R 85 " - pdb=" SG CYS R 126 " distance=2.04 Simple disulfide: pdb=" SG CYS R 226 " - pdb=" SG CYS R 296 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.03 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: 0.80 Conformation dependent library (CDL) restraints added in 423.6 milliseconds 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2212 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 12 sheets defined 42.8% alpha, 19.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.22 Creating SS restraints... Processing helix chain 'P' and resid 7 through 35 Processing helix chain 'R' and resid 31 through 53 Processing helix chain 'R' and resid 137 through 169 removed outlier: 3.653A pdb=" N PHE R 143 " --> pdb=" O GLU R 139 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N SER R 157 " --> pdb=" O ALA R 153 " (cutoff:3.500A) Processing helix chain 'R' and resid 170 through 173 Processing helix chain 'R' and resid 174 through 205 Processing helix chain 'R' and resid 206 through 215 Processing helix chain 'R' and resid 223 through 256 removed outlier: 3.628A pdb=" N ARG R 227 " --> pdb=" O SER R 223 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N PHE R 230 " --> pdb=" O CYS R 226 " (cutoff:3.500A) Processing helix chain 'R' and resid 261 through 275 Processing helix chain 'R' and resid 277 through 292 removed outlier: 3.580A pdb=" N VAL R 282 " --> pdb=" O LEU R 278 " (cutoff:3.500A) Proline residue: R 283 - end of helix Processing helix chain 'R' and resid 302 through 338 removed outlier: 3.692A pdb=" N ILE R 308 " --> pdb=" O ASN R 304 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N ILE R 309 " --> pdb=" O TYR R 305 " (cutoff:3.500A) Proline residue: R 312 - end of helix Processing helix chain 'R' and resid 345 through 361 Proline residue: R 358 - end of helix Processing helix chain 'R' and resid 362 through 366 Processing helix chain 'R' and resid 376 through 393 Processing helix chain 'R' and resid 393 through 403 Processing helix chain 'R' and resid 406 through 422 Processing helix chain 'A' and resid 12 through 39 Processing helix chain 'A' and resid 49 through 51 No H-bonds generated for 'chain 'A' and resid 49 through 51' Processing helix chain 'A' and resid 52 through 63 removed outlier: 3.592A pdb=" N LEU A 63 " --> pdb=" O GLN A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 279 Processing helix chain 'A' and resid 293 through 303 removed outlier: 4.100A pdb=" N GLU A 299 " --> pdb=" O ASP A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 312 removed outlier: 3.902A pdb=" N TYR A 311 " --> pdb=" O LYS A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 318 Processing helix chain 'A' and resid 331 through 351 removed outlier: 3.578A pdb=" N ALA A 351 " --> pdb=" O ARG A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 removed outlier: 3.512A pdb=" N PHE A 376 " --> pdb=" O ILE A 372 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 24 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'B' and resid 35 through 37 No H-bonds generated for 'chain 'B' and resid 35 through 37' Processing helix chain 'G' and resid 9 through 24 removed outlier: 3.860A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 removed outlier: 3.570A pdb=" N ASP G 36 " --> pdb=" O LYS G 32 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LEU G 37 " --> pdb=" O ALA G 33 " (cutoff:3.500A) Processing helix chain 'N' and resid 28 through 32 Processing helix chain 'N' and resid 62 through 65 Processing helix chain 'N' and resid 87 through 91 Processing sheet with id=AA1, first strand: chain 'R' and resid 65 through 66 removed outlier: 3.894A pdb=" N THR R 65 " --> pdb=" O TRP R 72 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N TRP R 72 " --> pdb=" O THR R 65 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'R' and resid 80 through 84 removed outlier: 3.632A pdb=" N TYR R 101 " --> pdb=" O ASP R 122 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 208 through 214 removed outlier: 6.474A pdb=" N HIS A 41 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N PHE A 222 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N LEU A 43 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 9.102A pdb=" N ALA A 243 " --> pdb=" O THR A 40 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 46 through 51 removed outlier: 5.540A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.528A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 100 through 105 removed outlier: 4.141A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.512A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.684A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.911A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.515A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.378A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ASP B 303 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AB3, first strand: chain 'N' and resid 10 through 11 removed outlier: 6.970A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) 491 hydrogen bonds defined for protein. 1401 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.57 Time building geometry restraints manager: 1.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 3039 1.34 - 1.46: 2354 1.46 - 1.58: 4366 1.58 - 1.71: 0 1.71 - 1.83: 76 Bond restraints: 9835 Sorted by residual: bond pdb=" C14 HNO R 501 " pdb=" N15 HNO R 501 " ideal model delta sigma weight residual 1.348 1.457 -0.109 2.00e-02 2.50e+03 2.99e+01 bond pdb=" C20 HNO R 501 " pdb=" C21 HNO R 501 " ideal model delta sigma weight residual 1.418 1.357 0.061 2.00e-02 2.50e+03 9.43e+00 bond pdb=" C12 HNO R 501 " pdb=" C14 HNO R 501 " ideal model delta sigma weight residual 1.450 1.399 0.051 2.00e-02 2.50e+03 6.62e+00 bond pdb=" C24 HNO R 501 " pdb="CL2 HNO R 501 " ideal model delta sigma weight residual 1.740 1.784 -0.044 2.00e-02 2.50e+03 4.95e+00 bond pdb=" C23 HNO R 501 " pdb="CL1 HNO R 501 " ideal model delta sigma weight residual 1.741 1.785 -0.044 2.00e-02 2.50e+03 4.94e+00 ... (remaining 9830 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.14: 13007 2.14 - 4.28: 308 4.28 - 6.42: 43 6.42 - 8.55: 12 8.55 - 10.69: 2 Bond angle restraints: 13372 Sorted by residual: angle pdb=" CA TYR R 148 " pdb=" CB TYR R 148 " pdb=" CG TYR R 148 " ideal model delta sigma weight residual 113.90 122.27 -8.37 1.80e+00 3.09e-01 2.16e+01 angle pdb=" C GLY R 275 " pdb=" N VAL R 276 " pdb=" CA VAL R 276 " ideal model delta sigma weight residual 120.24 123.02 -2.78 6.30e-01 2.52e+00 1.95e+01 angle pdb=" CB MET B 61 " pdb=" CG MET B 61 " pdb=" SD MET B 61 " ideal model delta sigma weight residual 112.70 102.01 10.69 3.00e+00 1.11e-01 1.27e+01 angle pdb=" N VAL R 259 " pdb=" CA VAL R 259 " pdb=" C VAL R 259 " ideal model delta sigma weight residual 106.85 111.78 -4.93 1.42e+00 4.96e-01 1.21e+01 angle pdb=" C VAL N 48 " pdb=" N SER N 49 " pdb=" CA SER N 49 " ideal model delta sigma weight residual 121.64 115.96 5.68 1.70e+00 3.46e-01 1.12e+01 ... (remaining 13367 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.59: 5873 24.59 - 49.18: 227 49.18 - 73.77: 36 73.77 - 98.35: 8 98.35 - 122.94: 3 Dihedral angle restraints: 6147 sinusoidal: 2726 harmonic: 3421 Sorted by residual: dihedral pdb=" CB CYS N 99 " pdb=" SG CYS N 99 " pdb=" SG CYS N 107 " pdb=" CB CYS N 107 " ideal model delta sinusoidal sigma weight residual -86.00 -24.13 -61.87 1 1.00e+01 1.00e-02 5.07e+01 dihedral pdb=" CA CYS N 99 " pdb=" C CYS N 99 " pdb=" N PRO N 100 " pdb=" CA PRO N 100 " ideal model delta harmonic sigma weight residual -180.00 -146.08 -33.92 0 5.00e+00 4.00e-02 4.60e+01 dihedral pdb=" CB CYS R 46 " pdb=" SG CYS R 46 " pdb=" SG CYS R 71 " pdb=" CB CYS R 71 " ideal model delta sinusoidal sigma weight residual -86.00 -144.37 58.37 1 1.00e+01 1.00e-02 4.56e+01 ... (remaining 6144 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 1309 0.077 - 0.154: 157 0.154 - 0.231: 10 0.231 - 0.308: 8 0.308 - 0.385: 6 Chirality restraints: 1490 Sorted by residual: chirality pdb=" C14 CLR R 506 " pdb=" C13 CLR R 506 " pdb=" C15 CLR R 506 " pdb=" C8 CLR R 506 " both_signs ideal model delta sigma weight residual False -2.32 -2.70 0.39 2.00e-01 2.50e+01 3.71e+00 chirality pdb=" C14 CLR R 508 " pdb=" C13 CLR R 508 " pdb=" C15 CLR R 508 " pdb=" C8 CLR R 508 " both_signs ideal model delta sigma weight residual False -2.32 -2.70 0.38 2.00e-01 2.50e+01 3.64e+00 chirality pdb=" C14 CLR R 505 " pdb=" C13 CLR R 505 " pdb=" C15 CLR R 505 " pdb=" C8 CLR R 505 " both_signs ideal model delta sigma weight residual False -2.32 -2.67 0.35 2.00e-01 2.50e+01 3.09e+00 ... (remaining 1487 not shown) Planarity restraints: 1658 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS A 357 " 0.023 2.00e-02 2.50e+03 2.77e-02 1.15e+01 pdb=" CG HIS A 357 " -0.058 2.00e-02 2.50e+03 pdb=" ND1 HIS A 357 " 0.021 2.00e-02 2.50e+03 pdb=" CD2 HIS A 357 " 0.010 2.00e-02 2.50e+03 pdb=" CE1 HIS A 357 " -0.009 2.00e-02 2.50e+03 pdb=" NE2 HIS A 357 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR R 148 " -0.032 2.00e-02 2.50e+03 2.20e-02 9.66e+00 pdb=" CG TYR R 148 " 0.052 2.00e-02 2.50e+03 pdb=" CD1 TYR R 148 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 TYR R 148 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR R 148 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR R 148 " -0.006 2.00e-02 2.50e+03 pdb=" CZ TYR R 148 " -0.005 2.00e-02 2.50e+03 pdb=" OH TYR R 148 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 234 " -0.008 2.00e-02 2.50e+03 1.66e-02 4.83e+00 pdb=" CG PHE B 234 " 0.034 2.00e-02 2.50e+03 pdb=" CD1 PHE B 234 " -0.023 2.00e-02 2.50e+03 pdb=" CD2 PHE B 234 " -0.010 2.00e-02 2.50e+03 pdb=" CE1 PHE B 234 " 0.011 2.00e-02 2.50e+03 pdb=" CE2 PHE B 234 " -0.002 2.00e-02 2.50e+03 pdb=" CZ PHE B 234 " -0.003 2.00e-02 2.50e+03 ... (remaining 1655 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 214 2.68 - 3.24: 9533 3.24 - 3.79: 16344 3.79 - 4.35: 22538 4.35 - 4.90: 36126 Nonbonded interactions: 84755 Sorted by model distance: nonbonded pdb=" OE2 GLU P 9 " pdb=" OH TYR R 152 " model vdw 2.126 3.040 nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.140 3.040 nonbonded pdb=" OH TYR A 318 " pdb=" OD2 ASP A 343 " model vdw 2.157 3.040 nonbonded pdb=" OH TYR A 253 " pdb=" O LYS A 307 " model vdw 2.180 3.040 nonbonded pdb=" O ARG N 98 " pdb=" OH TYR N 115 " model vdw 2.186 3.040 ... (remaining 84750 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: 0.710 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: 0.190 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 10.110 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 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:6.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7453 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 0.109 9842 Z= 0.300 Angle : 0.820 10.693 13384 Z= 0.443 Chirality : 0.058 0.385 1490 Planarity : 0.005 0.045 1658 Dihedral : 13.618 122.944 3917 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 0.30 % Allowed : 2.67 % Favored : 97.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.86 (0.23), residues: 1154 helix: -0.60 (0.22), residues: 454 sheet: -0.48 (0.29), residues: 265 loop : -0.31 (0.31), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 22 TYR 0.052 0.002 TYR R 148 PHE 0.034 0.003 PHE B 234 TRP 0.016 0.002 TRP B 82 HIS 0.032 0.003 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00649 ( 9835) covalent geometry : angle 0.81857 (13372) SS BOND : bond 0.00384 ( 6) SS BOND : angle 1.91301 ( 12) hydrogen bonds : bond 0.14509 ( 491) hydrogen bonds : angle 6.92061 ( 1401) Misc. bond : bond 0.00178 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 192 time to evaluate : 0.319 Fit side-chains revert: symmetry clash REVERT: R 265 ILE cc_start: 0.7346 (tp) cc_final: 0.7087 (tp) REVERT: R 293 ASP cc_start: 0.6091 (p0) cc_final: 0.5821 (p0) REVERT: A 20 ARG cc_start: 0.7116 (mtm-85) cc_final: 0.6863 (mtm-85) REVERT: A 299 GLU cc_start: 0.5919 (mt-10) cc_final: 0.5600 (tp30) REVERT: B 176 GLN cc_start: 0.8410 (tt0) cc_final: 0.8119 (tt0) REVERT: B 188 MET cc_start: 0.8517 (mmm) cc_final: 0.8235 (mmm) REVERT: B 220 GLN cc_start: 0.7838 (mt0) cc_final: 0.7214 (mt0) REVERT: B 273 ILE cc_start: 0.8114 (mt) cc_final: 0.7902 (mp) REVERT: G 21 MET cc_start: 0.4481 (ptp) cc_final: 0.3995 (pmm) outliers start: 3 outliers final: 3 residues processed: 193 average time/residue: 0.6721 time to fit residues: 137.3978 Evaluate side-chains 150 residues out of total 1013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 147 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 260 LEU Chi-restraints excluded: chain A residue 212 PHE Chi-restraints excluded: chain B residue 59 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 108 optimal weight: 0.9990 chunk 49 optimal weight: 0.8980 chunk 97 optimal weight: 0.8980 chunk 113 optimal weight: 0.9980 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 20.0000 chunk 62 optimal weight: 10.0000 chunk 51 optimal weight: 0.8980 chunk 100 optimal weight: 0.5980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 177 ASN R 180 HIS R 221 GLN R 302 ASN R 363 HIS A 14 ASN A 262 GLN A 278 ASN A 387 HIS B 155 ASN B 176 GLN B 268 ASN N 5 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4362 r_free = 0.4362 target = 0.199035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.142830 restraints weight = 10094.396| |-----------------------------------------------------------------------------| r_work (start): 0.3795 rms_B_bonded: 2.23 r_work: 0.3649 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3506 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7433 moved from start: 0.1668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 9842 Z= 0.166 Angle : 0.596 8.320 13384 Z= 0.313 Chirality : 0.043 0.179 1490 Planarity : 0.004 0.042 1658 Dihedral : 7.883 59.935 1749 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 2.17 % Allowed : 10.07 % Favored : 87.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.28 (0.24), residues: 1154 helix: 0.92 (0.23), residues: 448 sheet: -0.34 (0.29), residues: 250 loop : -0.06 (0.31), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG R 40 TYR 0.032 0.002 TYR R 148 PHE 0.018 0.002 PHE A 273 TRP 0.014 0.002 TRP R 243 HIS 0.006 0.001 HIS R 180 Details of bonding type rmsd covalent geometry : bond 0.00358 ( 9835) covalent geometry : angle 0.59455 (13372) SS BOND : bond 0.00398 ( 6) SS BOND : angle 1.52217 ( 12) hydrogen bonds : bond 0.04710 ( 491) hydrogen bonds : angle 5.20762 ( 1401) Misc. bond : bond 0.00069 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 160 time to evaluate : 0.473 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 40 ARG cc_start: 0.7869 (ttm-80) cc_final: 0.7653 (ttm-80) REVERT: R 126 CYS cc_start: 0.5347 (m) cc_final: 0.5104 (m) REVERT: R 228 LEU cc_start: 0.7965 (OUTLIER) cc_final: 0.7764 (mm) REVERT: R 265 ILE cc_start: 0.6998 (tp) cc_final: 0.6712 (tp) REVERT: R 293 ASP cc_start: 0.7461 (p0) cc_final: 0.7213 (p0) REVERT: R 414 ARG cc_start: 0.6965 (ttp-110) cc_final: 0.6728 (ttm110) REVERT: R 417 TRP cc_start: 0.7207 (t-100) cc_final: 0.6967 (t-100) REVERT: A 20 ARG cc_start: 0.6969 (mtm-85) cc_final: 0.6382 (mtm-85) REVERT: A 28 LYS cc_start: 0.7377 (mttt) cc_final: 0.6411 (pttp) REVERT: A 283 ARG cc_start: 0.7265 (mtm110) cc_final: 0.6470 (mmt180) REVERT: B 176 GLN cc_start: 0.8968 (tt0) cc_final: 0.8687 (tt0) REVERT: B 214 ARG cc_start: 0.7584 (OUTLIER) cc_final: 0.7245 (mmp80) REVERT: B 217 MET cc_start: 0.7391 (mmm) cc_final: 0.6585 (ptm) REVERT: B 325 MET cc_start: 0.7957 (mmm) cc_final: 0.7348 (mmm) REVERT: G 21 MET cc_start: 0.3715 (ptp) cc_final: 0.3190 (pmm) REVERT: N 5 GLN cc_start: 0.7688 (OUTLIER) cc_final: 0.7159 (tm-30) REVERT: N 35 ASN cc_start: 0.8186 (OUTLIER) cc_final: 0.7885 (m-40) REVERT: N 103 PHE cc_start: 0.7893 (m-80) cc_final: 0.7507 (m-80) REVERT: N 120 GLN cc_start: 0.8110 (mm110) cc_final: 0.7682 (mm110) outliers start: 22 outliers final: 6 residues processed: 172 average time/residue: 0.6285 time to fit residues: 114.8968 Evaluate side-chains 147 residues out of total 1013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 137 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 228 LEU Chi-restraints excluded: chain A residue 212 PHE Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain N residue 5 GLN Chi-restraints excluded: chain N residue 35 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 13 optimal weight: 3.9990 chunk 72 optimal weight: 2.9990 chunk 46 optimal weight: 0.0060 chunk 87 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 105 optimal weight: 1.9990 chunk 66 optimal weight: 10.0000 chunk 90 optimal weight: 0.0170 chunk 108 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 overall best weight: 1.6040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 407 ASN A 267 GLN B 268 ASN N 5 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4336 r_free = 0.4336 target = 0.196054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.138896 restraints weight = 10061.905| |-----------------------------------------------------------------------------| r_work (start): 0.3755 rms_B_bonded: 2.22 r_work: 0.3604 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3460 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7481 moved from start: 0.1935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 9842 Z= 0.218 Angle : 0.601 9.344 13384 Z= 0.318 Chirality : 0.045 0.222 1490 Planarity : 0.004 0.042 1658 Dihedral : 7.563 59.487 1745 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.67 % Allowed : 12.93 % Favored : 84.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.50 (0.25), residues: 1154 helix: 1.32 (0.24), residues: 445 sheet: -0.51 (0.30), residues: 252 loop : 0.02 (0.31), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 96 TYR 0.039 0.002 TYR R 148 PHE 0.021 0.002 PHE R 230 TRP 0.015 0.002 TRP R 243 HIS 0.009 0.002 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00495 ( 9835) covalent geometry : angle 0.59891 (13372) SS BOND : bond 0.00599 ( 6) SS BOND : angle 1.68797 ( 12) hydrogen bonds : bond 0.04702 ( 491) hydrogen bonds : angle 5.13137 ( 1401) Misc. bond : bond 0.00052 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 139 time to evaluate : 0.399 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 265 ILE cc_start: 0.7082 (tp) cc_final: 0.6807 (tp) REVERT: R 293 ASP cc_start: 0.7329 (p0) cc_final: 0.7066 (p0) REVERT: R 414 ARG cc_start: 0.7019 (ttp-110) cc_final: 0.6815 (ttm110) REVERT: R 417 TRP cc_start: 0.7201 (t-100) cc_final: 0.6987 (t-100) REVERT: A 20 ARG cc_start: 0.6921 (mtm-85) cc_final: 0.6394 (mtm-85) REVERT: A 28 LYS cc_start: 0.7404 (mttt) cc_final: 0.6426 (pttp) REVERT: A 372 ILE cc_start: 0.8748 (OUTLIER) cc_final: 0.8228 (mp) REVERT: B 138 GLU cc_start: 0.8650 (mt-10) cc_final: 0.8211 (mt-10) REVERT: B 214 ARG cc_start: 0.7497 (OUTLIER) cc_final: 0.6952 (mmp80) REVERT: B 217 MET cc_start: 0.7770 (mmm) cc_final: 0.6956 (ppp) REVERT: G 21 MET cc_start: 0.3729 (ptp) cc_final: 0.3224 (pmm) REVERT: N 5 GLN cc_start: 0.7647 (tt0) cc_final: 0.7147 (tm-30) REVERT: N 35 ASN cc_start: 0.8292 (OUTLIER) cc_final: 0.7929 (m-40) outliers start: 27 outliers final: 10 residues processed: 151 average time/residue: 0.6644 time to fit residues: 106.5873 Evaluate side-chains 144 residues out of total 1013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 131 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 228 LEU Chi-restraints excluded: chain R residue 260 LEU Chi-restraints excluded: chain R residue 309 ILE Chi-restraints excluded: chain A residue 212 PHE Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain B residue 42 ARG Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain N residue 35 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 47 optimal weight: 1.9990 chunk 108 optimal weight: 2.9990 chunk 11 optimal weight: 0.0870 chunk 95 optimal weight: 0.0370 chunk 24 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 63 optimal weight: 0.6980 overall best weight: 0.9640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 263 GLN R 374 HIS B 176 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4338 r_free = 0.4338 target = 0.197403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.141111 restraints weight = 10171.519| |-----------------------------------------------------------------------------| r_work (start): 0.3763 rms_B_bonded: 2.46 r_work: 0.3606 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3460 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7411 moved from start: 0.2188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9842 Z= 0.158 Angle : 0.541 8.892 13384 Z= 0.287 Chirality : 0.042 0.170 1490 Planarity : 0.004 0.041 1658 Dihedral : 7.208 57.433 1745 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 2.96 % Allowed : 14.12 % Favored : 82.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.76 (0.25), residues: 1154 helix: 1.66 (0.24), residues: 445 sheet: -0.45 (0.30), residues: 252 loop : 0.06 (0.32), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 283 TYR 0.037 0.002 TYR R 148 PHE 0.018 0.001 PHE R 230 TRP 0.014 0.001 TRP R 243 HIS 0.006 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00353 ( 9835) covalent geometry : angle 0.53946 (13372) SS BOND : bond 0.00250 ( 6) SS BOND : angle 1.56071 ( 12) hydrogen bonds : bond 0.04203 ( 491) hydrogen bonds : angle 4.92699 ( 1401) Misc. bond : bond 0.00034 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 141 time to evaluate : 0.242 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 40 ARG cc_start: 0.7992 (ttm-80) cc_final: 0.7782 (ttm-80) REVERT: R 121 ARG cc_start: 0.5060 (OUTLIER) cc_final: 0.4778 (ptt180) REVERT: R 228 LEU cc_start: 0.7957 (OUTLIER) cc_final: 0.7747 (mm) REVERT: R 265 ILE cc_start: 0.7007 (tp) cc_final: 0.6805 (tp) REVERT: R 293 ASP cc_start: 0.7481 (p0) cc_final: 0.7243 (p0) REVERT: R 353 THR cc_start: 0.8745 (m) cc_final: 0.8146 (p) REVERT: R 414 ARG cc_start: 0.6972 (ttp-110) cc_final: 0.6768 (ttm110) REVERT: A 17 LYS cc_start: 0.7056 (mttp) cc_final: 0.6843 (mtpp) REVERT: A 20 ARG cc_start: 0.6861 (mtm-85) cc_final: 0.6245 (mtm-85) REVERT: A 28 LYS cc_start: 0.7400 (mttt) cc_final: 0.6379 (pttp) REVERT: B 214 ARG cc_start: 0.7395 (OUTLIER) cc_final: 0.7094 (mmp80) REVERT: B 217 MET cc_start: 0.7728 (mmm) cc_final: 0.7174 (ppp) REVERT: B 252 LEU cc_start: 0.8582 (tt) cc_final: 0.8284 (tp) REVERT: G 21 MET cc_start: 0.3679 (ptp) cc_final: 0.3245 (pmm) REVERT: N 5 GLN cc_start: 0.7599 (tt0) cc_final: 0.7064 (tm-30) outliers start: 30 outliers final: 13 residues processed: 160 average time/residue: 0.5936 time to fit residues: 101.4789 Evaluate side-chains 147 residues out of total 1013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 131 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 121 ARG Chi-restraints excluded: chain R residue 228 LEU Chi-restraints excluded: chain R residue 260 LEU Chi-restraints excluded: chain R residue 309 ILE Chi-restraints excluded: chain A residue 212 PHE Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain B residue 42 ARG Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 258 ASP Chi-restraints excluded: chain N residue 3 GLN Chi-restraints excluded: chain N residue 35 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 14 optimal weight: 0.5980 chunk 43 optimal weight: 2.9990 chunk 82 optimal weight: 4.9990 chunk 1 optimal weight: 0.5980 chunk 15 optimal weight: 0.6980 chunk 77 optimal weight: 0.4980 chunk 50 optimal weight: 0.9990 chunk 4 optimal weight: 10.0000 chunk 51 optimal weight: 0.0970 chunk 33 optimal weight: 1.9990 chunk 63 optimal weight: 0.9990 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 263 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4359 r_free = 0.4359 target = 0.199702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.143541 restraints weight = 10158.983| |-----------------------------------------------------------------------------| r_work (start): 0.3799 rms_B_bonded: 2.26 r_work: 0.3655 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3510 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3510 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7377 moved from start: 0.2510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 9842 Z= 0.121 Angle : 0.510 8.726 13384 Z= 0.270 Chirality : 0.040 0.169 1490 Planarity : 0.004 0.040 1658 Dihedral : 6.788 57.019 1745 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 2.96 % Allowed : 14.71 % Favored : 82.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.02 (0.25), residues: 1154 helix: 2.00 (0.24), residues: 445 sheet: -0.33 (0.31), residues: 250 loop : 0.05 (0.32), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 283 TYR 0.038 0.002 TYR R 148 PHE 0.015 0.001 PHE R 230 TRP 0.014 0.001 TRP R 39 HIS 0.005 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00266 ( 9835) covalent geometry : angle 0.50781 (13372) SS BOND : bond 0.00254 ( 6) SS BOND : angle 1.64541 ( 12) hydrogen bonds : bond 0.03934 ( 491) hydrogen bonds : angle 4.71943 ( 1401) Misc. bond : bond 0.00024 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 148 time to evaluate : 0.411 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 265 ILE cc_start: 0.7226 (tp) cc_final: 0.6981 (tp) REVERT: R 293 ASP cc_start: 0.7415 (p0) cc_final: 0.7190 (p0) REVERT: R 353 THR cc_start: 0.8749 (m) cc_final: 0.8406 (m) REVERT: A 20 ARG cc_start: 0.6852 (mtm-85) cc_final: 0.6204 (mtp85) REVERT: A 21 GLU cc_start: 0.7204 (mt-10) cc_final: 0.6802 (pt0) REVERT: A 28 LYS cc_start: 0.7416 (mttt) cc_final: 0.6396 (pttp) REVERT: A 210 THR cc_start: 0.6946 (p) cc_final: 0.6645 (t) REVERT: A 283 ARG cc_start: 0.7176 (mtm110) cc_final: 0.6394 (mmt180) REVERT: B 188 MET cc_start: 0.8638 (mmm) cc_final: 0.8259 (mmm) REVERT: B 214 ARG cc_start: 0.7297 (OUTLIER) cc_final: 0.7082 (mmp80) REVERT: B 217 MET cc_start: 0.7633 (mmm) cc_final: 0.7249 (ppp) REVERT: B 252 LEU cc_start: 0.8563 (tt) cc_final: 0.8274 (tp) REVERT: B 258 ASP cc_start: 0.5644 (OUTLIER) cc_final: 0.5381 (m-30) REVERT: N 5 GLN cc_start: 0.7649 (tt0) cc_final: 0.7141 (tm-30) REVERT: N 103 PHE cc_start: 0.7953 (m-80) cc_final: 0.7642 (m-80) outliers start: 30 outliers final: 12 residues processed: 167 average time/residue: 0.5610 time to fit residues: 100.3823 Evaluate side-chains 150 residues out of total 1013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 136 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 50 LEU Chi-restraints excluded: chain R residue 100 VAL Chi-restraints excluded: chain R residue 309 ILE Chi-restraints excluded: chain A residue 212 PHE Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain B residue 42 ARG Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 258 ASP Chi-restraints excluded: chain N residue 35 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 22 optimal weight: 0.8980 chunk 89 optimal weight: 0.8980 chunk 84 optimal weight: 4.9990 chunk 35 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 95 optimal weight: 7.9990 chunk 82 optimal weight: 1.9990 chunk 78 optimal weight: 4.9990 chunk 49 optimal weight: 0.9990 chunk 10 optimal weight: 20.0000 chunk 54 optimal weight: 1.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 212 HIS R 263 GLN B 156 GLN B 220 GLN B 340 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4329 r_free = 0.4329 target = 0.196322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.139244 restraints weight = 10105.014| |-----------------------------------------------------------------------------| r_work (start): 0.3746 rms_B_bonded: 2.25 r_work: 0.3599 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3457 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7443 moved from start: 0.2458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 9842 Z= 0.193 Angle : 0.555 7.854 13384 Z= 0.295 Chirality : 0.043 0.195 1490 Planarity : 0.004 0.038 1658 Dihedral : 6.955 59.173 1745 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 3.26 % Allowed : 15.60 % Favored : 81.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.92 (0.25), residues: 1154 helix: 1.86 (0.24), residues: 443 sheet: -0.35 (0.31), residues: 251 loop : 0.06 (0.32), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG R 40 TYR 0.034 0.002 TYR R 148 PHE 0.020 0.002 PHE R 230 TRP 0.020 0.002 TRP R 264 HIS 0.006 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00441 ( 9835) covalent geometry : angle 0.55309 (13372) SS BOND : bond 0.00311 ( 6) SS BOND : angle 1.72044 ( 12) hydrogen bonds : bond 0.04304 ( 491) hydrogen bonds : angle 4.85862 ( 1401) Misc. bond : bond 0.00034 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 142 time to evaluate : 0.379 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 9 GLU cc_start: 0.7946 (OUTLIER) cc_final: 0.7629 (tp30) REVERT: R 121 ARG cc_start: 0.5087 (OUTLIER) cc_final: 0.4853 (ptt-90) REVERT: R 265 ILE cc_start: 0.7309 (tp) cc_final: 0.7051 (tp) REVERT: R 293 ASP cc_start: 0.7246 (p0) cc_final: 0.7029 (p0) REVERT: A 20 ARG cc_start: 0.6874 (mtm-85) cc_final: 0.6177 (mtp85) REVERT: A 21 GLU cc_start: 0.7240 (mt-10) cc_final: 0.6830 (pt0) REVERT: A 28 LYS cc_start: 0.7379 (mttt) cc_final: 0.6364 (pttp) REVERT: A 210 THR cc_start: 0.6903 (p) cc_final: 0.6590 (t) REVERT: B 156 GLN cc_start: 0.8202 (mt0) cc_final: 0.7808 (mt0) REVERT: B 214 ARG cc_start: 0.7355 (OUTLIER) cc_final: 0.6986 (mmp80) REVERT: B 217 MET cc_start: 0.7619 (mmm) cc_final: 0.7172 (ppp) REVERT: B 258 ASP cc_start: 0.5682 (OUTLIER) cc_final: 0.5444 (m-30) REVERT: G 21 MET cc_start: 0.3859 (ptp) cc_final: 0.3158 (pmm) REVERT: N 5 GLN cc_start: 0.7606 (tt0) cc_final: 0.7102 (tm-30) REVERT: N 35 ASN cc_start: 0.8274 (OUTLIER) cc_final: 0.7957 (m-40) outliers start: 33 outliers final: 17 residues processed: 166 average time/residue: 0.5434 time to fit residues: 96.6795 Evaluate side-chains 152 residues out of total 1013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 130 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 9 GLU Chi-restraints excluded: chain R residue 50 LEU Chi-restraints excluded: chain R residue 100 VAL Chi-restraints excluded: chain R residue 121 ARG Chi-restraints excluded: chain R residue 260 LEU Chi-restraints excluded: chain R residue 309 ILE Chi-restraints excluded: chain A residue 212 PHE Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain B residue 42 ARG Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 258 ASP Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain G residue 17 GLU Chi-restraints excluded: chain N residue 3 GLN Chi-restraints excluded: chain N residue 35 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 2 optimal weight: 1.9990 chunk 73 optimal weight: 4.9990 chunk 113 optimal weight: 0.9990 chunk 15 optimal weight: 2.9990 chunk 56 optimal weight: 0.9980 chunk 63 optimal weight: 0.6980 chunk 68 optimal weight: 7.9990 chunk 75 optimal weight: 2.9990 chunk 66 optimal weight: 5.9990 chunk 5 optimal weight: 0.9990 chunk 99 optimal weight: 20.0000 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 212 HIS R 263 GLN B 176 GLN B 220 GLN B 340 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4331 r_free = 0.4331 target = 0.196599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.139739 restraints weight = 10090.380| |-----------------------------------------------------------------------------| r_work (start): 0.3756 rms_B_bonded: 2.25 r_work: 0.3609 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3467 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7430 moved from start: 0.2601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9842 Z= 0.170 Angle : 0.553 8.005 13384 Z= 0.292 Chirality : 0.043 0.223 1490 Planarity : 0.004 0.042 1658 Dihedral : 6.878 58.782 1745 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 3.06 % Allowed : 16.29 % Favored : 80.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.94 (0.25), residues: 1154 helix: 1.96 (0.24), residues: 443 sheet: -0.37 (0.31), residues: 252 loop : 0.00 (0.31), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 283 TYR 0.031 0.002 TYR R 148 PHE 0.019 0.002 PHE R 230 TRP 0.022 0.002 TRP R 264 HIS 0.006 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00386 ( 9835) covalent geometry : angle 0.55156 (13372) SS BOND : bond 0.00294 ( 6) SS BOND : angle 1.56196 ( 12) hydrogen bonds : bond 0.04206 ( 491) hydrogen bonds : angle 4.82656 ( 1401) Misc. bond : bond 0.00022 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 143 time to evaluate : 0.384 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: P 9 GLU cc_start: 0.7931 (OUTLIER) cc_final: 0.7676 (tp30) REVERT: R 260 LEU cc_start: 0.6426 (OUTLIER) cc_final: 0.6225 (mt) REVERT: R 265 ILE cc_start: 0.7340 (tp) cc_final: 0.7079 (tp) REVERT: R 293 ASP cc_start: 0.7220 (p0) cc_final: 0.6998 (p0) REVERT: R 353 THR cc_start: 0.8726 (m) cc_final: 0.8362 (m) REVERT: R 414 ARG cc_start: 0.7229 (ttm110) cc_final: 0.6841 (ttm110) REVERT: A 20 ARG cc_start: 0.6843 (mtm-85) cc_final: 0.6189 (mtp85) REVERT: A 21 GLU cc_start: 0.7214 (mt-10) cc_final: 0.6822 (pt0) REVERT: A 28 LYS cc_start: 0.7368 (mttt) cc_final: 0.6361 (pttp) REVERT: A 210 THR cc_start: 0.6885 (p) cc_final: 0.6577 (t) REVERT: A 278 ASN cc_start: 0.8623 (m-40) cc_final: 0.8357 (m110) REVERT: A 283 ARG cc_start: 0.7276 (mtm110) cc_final: 0.6380 (mmt180) REVERT: B 217 MET cc_start: 0.7439 (mmm) cc_final: 0.7097 (ppp) REVERT: B 252 LEU cc_start: 0.8587 (tt) cc_final: 0.8280 (tp) REVERT: B 258 ASP cc_start: 0.5630 (OUTLIER) cc_final: 0.5428 (m-30) REVERT: G 21 MET cc_start: 0.3838 (ptp) cc_final: 0.3307 (pmm) REVERT: N 5 GLN cc_start: 0.7622 (tt0) cc_final: 0.7117 (tm-30) REVERT: N 35 ASN cc_start: 0.8197 (OUTLIER) cc_final: 0.7923 (m-40) outliers start: 31 outliers final: 15 residues processed: 164 average time/residue: 0.5837 time to fit residues: 102.4548 Evaluate side-chains 153 residues out of total 1013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 134 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 9 GLU Chi-restraints excluded: chain R residue 100 VAL Chi-restraints excluded: chain R residue 260 LEU Chi-restraints excluded: chain R residue 309 ILE Chi-restraints excluded: chain A residue 212 PHE Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain B residue 42 ARG Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 258 ASP Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain G residue 17 GLU Chi-restraints excluded: chain N residue 3 GLN Chi-restraints excluded: chain N residue 35 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 71 optimal weight: 2.9990 chunk 90 optimal weight: 0.0670 chunk 68 optimal weight: 5.9990 chunk 52 optimal weight: 0.9980 chunk 8 optimal weight: 7.9990 chunk 63 optimal weight: 1.9990 chunk 73 optimal weight: 0.6980 chunk 54 optimal weight: 1.9990 chunk 51 optimal weight: 4.9990 chunk 70 optimal weight: 0.4980 chunk 113 optimal weight: 0.7980 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 212 HIS R 263 GLN B 156 GLN B 176 GLN B 220 GLN B 340 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4352 r_free = 0.4352 target = 0.199004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.143030 restraints weight = 10101.789| |-----------------------------------------------------------------------------| r_work (start): 0.3782 rms_B_bonded: 2.57 r_work: 0.3621 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7252 moved from start: 0.2754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9842 Z= 0.128 Angle : 0.524 7.832 13384 Z= 0.275 Chirality : 0.041 0.194 1490 Planarity : 0.004 0.039 1658 Dihedral : 6.594 57.336 1745 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 2.86 % Allowed : 16.98 % Favored : 80.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.02 (0.25), residues: 1154 helix: 2.03 (0.24), residues: 451 sheet: -0.33 (0.32), residues: 240 loop : -0.03 (0.31), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 283 TYR 0.029 0.002 TYR R 148 PHE 0.018 0.001 PHE R 230 TRP 0.023 0.001 TRP R 264 HIS 0.005 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00285 ( 9835) covalent geometry : angle 0.52222 (13372) SS BOND : bond 0.00264 ( 6) SS BOND : angle 1.36549 ( 12) hydrogen bonds : bond 0.03929 ( 491) hydrogen bonds : angle 4.66135 ( 1401) Misc. bond : bond 0.00011 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 136 time to evaluate : 0.377 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 40 ARG cc_start: 0.7891 (ttm-80) cc_final: 0.7202 (mtp180) REVERT: R 211 GLN cc_start: 0.7476 (mm-40) cc_final: 0.6967 (tp-100) REVERT: R 265 ILE cc_start: 0.7318 (tp) cc_final: 0.7022 (tp) REVERT: R 293 ASP cc_start: 0.7079 (p0) cc_final: 0.6713 (p0) REVERT: R 414 ARG cc_start: 0.7186 (ttm110) cc_final: 0.6768 (ttm110) REVERT: A 20 ARG cc_start: 0.6772 (mtm-85) cc_final: 0.6179 (mtm-85) REVERT: A 21 GLU cc_start: 0.7069 (mt-10) cc_final: 0.6727 (pt0) REVERT: A 28 LYS cc_start: 0.7310 (mttt) cc_final: 0.6318 (pttp) REVERT: A 210 THR cc_start: 0.6957 (p) cc_final: 0.6677 (t) REVERT: A 283 ARG cc_start: 0.7052 (mtm110) cc_final: 0.6309 (mmt180) REVERT: A 389 ARG cc_start: 0.7662 (ttp-110) cc_final: 0.7401 (mtm110) REVERT: B 96 ARG cc_start: 0.8516 (mtm110) cc_final: 0.7546 (mmt-90) REVERT: B 188 MET cc_start: 0.8555 (mmm) cc_final: 0.8153 (mmm) REVERT: B 252 LEU cc_start: 0.8445 (tt) cc_final: 0.8125 (tp) REVERT: G 21 MET cc_start: 0.3830 (ptp) cc_final: 0.3342 (pmm) REVERT: G 50 LEU cc_start: 0.7623 (mt) cc_final: 0.7008 (mp) REVERT: N 5 GLN cc_start: 0.7462 (tt0) cc_final: 0.7066 (tm-30) outliers start: 29 outliers final: 17 residues processed: 158 average time/residue: 0.5604 time to fit residues: 94.9122 Evaluate side-chains 148 residues out of total 1013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 131 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 50 LEU Chi-restraints excluded: chain R residue 100 VAL Chi-restraints excluded: chain R residue 309 ILE Chi-restraints excluded: chain A residue 212 PHE Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain B residue 42 ARG Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain G residue 17 GLU Chi-restraints excluded: chain N residue 3 GLN Chi-restraints excluded: chain N residue 35 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 7 optimal weight: 9.9990 chunk 0 optimal weight: 4.9990 chunk 56 optimal weight: 0.8980 chunk 39 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 chunk 58 optimal weight: 0.0010 chunk 9 optimal weight: 0.8980 chunk 69 optimal weight: 0.7980 chunk 95 optimal weight: 1.9990 chunk 4 optimal weight: 3.9990 chunk 85 optimal weight: 3.9990 overall best weight: 0.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 212 HIS R 263 GLN A 278 ASN ** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4351 r_free = 0.4351 target = 0.198958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.142626 restraints weight = 9998.370| |-----------------------------------------------------------------------------| r_work (start): 0.3789 rms_B_bonded: 2.22 r_work: 0.3644 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3500 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3500 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7400 moved from start: 0.2856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9842 Z= 0.135 Angle : 0.531 7.489 13384 Z= 0.279 Chirality : 0.042 0.211 1490 Planarity : 0.004 0.039 1658 Dihedral : 6.488 56.566 1745 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.47 % Allowed : 17.87 % Favored : 79.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.10 (0.25), residues: 1154 helix: 2.16 (0.24), residues: 443 sheet: -0.29 (0.31), residues: 255 loop : 0.02 (0.31), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 283 TYR 0.025 0.002 TYR R 148 PHE 0.017 0.001 PHE R 230 TRP 0.026 0.001 TRP R 264 HIS 0.005 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00303 ( 9835) covalent geometry : angle 0.52921 (13372) SS BOND : bond 0.00249 ( 6) SS BOND : angle 1.40494 ( 12) hydrogen bonds : bond 0.03954 ( 491) hydrogen bonds : angle 4.65583 ( 1401) Misc. bond : bond 0.00017 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 132 time to evaluate : 0.333 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 211 GLN cc_start: 0.7503 (mm-40) cc_final: 0.7007 (tp-100) REVERT: R 265 ILE cc_start: 0.7351 (tp) cc_final: 0.7103 (tp) REVERT: R 293 ASP cc_start: 0.7210 (p0) cc_final: 0.6905 (p0) REVERT: R 414 ARG cc_start: 0.7194 (ttm110) cc_final: 0.6761 (ttm110) REVERT: A 20 ARG cc_start: 0.6783 (mtm-85) cc_final: 0.6268 (mtm-85) REVERT: A 21 GLU cc_start: 0.7132 (mt-10) cc_final: 0.6747 (pt0) REVERT: A 28 LYS cc_start: 0.7394 (mttt) cc_final: 0.6369 (pttp) REVERT: A 278 ASN cc_start: 0.8568 (m-40) cc_final: 0.8340 (m-40) REVERT: A 283 ARG cc_start: 0.7211 (mtm110) cc_final: 0.6352 (mmt180) REVERT: A 380 ARG cc_start: 0.7858 (mtp180) cc_final: 0.7527 (mtp180) REVERT: A 389 ARG cc_start: 0.7884 (ttp-110) cc_final: 0.7525 (mtm110) REVERT: B 96 ARG cc_start: 0.8598 (mtm110) cc_final: 0.7559 (mmt-90) REVERT: B 252 LEU cc_start: 0.8517 (tt) cc_final: 0.8204 (tp) REVERT: B 340 ASN cc_start: 0.7888 (OUTLIER) cc_final: 0.7634 (m-40) REVERT: G 21 MET cc_start: 0.3816 (ptp) cc_final: 0.3308 (pmm) REVERT: G 50 LEU cc_start: 0.7709 (mt) cc_final: 0.7074 (mp) REVERT: N 5 GLN cc_start: 0.7562 (tt0) cc_final: 0.7103 (tm-30) REVERT: N 114 THR cc_start: 0.8014 (p) cc_final: 0.7593 (m) outliers start: 25 outliers final: 19 residues processed: 149 average time/residue: 0.5473 time to fit residues: 87.5680 Evaluate side-chains 152 residues out of total 1013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 132 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 100 VAL Chi-restraints excluded: chain R residue 309 ILE Chi-restraints excluded: chain R residue 346 LYS Chi-restraints excluded: chain A residue 212 PHE Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain B residue 42 ARG Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain G residue 17 GLU Chi-restraints excluded: chain N residue 3 GLN Chi-restraints excluded: chain N residue 35 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 8 optimal weight: 5.9990 chunk 101 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 chunk 75 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 69 optimal weight: 0.5980 chunk 30 optimal weight: 0.8980 chunk 83 optimal weight: 0.3980 chunk 61 optimal weight: 4.9990 chunk 79 optimal weight: 0.7980 chunk 26 optimal weight: 0.4980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 212 HIS R 263 GLN B 35 ASN ** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4355 r_free = 0.4355 target = 0.199317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.142955 restraints weight = 10028.756| |-----------------------------------------------------------------------------| r_work (start): 0.3791 rms_B_bonded: 2.25 r_work: 0.3647 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3501 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7385 moved from start: 0.2899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9842 Z= 0.130 Angle : 0.529 7.492 13384 Z= 0.277 Chirality : 0.042 0.228 1490 Planarity : 0.004 0.040 1658 Dihedral : 6.428 56.953 1745 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 2.17 % Allowed : 18.16 % Favored : 79.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.12 (0.25), residues: 1154 helix: 2.20 (0.23), residues: 443 sheet: -0.31 (0.31), residues: 250 loop : 0.01 (0.31), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG R 40 TYR 0.014 0.002 TYR R 69 PHE 0.016 0.001 PHE R 230 TRP 0.027 0.001 TRP R 264 HIS 0.007 0.001 HIS R 212 Details of bonding type rmsd covalent geometry : bond 0.00291 ( 9835) covalent geometry : angle 0.52748 (13372) SS BOND : bond 0.00255 ( 6) SS BOND : angle 1.33370 ( 12) hydrogen bonds : bond 0.03911 ( 491) hydrogen bonds : angle 4.63580 ( 1401) Misc. bond : bond 0.00018 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 134 time to evaluate : 0.383 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 40 ARG cc_start: 0.7900 (ttm-80) cc_final: 0.7263 (mtp180) REVERT: R 265 ILE cc_start: 0.7339 (tp) cc_final: 0.7078 (tp) REVERT: R 293 ASP cc_start: 0.7205 (p0) cc_final: 0.6918 (p0) REVERT: R 414 ARG cc_start: 0.7153 (ttm110) cc_final: 0.6717 (ttm110) REVERT: A 17 LYS cc_start: 0.7047 (mttp) cc_final: 0.6825 (mtpp) REVERT: A 20 ARG cc_start: 0.6795 (mtm-85) cc_final: 0.6172 (mtm-85) REVERT: A 21 GLU cc_start: 0.7130 (mt-10) cc_final: 0.6774 (pt0) REVERT: A 28 LYS cc_start: 0.7376 (mttt) cc_final: 0.6353 (pttp) REVERT: A 278 ASN cc_start: 0.8608 (m-40) cc_final: 0.8386 (m-40) REVERT: A 283 ARG cc_start: 0.7209 (mtm110) cc_final: 0.6344 (mmt180) REVERT: A 380 ARG cc_start: 0.7824 (mtp180) cc_final: 0.7482 (mtp180) REVERT: A 389 ARG cc_start: 0.7817 (ttp-110) cc_final: 0.7501 (mtm110) REVERT: B 96 ARG cc_start: 0.8604 (mtm110) cc_final: 0.7606 (mmt180) REVERT: B 252 LEU cc_start: 0.8498 (tt) cc_final: 0.8181 (tp) REVERT: G 21 MET cc_start: 0.3755 (ptp) cc_final: 0.3250 (pmm) REVERT: G 50 LEU cc_start: 0.7656 (mt) cc_final: 0.7020 (mp) REVERT: N 5 GLN cc_start: 0.7586 (tt0) cc_final: 0.7091 (tm-30) REVERT: N 114 THR cc_start: 0.8014 (p) cc_final: 0.7581 (m) outliers start: 22 outliers final: 18 residues processed: 149 average time/residue: 0.5675 time to fit residues: 90.9507 Evaluate side-chains 145 residues out of total 1013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 127 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 100 VAL Chi-restraints excluded: chain R residue 148 TYR Chi-restraints excluded: chain R residue 309 ILE Chi-restraints excluded: chain R residue 346 LYS Chi-restraints excluded: chain A residue 212 PHE Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain B residue 42 ARG Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain G residue 17 GLU Chi-restraints excluded: chain N residue 3 GLN Chi-restraints excluded: chain N residue 35 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 107 optimal weight: 0.8980 chunk 40 optimal weight: 3.9990 chunk 81 optimal weight: 4.9990 chunk 32 optimal weight: 0.9980 chunk 33 optimal weight: 6.9990 chunk 112 optimal weight: 0.7980 chunk 114 optimal weight: 0.8980 chunk 16 optimal weight: 0.9980 chunk 72 optimal weight: 0.5980 chunk 28 optimal weight: 0.9980 chunk 29 optimal weight: 0.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 212 HIS ** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** 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 = 0.4346 r_free = 0.4346 target = 0.198400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.142093 restraints weight = 10061.565| |-----------------------------------------------------------------------------| r_work (start): 0.3781 rms_B_bonded: 2.23 r_work: 0.3637 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3492 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7411 moved from start: 0.2938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9842 Z= 0.144 Angle : 0.537 7.361 13384 Z= 0.281 Chirality : 0.043 0.257 1490 Planarity : 0.004 0.040 1658 Dihedral : 6.451 56.357 1745 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.47 % Allowed : 18.46 % Favored : 79.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.09 (0.25), residues: 1154 helix: 2.18 (0.23), residues: 445 sheet: -0.34 (0.31), residues: 251 loop : -0.02 (0.31), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG R 40 TYR 0.017 0.002 TYR R 148 PHE 0.017 0.001 PHE R 230 TRP 0.027 0.001 TRP R 264 HIS 0.006 0.001 HIS R 212 Details of bonding type rmsd covalent geometry : bond 0.00326 ( 9835) covalent geometry : angle 0.53577 (13372) SS BOND : bond 0.00221 ( 6) SS BOND : angle 1.39053 ( 12) hydrogen bonds : bond 0.03982 ( 491) hydrogen bonds : angle 4.65480 ( 1401) Misc. bond : bond 0.00013 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4925.72 seconds wall clock time: 84 minutes 20.46 seconds (5060.46 seconds total)