Starting phenix.real_space_refine on Wed Aug 5 17:12:21 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8j12_35912/08_2026/8j12_35912.cif Found real_map, /net/cci-nas-00/data/ceres_data/8j12_35912/08_2026/8j12_35912.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.08 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/8j12_35912/08_2026/8j12_35912.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8j12_35912/08_2026/8j12_35912.cif" model { file = "/net/cci-nas-00/data/ceres_data/8j12_35912/08_2026/8j12_35912.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8j12_35912/08_2026/8j12_35912.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8j12_35912/08_2026/8j12_35912.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8j12_35912/08_2026/8j12_35912.map" } resolution = 3.08 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.008 sd= 0.070 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: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 194 5.49 5 Mg 7 5.21 5 S 32 5.16 5 C 6014 2.51 5 N 1933 2.21 5 O 2522 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10704 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 424, 3435 Classifications: {'peptide': 424} Link IDs: {'PTRANS': 10, 'TRANS': 413} Chain: "B" Number of atoms: 3140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 385, 3140 Classifications: {'peptide': 385} Link IDs: {'PTRANS': 9, 'TRANS': 375} Chain breaks: 4 Chain: "D" Number of atoms: 570 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 570 Classifications: {'DNA': 28} Link IDs: {'rna3p': 27} Chain: "E" Number of atoms: 224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 224 Classifications: {'DNA': 11} Link IDs: {'rna3p': 10} Chain: "C" Number of atoms: 3326 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 3326 Classifications: {'RNAv2': 155} Modifications used: {'rna2p_pur': 16, 'rna2p_pyr': 3, 'rna3p_pur': 74, 'rna3p_pyr': 62} Link IDs: {'rna2p': 19, 'rna3p': 135} Chain breaks: 1 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Unusual residues: {' MG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 3061 SG CYS A 372 13.353 60.597 78.620 1.00115.98 S ATOM 3082 SG CYS A 375 11.566 59.491 76.936 1.00102.76 S ATOM 3199 SG CYS A 391 11.892 63.391 77.544 1.00123.59 S ATOM 3221 SG CYS A 394 11.130 63.187 79.407 1.00136.00 S ATOM 6247 SG CYS B 372 44.242 92.363 50.170 1.00119.09 S ATOM 6268 SG CYS B 375 42.206 94.917 48.341 1.00122.36 S ATOM 6348 SG CYS B 391 41.180 92.979 50.246 1.00124.59 S ATOM 6370 SG CYS B 394 40.978 91.410 48.958 1.00112.13 S Time building chain proxies: 2.35, per 1000 atoms: 0.22 Number of scatterers: 10704 At special positions: 0 Unit cell: (115.536, 116.864, 131.472, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 32 16.00 P 194 15.00 Mg 7 11.99 O 2522 8.00 N 1933 7.00 C 6014 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.80 Conformation dependent library (CDL) restraints added in 192.2 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 502 " pdb="ZN ZN A 502 " - pdb=" SG CYS A 375 " pdb="ZN ZN A 502 " - pdb=" SG CYS A 394 " pdb="ZN ZN A 502 " - pdb=" SG CYS A 391 " pdb="ZN ZN A 502 " - pdb=" SG CYS A 372 " pdb=" ZN B 502 " pdb="ZN ZN B 502 " - pdb=" SG CYS B 394 " pdb="ZN ZN B 502 " - pdb=" SG CYS B 375 " pdb="ZN ZN B 502 " - pdb=" SG CYS B 372 " pdb="ZN ZN B 502 " - pdb=" SG CYS B 391 " Number of angles added : 12 1594 Ramachandran restraints generated. 797 Oldfield, 0 Emsley, 797 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1516 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 9 sheets defined 49.1% alpha, 18.2% beta 76 base pairs and 119 stacking pairs defined. Time for finding SS restraints: 0.94 Creating SS restraints... Processing helix chain 'A' and resid 16 through 57 Processing helix chain 'A' and resid 70 through 83 removed outlier: 3.630A pdb=" N TYR A 74 " --> pdb=" O ASN A 70 " (cutoff:3.500A) removed outlier: 4.984A pdb=" N THR A 81 " --> pdb=" O HIS A 77 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N LYS A 82 " --> pdb=" O THR A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 105 removed outlier: 3.579A pdb=" N TYR A 105 " --> pdb=" O ARG A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 112 Processing helix chain 'A' and resid 128 through 130 No H-bonds generated for 'chain 'A' and resid 128 through 130' Processing helix chain 'A' and resid 150 through 158 Processing helix chain 'A' and resid 171 through 183 removed outlier: 3.770A pdb=" N THR A 175 " --> pdb=" O GLY A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 266 removed outlier: 4.616A pdb=" N ARG A 254 " --> pdb=" O ILE A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 269 No H-bonds generated for 'chain 'A' and resid 267 through 269' Processing helix chain 'A' and resid 279 through 284 Processing helix chain 'A' and resid 285 through 291 removed outlier: 3.724A pdb=" N GLN A 289 " --> pdb=" O PRO A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 317 Processing helix chain 'A' and resid 326 through 330 Processing helix chain 'A' and resid 341 through 356 Processing helix chain 'A' and resid 400 through 410 Processing helix chain 'A' and resid 412 through 422 Processing helix chain 'B' and resid 16 through 46 Processing helix chain 'B' and resid 51 through 55 Processing helix chain 'B' and resid 70 through 80 removed outlier: 3.556A pdb=" N TYR B 74 " --> pdb=" O ASN B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 87 through 105 Processing helix chain 'B' and resid 105 through 112 Processing helix chain 'B' and resid 128 through 130 No H-bonds generated for 'chain 'B' and resid 128 through 130' Processing helix chain 'B' and resid 150 through 158 removed outlier: 3.564A pdb=" N GLN B 155 " --> pdb=" O ASN B 151 " (cutoff:3.500A) Processing helix chain 'B' and resid 171 through 183 removed outlier: 4.349A pdb=" N THR B 175 " --> pdb=" O GLY B 171 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N ILE B 176 " --> pdb=" O ALA B 172 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 266 removed outlier: 3.875A pdb=" N ARG B 266 " --> pdb=" O ILE B 262 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 317 Processing helix chain 'B' and resid 341 through 356 Processing helix chain 'B' and resid 400 through 410 Processing helix chain 'B' and resid 412 through 421 removed outlier: 3.552A pdb=" N ILE B 416 " --> pdb=" O ASN B 412 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE B 421 " --> pdb=" O ILE B 417 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 1 through 5 removed outlier: 3.809A pdb=" N PHE A 209 " --> pdb=" O MET A 1 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 1 through 5 removed outlier: 3.809A pdb=" N PHE A 209 " --> pdb=" O MET A 1 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 9 through 12 removed outlier: 6.797A pdb=" N ILE A 166 " --> pdb=" O VAL A 10 " (cutoff:3.500A) removed outlier: 7.380A pdb=" N SER A 164 " --> pdb=" O PRO A 12 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N TYR A 142 " --> pdb=" O ILE A 167 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 243 through 244 removed outlier: 4.341A pdb=" N GLU A 324 " --> pdb=" O ILE A 224 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 388 through 391 Processing sheet with id=AA6, first strand: chain 'B' and resid 125 through 127 removed outlier: 3.505A pdb=" N GLN B 191 " --> pdb=" O ASN B 204 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LYS B 200 " --> pdb=" O ASP B 195 " (cutoff:3.500A) removed outlier: 5.150A pdb=" N TRP B 201 " --> pdb=" O ILE B 9 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N ILE B 166 " --> pdb=" O VAL B 10 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N SER B 164 " --> pdb=" O PRO B 12 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 125 through 127 removed outlier: 3.505A pdb=" N GLN B 191 " --> pdb=" O ASN B 204 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LYS B 200 " --> pdb=" O ASP B 195 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 242 through 243 removed outlier: 8.149A pdb=" N CYS B 318 " --> pdb=" O LEU B 218 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N LYS B 220 " --> pdb=" O CYS B 318 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLN B 322 " --> pdb=" O MET B 222 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N GLU B 324 " --> pdb=" O ILE B 224 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N LEU B 226 " --> pdb=" O GLU B 324 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N GLY B 319 " --> pdb=" O LYS B 359 " (cutoff:3.500A) removed outlier: 8.029A pdb=" N ILE B 361 " --> pdb=" O GLY B 319 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N ILE B 321 " --> pdb=" O ILE B 361 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N ILE B 363 " --> pdb=" O ILE B 321 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N MET B 323 " --> pdb=" O ILE B 363 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 388 through 390 removed outlier: 3.567A pdb=" N ALA B 398 " --> pdb=" O PHE B 389 " (cutoff:3.500A) 364 hydrogen bonds defined for protein. 1020 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 189 hydrogen bonds 346 hydrogen bond angles 0 basepair planarities 76 basepair parallelities 119 stacking parallelities Total time for adding SS restraints: 1.80 Time building geometry restraints manager: 1.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 2552 1.33 - 1.45: 3267 1.45 - 1.57: 5045 1.57 - 1.69: 384 1.69 - 1.81: 54 Bond restraints: 11302 Sorted by residual: bond pdb=" C3' DT D 14 " pdb=" C2' DT D 14 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.56e+00 bond pdb=" C4' DT E -3 " pdb=" C3' DT E -3 " ideal model delta sigma weight residual 1.529 1.504 0.025 1.00e-02 1.00e+04 6.11e+00 bond pdb=" C3' DC D 17 " pdb=" C2' DC D 17 " ideal model delta sigma weight residual 1.516 1.535 -0.019 8.00e-03 1.56e+04 5.63e+00 bond pdb=" C3' DT D 16 " pdb=" C2' DT D 16 " ideal model delta sigma weight residual 1.516 1.535 -0.019 8.00e-03 1.56e+04 5.44e+00 bond pdb=" C3' DC D 10 " pdb=" C2' DC D 10 " ideal model delta sigma weight residual 1.516 1.534 -0.018 8.00e-03 1.56e+04 4.98e+00 ... (remaining 11297 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.07: 14985 1.07 - 2.15: 653 2.15 - 3.22: 439 3.22 - 4.29: 52 4.29 - 5.36: 33 Bond angle restraints: 16162 Sorted by residual: angle pdb=" O4' DT E -3 " pdb=" C4' DT E -3 " pdb=" C3' DT E -3 " ideal model delta sigma weight residual 106.00 103.29 2.71 6.00e-01 2.78e+00 2.04e+01 angle pdb=" N3 DT D 19 " pdb=" C4 DT D 19 " pdb=" O4 DT D 19 " ideal model delta sigma weight residual 119.90 122.49 -2.59 6.00e-01 2.78e+00 1.86e+01 angle pdb=" N3 DT D 15 " pdb=" C4 DT D 15 " pdb=" O4 DT D 15 " ideal model delta sigma weight residual 119.90 122.48 -2.58 6.00e-01 2.78e+00 1.85e+01 angle pdb=" N3 DT D 16 " pdb=" C4 DT D 16 " pdb=" O4 DT D 16 " ideal model delta sigma weight residual 119.90 122.46 -2.56 6.00e-01 2.78e+00 1.82e+01 angle pdb=" N3 DT E -2 " pdb=" C4 DT E -2 " pdb=" O4 DT E -2 " ideal model delta sigma weight residual 119.90 122.42 -2.52 6.00e-01 2.78e+00 1.76e+01 ... (remaining 16157 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.74: 5327 17.74 - 35.47: 616 35.47 - 53.21: 296 53.21 - 70.94: 127 70.94 - 88.68: 14 Dihedral angle restraints: 6380 sinusoidal: 4013 harmonic: 2367 Sorted by residual: dihedral pdb=" C4' G C -6 " pdb=" C3' G C -6 " pdb=" C2' G C -6 " pdb=" C1' G C -6 " ideal model delta sinusoidal sigma weight residual 36.34 -37.60 73.94 1 3.10e+00 1.04e-01 7.23e+02 dihedral pdb=" C4' G C-141 " pdb=" C3' G C-141 " pdb=" C2' G C-141 " pdb=" C1' G C-141 " ideal model delta sinusoidal sigma weight residual 36.34 -36.91 73.25 1 3.10e+00 1.04e-01 7.11e+02 dihedral pdb=" C4' G C-131 " pdb=" C3' G C-131 " pdb=" C2' G C-131 " pdb=" C1' G C-131 " ideal model delta sinusoidal sigma weight residual 36.34 -36.38 72.72 1 3.10e+00 1.04e-01 7.02e+02 ... (remaining 6377 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 1508 0.060 - 0.120: 178 0.120 - 0.180: 15 0.180 - 0.240: 155 0.240 - 0.301: 38 Chirality restraints: 1894 Sorted by residual: chirality pdb=" C2' U C-148 " pdb=" C3' U C-148 " pdb=" O2' U C-148 " pdb=" C1' U C-148 " both_signs ideal model delta sigma weight residual False -2.79 -2.49 -0.30 2.00e-01 2.50e+01 2.26e+00 chirality pdb=" C3' G C 0 " pdb=" C4' G C 0 " pdb=" O3' G C 0 " pdb=" C2' G C 0 " both_signs ideal model delta sigma weight residual False -2.50 -2.80 0.30 2.00e-01 2.50e+01 2.21e+00 chirality pdb=" C2' A C -93 " pdb=" C3' A C -93 " pdb=" O2' A C -93 " pdb=" C1' A C -93 " both_signs ideal model delta sigma weight residual False -2.79 -2.50 -0.29 2.00e-01 2.50e+01 2.09e+00 ... (remaining 1891 not shown) Planarity restraints: 1352 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' C C -72 " 0.022 2.00e-02 2.50e+03 1.27e-02 3.64e+00 pdb=" N1 C C -72 " -0.025 2.00e-02 2.50e+03 pdb=" C2 C C -72 " 0.012 2.00e-02 2.50e+03 pdb=" O2 C C -72 " -0.009 2.00e-02 2.50e+03 pdb=" N3 C C -72 " -0.003 2.00e-02 2.50e+03 pdb=" C4 C C -72 " 0.005 2.00e-02 2.50e+03 pdb=" N4 C C -72 " 0.006 2.00e-02 2.50e+03 pdb=" C5 C C -72 " -0.002 2.00e-02 2.50e+03 pdb=" C6 C C -72 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A C-106 " 0.024 2.00e-02 2.50e+03 1.08e-02 3.18e+00 pdb=" N9 A C-106 " -0.025 2.00e-02 2.50e+03 pdb=" C8 A C-106 " -0.003 2.00e-02 2.50e+03 pdb=" N7 A C-106 " -0.001 2.00e-02 2.50e+03 pdb=" C5 A C-106 " 0.001 2.00e-02 2.50e+03 pdb=" C6 A C-106 " 0.004 2.00e-02 2.50e+03 pdb=" N6 A C-106 " 0.007 2.00e-02 2.50e+03 pdb=" N1 A C-106 " 0.002 2.00e-02 2.50e+03 pdb=" C2 A C-106 " -0.006 2.00e-02 2.50e+03 pdb=" N3 A C-106 " -0.002 2.00e-02 2.50e+03 pdb=" C4 A C-106 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A C-114 " 0.022 2.00e-02 2.50e+03 1.05e-02 3.03e+00 pdb=" N9 A C-114 " -0.026 2.00e-02 2.50e+03 pdb=" C8 A C-114 " -0.001 2.00e-02 2.50e+03 pdb=" N7 A C-114 " 0.001 2.00e-02 2.50e+03 pdb=" C5 A C-114 " -0.000 2.00e-02 2.50e+03 pdb=" C6 A C-114 " 0.003 2.00e-02 2.50e+03 pdb=" N6 A C-114 " 0.005 2.00e-02 2.50e+03 pdb=" N1 A C-114 " 0.001 2.00e-02 2.50e+03 pdb=" C2 A C-114 " -0.001 2.00e-02 2.50e+03 pdb=" N3 A C-114 " -0.003 2.00e-02 2.50e+03 pdb=" C4 A C-114 " -0.001 2.00e-02 2.50e+03 ... (remaining 1349 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 441 2.69 - 3.25: 9496 3.25 - 3.80: 19030 3.80 - 4.35: 24654 4.35 - 4.90: 36427 Nonbonded interactions: 90048 Sorted by model distance: nonbonded pdb=" O LEU B 337 " pdb=" OH TYR B 342 " model vdw 2.144 3.040 nonbonded pdb=" O ILE B 416 " pdb=" OG SER B 420 " model vdw 2.234 3.040 nonbonded pdb=" OH TYR A 76 " pdb=" OP2 DT E -3 " model vdw 2.241 3.040 nonbonded pdb=" O LEU A 337 " pdb=" OH TYR A 342 " model vdw 2.244 3.040 nonbonded pdb=" O2' C C-103 " pdb=" OP2 U C -5 " model vdw 2.264 3.040 ... (remaining 90043 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 55 or resid 66 through 267 or resid 285 through \ 326 or resid 331 through 379 or resid 385 through 421 or resid 501 through 502)) \ selection = chain 'B' } 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: 0.110 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: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.540 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 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 : 0.004 0.102 11310 Z= 0.258 Angle : 1.152 61.226 16174 Z= 0.421 Chirality : 0.083 0.301 1894 Planarity : 0.003 0.033 1352 Dihedral : 18.497 88.680 4864 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 2.14 % Allowed : 10.54 % Favored : 87.32 % 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: 0.80 (0.30), residues: 797 helix: 2.30 (0.26), residues: 360 sheet: -0.68 (0.43), residues: 146 loop : -1.09 (0.36), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 298 TYR 0.016 0.001 TYR A 351 PHE 0.008 0.001 PHE A 209 TRP 0.011 0.001 TRP A 43 HIS 0.003 0.001 HIS A 238 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.25 (11302) covalent geometry : angle 0.69044 / 0.39 (16162) hydrogen bonds : bond 0.14816 / 9.76 ( 540) hydrogen bonds : angle 5.60407 / 3.90 ( 1366) metal coordination : bond 0.06498 / 4.76 ( 8) metal coordination : angle 33.85833 / 21.38 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1594 Ramachandran restraints generated. 797 Oldfield, 0 Emsley, 797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1594 Ramachandran restraints generated. 797 Oldfield, 0 Emsley, 797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 232 time to evaluate : 0.227 Fit side-chains revert: symmetry clash REVERT: A 8 GLU cc_start: 0.7854 (tt0) cc_final: 0.7622 (tt0) REVERT: A 30 GLU cc_start: 0.7682 (mm-30) cc_final: 0.7391 (mm-30) REVERT: A 53 LYS cc_start: 0.8731 (tttt) cc_final: 0.8472 (ttmt) REVERT: A 70 ASN cc_start: 0.8117 (m-40) cc_final: 0.7877 (m110) REVERT: A 82 LYS cc_start: 0.8524 (ttmt) cc_final: 0.8102 (mtmm) REVERT: A 130 GLU cc_start: 0.8312 (mp0) cc_final: 0.7842 (mp0) REVERT: A 133 SER cc_start: 0.8778 (t) cc_final: 0.8552 (t) REVERT: A 145 SER cc_start: 0.8782 (m) cc_final: 0.8454 (p) REVERT: A 155 GLN cc_start: 0.7820 (tt0) cc_final: 0.7616 (tt0) REVERT: A 197 ARG cc_start: 0.7827 (ttt180) cc_final: 0.7596 (ttt180) REVERT: A 242 ARG cc_start: 0.8311 (mtm180) cc_final: 0.8077 (mtt180) REVERT: A 244 LYS cc_start: 0.8611 (pttt) cc_final: 0.8378 (ptpp) REVERT: A 258 GLU cc_start: 0.7293 (mt-10) cc_final: 0.7075 (mt-10) REVERT: A 262 ILE cc_start: 0.8391 (mt) cc_final: 0.8141 (mm) REVERT: A 311 ASP cc_start: 0.8174 (m-30) cc_final: 0.7935 (m-30) REVERT: A 341 THR cc_start: 0.6745 (t) cc_final: 0.6184 (t) REVERT: A 344 ASP cc_start: 0.7735 (t0) cc_final: 0.7454 (m-30) REVERT: B 100 ASP cc_start: 0.8096 (m-30) cc_final: 0.7771 (m-30) REVERT: B 101 ARG cc_start: 0.8774 (OUTLIER) cc_final: 0.8491 (ttt-90) REVERT: B 129 LYS cc_start: 0.8838 (tttt) cc_final: 0.8519 (tttp) REVERT: B 133 SER cc_start: 0.9035 (t) cc_final: 0.8574 (p) REVERT: B 136 ARG cc_start: 0.8200 (ttt180) cc_final: 0.7716 (ttt-90) REVERT: B 150 SER cc_start: 0.8688 (t) cc_final: 0.8439 (p) REVERT: B 174 LYS cc_start: 0.8342 (tttt) cc_final: 0.7596 (tppp) REVERT: B 178 ASP cc_start: 0.8051 (m-30) cc_final: 0.7413 (m-30) REVERT: B 200 LYS cc_start: 0.8551 (mttt) cc_final: 0.8324 (mttm) REVERT: B 220 LYS cc_start: 0.7913 (mttt) cc_final: 0.7653 (mmtp) REVERT: B 221 ILE cc_start: 0.8277 (mp) cc_final: 0.7830 (mm) REVERT: B 234 MET cc_start: 0.8834 (mtm) cc_final: 0.8594 (mtt) REVERT: B 289 GLN cc_start: 0.8134 (mm-40) cc_final: 0.7729 (mm-40) REVERT: B 316 GLU cc_start: 0.8026 (mm-30) cc_final: 0.7815 (mm-30) REVERT: B 320 THR cc_start: 0.8533 (p) cc_final: 0.8329 (p) REVERT: B 379 ASP cc_start: 0.7272 (m-30) cc_final: 0.6753 (m-30) outliers start: 15 outliers final: 5 residues processed: 246 average time/residue: 0.1185 time to fit residues: 38.0384 Evaluate side-chains 191 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 185 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain B residue 101 ARG Chi-restraints excluded: chain B residue 224 ILE Chi-restraints excluded: chain B residue 233 TYR Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 416 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 49 optimal weight: 6.9990 chunk 97 optimal weight: 6.9990 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 7.9990 chunk 33 optimal weight: 10.0000 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 6.9990 chunk 51 optimal weight: 4.9990 chunk 38 optimal weight: 0.0070 chunk 61 optimal weight: 4.9990 chunk 45 optimal weight: 0.7980 overall best weight: 3.1604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 56 HIS A 194 HIS ** A 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 322 GLN A 366 GLN A 370 GLN B 26 GLN ** B 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 256 GLN ** B 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 407 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.118111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.098012 restraints weight = 17555.947| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 1.68 r_work: 0.3178 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3044 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.1511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 11310 Z= 0.279 Angle : 1.342 52.663 16174 Z= 0.523 Chirality : 0.107 1.185 1894 Planarity : 0.005 0.064 1352 Dihedral : 18.677 139.535 3218 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 3.56 % Allowed : 16.10 % Favored : 80.34 % 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: 0.93 (0.30), residues: 797 helix: 2.45 (0.26), residues: 365 sheet: -0.68 (0.43), residues: 147 loop : -1.12 (0.36), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 255 TYR 0.015 0.002 TYR B 342 PHE 0.027 0.002 PHE B 389 TRP 0.012 0.002 TRP A 43 HIS 0.004 0.001 HIS A 303 Details of bonding type rmsd/Z covalent geometry : bond 0.00586 / 0.28 (11302) covalent geometry : angle 1.16930 / 0.51 (16162) hydrogen bonds : bond 0.05920 / 3.91 ( 540) hydrogen bonds : angle 4.23619 / 3.04 ( 1366) metal coordination : bond 0.01906 / 1.12 ( 8) metal coordination : angle 24.17296 / 13.06 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1594 Ramachandran restraints generated. 797 Oldfield, 0 Emsley, 797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1594 Ramachandran restraints generated. 797 Oldfield, 0 Emsley, 797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 189 time to evaluate : 0.298 Fit side-chains revert: symmetry clash REVERT: A 82 LYS cc_start: 0.8668 (ttmt) cc_final: 0.8446 (ttmt) REVERT: A 130 GLU cc_start: 0.8291 (mp0) cc_final: 0.7834 (mp0) REVERT: A 145 SER cc_start: 0.8679 (m) cc_final: 0.8450 (p) REVERT: A 262 ILE cc_start: 0.8447 (mt) cc_final: 0.8216 (mm) REVERT: A 285 LYS cc_start: 0.8395 (tttt) cc_final: 0.8148 (tttm) REVERT: A 289 GLN cc_start: 0.8035 (mt0) cc_final: 0.7457 (mp10) REVERT: A 311 ASP cc_start: 0.8092 (m-30) cc_final: 0.7806 (m-30) REVERT: A 344 ASP cc_start: 0.7849 (OUTLIER) cc_final: 0.7468 (m-30) REVERT: B 100 ASP cc_start: 0.7873 (m-30) cc_final: 0.7629 (m-30) REVERT: B 133 SER cc_start: 0.9075 (t) cc_final: 0.8632 (p) REVERT: B 200 LYS cc_start: 0.8579 (mttt) cc_final: 0.8345 (mttp) REVERT: B 221 ILE cc_start: 0.8031 (mp) cc_final: 0.7721 (mm) REVERT: B 244 LYS cc_start: 0.8687 (pttt) cc_final: 0.8441 (pttm) REVERT: B 289 GLN cc_start: 0.7934 (mm-40) cc_final: 0.7588 (mm-40) REVERT: B 316 GLU cc_start: 0.8132 (mm-30) cc_final: 0.7895 (mm-30) REVERT: B 417 ILE cc_start: 0.8976 (OUTLIER) cc_final: 0.8765 (tt) outliers start: 25 outliers final: 16 residues processed: 203 average time/residue: 0.1182 time to fit residues: 31.5261 Evaluate side-chains 204 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 186 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 0 SER Chi-restraints excluded: chain A residue 46 MET Chi-restraints excluded: chain A residue 138 ASN Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 344 ASP Chi-restraints excluded: chain A residue 361 ILE Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain B residue 217 ASP Chi-restraints excluded: chain B residue 224 ILE Chi-restraints excluded: chain B residue 233 TYR Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 318 CYS Chi-restraints excluded: chain B residue 350 ILE Chi-restraints excluded: chain B residue 359 LYS Chi-restraints excluded: chain B residue 401 ASP Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain B residue 417 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 2 optimal weight: 0.8980 chunk 18 optimal weight: 6.9990 chunk 56 optimal weight: 5.9990 chunk 64 optimal weight: 0.8980 chunk 93 optimal weight: 6.9990 chunk 58 optimal weight: 5.9990 chunk 86 optimal weight: 7.9990 chunk 53 optimal weight: 3.9990 chunk 4 optimal weight: 4.9990 chunk 16 optimal weight: 3.9990 chunk 19 optimal weight: 6.9990 overall best weight: 2.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 366 GLN B 256 GLN ** B 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 403 ASN B 407 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.118206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.098135 restraints weight = 17632.904| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 1.71 r_work: 0.3186 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3049 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.1933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 11310 Z= 0.244 Angle : 0.962 18.228 16174 Z= 0.423 Chirality : 0.081 0.851 1894 Planarity : 0.004 0.055 1352 Dihedral : 19.031 163.674 3213 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 3.85 % Allowed : 17.52 % Favored : 78.63 % 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: 0.91 (0.30), residues: 797 helix: 2.49 (0.26), residues: 365 sheet: -0.82 (0.41), residues: 147 loop : -1.13 (0.36), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 255 TYR 0.018 0.002 TYR A 351 PHE 0.025 0.002 PHE B 389 TRP 0.011 0.002 TRP A 43 HIS 0.003 0.001 HIS A 238 Details of bonding type rmsd/Z covalent geometry : bond 0.00521 / 0.24 (11302) covalent geometry : angle 0.93690 / 0.42 (16162) hydrogen bonds : bond 0.06216 / 4.35 ( 540) hydrogen bonds : angle 3.96253 / 2.87 ( 1366) metal coordination : bond 0.01212 / 0.73 ( 8) metal coordination : angle 8.11786 / 5.67 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1594 Ramachandran restraints generated. 797 Oldfield, 0 Emsley, 797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1594 Ramachandran restraints generated. 797 Oldfield, 0 Emsley, 797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 183 time to evaluate : 0.197 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 130 GLU cc_start: 0.8260 (mp0) cc_final: 0.7969 (mp0) REVERT: A 262 ILE cc_start: 0.8464 (mt) cc_final: 0.8217 (mm) REVERT: A 280 ARG cc_start: 0.8273 (ttm110) cc_final: 0.7979 (ttm110) REVERT: A 285 LYS cc_start: 0.8414 (tttt) cc_final: 0.8104 (tttm) REVERT: A 289 GLN cc_start: 0.8051 (mt0) cc_final: 0.7674 (mp10) REVERT: A 311 ASP cc_start: 0.8123 (m-30) cc_final: 0.7836 (m-30) REVERT: A 344 ASP cc_start: 0.7866 (OUTLIER) cc_final: 0.7407 (m-30) REVERT: B 133 SER cc_start: 0.9046 (t) cc_final: 0.8605 (p) REVERT: B 200 LYS cc_start: 0.8538 (mttt) cc_final: 0.8284 (mttm) REVERT: B 221 ILE cc_start: 0.8012 (mp) cc_final: 0.7645 (mt) REVERT: B 244 LYS cc_start: 0.8645 (pttt) cc_final: 0.8367 (pttm) REVERT: B 289 GLN cc_start: 0.7776 (mm-40) cc_final: 0.7439 (mm-40) REVERT: B 417 ILE cc_start: 0.8957 (OUTLIER) cc_final: 0.8750 (tt) outliers start: 27 outliers final: 19 residues processed: 195 average time/residue: 0.1143 time to fit residues: 29.3558 Evaluate side-chains 193 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 172 time to evaluate : 0.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 0 SER Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 46 MET Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 138 ASN Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 344 ASP Chi-restraints excluded: chain A residue 361 ILE Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain B residue 210 GLU Chi-restraints excluded: chain B residue 217 ASP Chi-restraints excluded: chain B residue 224 ILE Chi-restraints excluded: chain B residue 233 TYR Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 318 CYS Chi-restraints excluded: chain B residue 350 ILE Chi-restraints excluded: chain B residue 359 LYS Chi-restraints excluded: chain B residue 401 ASP Chi-restraints excluded: chain B residue 413 ILE Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain B residue 417 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 92 optimal weight: 7.9990 chunk 73 optimal weight: 4.9990 chunk 43 optimal weight: 0.0770 chunk 63 optimal weight: 10.0000 chunk 66 optimal weight: 0.8980 chunk 37 optimal weight: 4.9990 chunk 6 optimal weight: 0.7980 chunk 72 optimal weight: 0.9990 chunk 97 optimal weight: 6.9990 chunk 76 optimal weight: 0.5980 chunk 34 optimal weight: 5.9990 overall best weight: 0.6740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 366 GLN B 26 GLN ** B 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 366 GLN ** B 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 407 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.121933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.102053 restraints weight = 17844.105| |-----------------------------------------------------------------------------| r_work (start): 0.3364 rms_B_bonded: 1.73 r_work: 0.3247 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3111 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.2249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11310 Z= 0.141 Angle : 0.845 13.017 16174 Z= 0.373 Chirality : 0.069 0.756 1894 Planarity : 0.003 0.032 1352 Dihedral : 18.835 173.420 3213 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 4.27 % Allowed : 18.09 % Favored : 77.64 % 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: 1.32 (0.30), residues: 797 helix: 2.90 (0.25), residues: 365 sheet: -0.59 (0.39), residues: 156 loop : -1.07 (0.37), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 254 TYR 0.018 0.001 TYR B 202 PHE 0.017 0.001 PHE B 389 TRP 0.007 0.001 TRP A 43 HIS 0.004 0.001 HIS A 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.14 (11302) covalent geometry : angle 0.83543 / 0.37 (16162) hydrogen bonds : bond 0.05247 / 3.78 ( 540) hydrogen bonds : angle 3.64743 / 2.64 ( 1366) metal coordination : bond 0.00622 / 0.36 ( 8) metal coordination : angle 4.64975 / 3.68 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1594 Ramachandran restraints generated. 797 Oldfield, 0 Emsley, 797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1594 Ramachandran restraints generated. 797 Oldfield, 0 Emsley, 797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 175 time to evaluate : 0.194 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 GLU cc_start: 0.8305 (mp0) cc_final: 0.7998 (mp0) REVERT: A 233 TYR cc_start: 0.8039 (OUTLIER) cc_final: 0.7205 (m-80) REVERT: A 258 GLU cc_start: 0.7540 (mt-10) cc_final: 0.7151 (mt-10) REVERT: A 262 ILE cc_start: 0.8373 (mt) cc_final: 0.8094 (mm) REVERT: A 280 ARG cc_start: 0.8131 (ttm110) cc_final: 0.7877 (ttm170) REVERT: A 285 LYS cc_start: 0.8223 (tttt) cc_final: 0.7979 (tttm) REVERT: A 344 ASP cc_start: 0.7746 (t0) cc_final: 0.7469 (t0) REVERT: A 399 ASN cc_start: 0.7572 (t0) cc_final: 0.7273 (t0) REVERT: B 11 LYS cc_start: 0.8690 (pttt) cc_final: 0.8431 (pttp) REVERT: B 100 ASP cc_start: 0.7888 (m-30) cc_final: 0.7670 (m-30) REVERT: B 133 SER cc_start: 0.8970 (t) cc_final: 0.8464 (p) REVERT: B 200 LYS cc_start: 0.8483 (mttt) cc_final: 0.8190 (mttp) REVERT: B 244 LYS cc_start: 0.8649 (pttt) cc_final: 0.8340 (pttm) REVERT: B 300 THR cc_start: 0.8625 (m) cc_final: 0.8178 (p) REVERT: B 366 GLN cc_start: 0.7659 (tp40) cc_final: 0.7343 (tm-30) REVERT: B 417 ILE cc_start: 0.8948 (OUTLIER) cc_final: 0.8673 (tt) outliers start: 30 outliers final: 18 residues processed: 187 average time/residue: 0.1156 time to fit residues: 28.2452 Evaluate side-chains 195 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 175 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 46 MET Chi-restraints excluded: chain A residue 138 ASN Chi-restraints excluded: chain A residue 233 TYR Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 361 ILE Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 217 ASP Chi-restraints excluded: chain B residue 224 ILE Chi-restraints excluded: chain B residue 233 TYR Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 318 CYS Chi-restraints excluded: chain B residue 350 ILE Chi-restraints excluded: chain B residue 359 LYS Chi-restraints excluded: chain B residue 401 ASP Chi-restraints excluded: chain B residue 413 ILE Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain B residue 417 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 19 optimal weight: 9.9990 chunk 12 optimal weight: 0.0970 chunk 52 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 chunk 38 optimal weight: 20.0000 chunk 61 optimal weight: 3.9990 chunk 7 optimal weight: 5.9990 chunk 46 optimal weight: 0.9980 chunk 33 optimal weight: 10.0000 chunk 54 optimal weight: 5.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 366 GLN ** B 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 407 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.121235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.101285 restraints weight = 17637.790| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 1.77 r_work: 0.3234 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3097 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.2389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 11310 Z= 0.152 Angle : 0.805 11.501 16174 Z= 0.358 Chirality : 0.067 0.714 1894 Planarity : 0.003 0.040 1352 Dihedral : 18.806 177.392 3213 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 4.42 % Allowed : 18.52 % Favored : 77.07 % 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: 1.36 (0.30), residues: 797 helix: 2.93 (0.25), residues: 365 sheet: -0.49 (0.39), residues: 156 loop : -1.09 (0.37), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 280 TYR 0.016 0.001 TYR A 351 PHE 0.013 0.001 PHE B 389 TRP 0.007 0.001 TRP A 43 HIS 0.004 0.001 HIS A 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.15 (11302) covalent geometry : angle 0.79899 / 0.36 (16162) hydrogen bonds : bond 0.05330 / 3.86 ( 540) hydrogen bonds : angle 3.60165 / 2.62 ( 1366) metal coordination : bond 0.00612 / 0.35 ( 8) metal coordination : angle 3.80668 / 2.89 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1594 Ramachandran restraints generated. 797 Oldfield, 0 Emsley, 797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1594 Ramachandran restraints generated. 797 Oldfield, 0 Emsley, 797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 175 time to evaluate : 0.185 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 LYS cc_start: 0.8869 (ttmt) cc_final: 0.8445 (tmtt) REVERT: A 130 GLU cc_start: 0.8315 (mp0) cc_final: 0.7993 (mp0) REVERT: A 222 MET cc_start: 0.8457 (ttm) cc_final: 0.8182 (ttt) REVERT: A 258 GLU cc_start: 0.7579 (mt-10) cc_final: 0.7170 (mt-10) REVERT: A 262 ILE cc_start: 0.8439 (mt) cc_final: 0.8178 (mm) REVERT: A 285 LYS cc_start: 0.8249 (tttt) cc_final: 0.7998 (tttm) REVERT: A 344 ASP cc_start: 0.7841 (OUTLIER) cc_final: 0.7539 (t0) REVERT: B 11 LYS cc_start: 0.8602 (pttt) cc_final: 0.8193 (pttp) REVERT: B 133 SER cc_start: 0.8987 (t) cc_final: 0.8514 (p) REVERT: B 166 ILE cc_start: 0.8886 (OUTLIER) cc_final: 0.8579 (mt) REVERT: B 200 LYS cc_start: 0.8541 (mttt) cc_final: 0.8254 (mttm) REVERT: B 224 ILE cc_start: 0.7507 (OUTLIER) cc_final: 0.7267 (tt) REVERT: B 244 LYS cc_start: 0.8654 (pttt) cc_final: 0.8359 (pttm) REVERT: B 366 GLN cc_start: 0.7707 (tp40) cc_final: 0.7402 (tm-30) REVERT: B 417 ILE cc_start: 0.8940 (OUTLIER) cc_final: 0.8664 (tt) outliers start: 31 outliers final: 21 residues processed: 191 average time/residue: 0.1149 time to fit residues: 28.6633 Evaluate side-chains 196 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 171 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 46 MET Chi-restraints excluded: chain A residue 138 ASN Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 344 ASP Chi-restraints excluded: chain A residue 359 LYS Chi-restraints excluded: chain A residue 361 ILE Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain B residue 114 MET Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 166 ILE Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 210 GLU Chi-restraints excluded: chain B residue 217 ASP Chi-restraints excluded: chain B residue 224 ILE Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 350 ILE Chi-restraints excluded: chain B residue 359 LYS Chi-restraints excluded: chain B residue 401 ASP Chi-restraints excluded: chain B residue 413 ILE Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain B residue 417 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 6 optimal weight: 6.9990 chunk 12 optimal weight: 1.9990 chunk 89 optimal weight: 7.9990 chunk 19 optimal weight: 4.9990 chunk 69 optimal weight: 7.9990 chunk 58 optimal weight: 6.9990 chunk 36 optimal weight: 5.9990 chunk 26 optimal weight: 7.9990 chunk 71 optimal weight: 4.9990 chunk 95 optimal weight: 10.0000 chunk 97 optimal weight: 5.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 407 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.115974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.096087 restraints weight = 17720.314| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 1.70 r_work: 0.3146 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3008 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.2396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.054 11310 Z= 0.350 Angle : 0.952 13.682 16174 Z= 0.425 Chirality : 0.076 0.856 1894 Planarity : 0.004 0.053 1352 Dihedral : 19.036 172.708 3211 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 5.13 % Allowed : 18.23 % Favored : 76.64 % 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: 0.88 (0.29), residues: 797 helix: 2.41 (0.25), residues: 365 sheet: -0.51 (0.39), residues: 156 loop : -1.29 (0.36), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 136 TYR 0.020 0.002 TYR A 351 PHE 0.035 0.003 PHE B 389 TRP 0.013 0.002 TRP B 43 HIS 0.004 0.001 HIS A 238 Details of bonding type rmsd/Z covalent geometry : bond 0.00759 / 0.35 (11302) covalent geometry : angle 0.94445 / 0.42 (16162) hydrogen bonds : bond 0.06596 / 4.55 ( 540) hydrogen bonds : angle 3.81748 / 2.74 ( 1366) metal coordination : bond 0.01208 / 0.74 ( 8) metal coordination : angle 4.63100 / 3.05 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1594 Ramachandran restraints generated. 797 Oldfield, 0 Emsley, 797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1594 Ramachandran restraints generated. 797 Oldfield, 0 Emsley, 797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 173 time to evaluate : 0.215 Fit side-chains revert: symmetry clash REVERT: A 130 GLU cc_start: 0.8350 (mp0) cc_final: 0.7975 (mp0) REVERT: A 254 ARG cc_start: 0.7101 (ttt180) cc_final: 0.6826 (ttt180) REVERT: A 262 ILE cc_start: 0.8371 (mt) cc_final: 0.8093 (mm) REVERT: A 280 ARG cc_start: 0.8238 (ttm110) cc_final: 0.7997 (ttm170) REVERT: A 285 LYS cc_start: 0.8450 (tttt) cc_final: 0.8220 (tttm) REVERT: A 344 ASP cc_start: 0.7902 (OUTLIER) cc_final: 0.7454 (m-30) REVERT: B 200 LYS cc_start: 0.8556 (mttt) cc_final: 0.8307 (mttp) REVERT: B 289 GLN cc_start: 0.7678 (mm-40) cc_final: 0.7364 (mm-40) REVERT: B 300 THR cc_start: 0.8713 (m) cc_final: 0.8269 (p) REVERT: B 417 ILE cc_start: 0.8716 (OUTLIER) cc_final: 0.8453 (tt) outliers start: 36 outliers final: 26 residues processed: 193 average time/residue: 0.1134 time to fit residues: 28.8060 Evaluate side-chains 197 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 169 time to evaluate : 0.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 0 SER Chi-restraints excluded: chain A residue 46 MET Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain A residue 138 ASN Chi-restraints excluded: chain A residue 252 ASN Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 344 ASP Chi-restraints excluded: chain A residue 359 LYS Chi-restraints excluded: chain A residue 361 ILE Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain B residue 114 MET Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 210 GLU Chi-restraints excluded: chain B residue 217 ASP Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 318 CYS Chi-restraints excluded: chain B residue 350 ILE Chi-restraints excluded: chain B residue 359 LYS Chi-restraints excluded: chain B residue 363 ILE Chi-restraints excluded: chain B residue 401 ASP Chi-restraints excluded: chain B residue 413 ILE Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain B residue 417 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 88 optimal weight: 6.9990 chunk 39 optimal weight: 4.9990 chunk 6 optimal weight: 4.9990 chunk 17 optimal weight: 1.9990 chunk 24 optimal weight: 6.9990 chunk 30 optimal weight: 0.9980 chunk 72 optimal weight: 0.0040 chunk 31 optimal weight: 0.9980 chunk 96 optimal weight: 5.9990 chunk 86 optimal weight: 6.9990 chunk 62 optimal weight: 8.9990 overall best weight: 1.7996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 407 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.118950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.098818 restraints weight = 17763.720| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 1.77 r_work: 0.3189 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3051 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.2445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 11310 Z= 0.178 Angle : 0.836 11.508 16174 Z= 0.373 Chirality : 0.068 0.730 1894 Planarity : 0.004 0.055 1352 Dihedral : 18.914 176.602 3209 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 4.42 % Allowed : 20.37 % Favored : 75.21 % 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: 1.16 (0.30), residues: 797 helix: 2.68 (0.25), residues: 366 sheet: -0.48 (0.38), residues: 156 loop : -1.16 (0.37), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 254 TYR 0.018 0.001 TYR A 351 PHE 0.029 0.002 PHE B 389 TRP 0.009 0.001 TRP A 43 HIS 0.002 0.001 HIS A 303 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.18 (11302) covalent geometry : angle 0.82964 / 0.37 (16162) hydrogen bonds : bond 0.05516 / 3.90 ( 540) hydrogen bonds : angle 3.67420 / 2.65 ( 1366) metal coordination : bond 0.00699 / 0.39 ( 8) metal coordination : angle 3.74963 / 2.68 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1594 Ramachandran restraints generated. 797 Oldfield, 0 Emsley, 797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1594 Ramachandran restraints generated. 797 Oldfield, 0 Emsley, 797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 172 time to evaluate : 0.202 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 130 GLU cc_start: 0.8325 (mp0) cc_final: 0.7981 (mp0) REVERT: A 254 ARG cc_start: 0.6997 (ttt180) cc_final: 0.6730 (ttt180) REVERT: A 258 GLU cc_start: 0.7291 (mt-10) cc_final: 0.7062 (mt-10) REVERT: A 262 ILE cc_start: 0.8426 (mt) cc_final: 0.8162 (mm) REVERT: A 280 ARG cc_start: 0.8164 (ttm110) cc_final: 0.7819 (ttm170) REVERT: A 285 LYS cc_start: 0.8418 (tttt) cc_final: 0.8182 (tttm) REVERT: A 344 ASP cc_start: 0.7863 (OUTLIER) cc_final: 0.7370 (m-30) REVERT: B 133 SER cc_start: 0.9044 (t) cc_final: 0.8518 (p) REVERT: B 135 ASN cc_start: 0.8582 (t0) cc_final: 0.8161 (t0) REVERT: B 178 ASP cc_start: 0.8067 (m-30) cc_final: 0.7451 (m-30) REVERT: B 200 LYS cc_start: 0.8522 (mttt) cc_final: 0.8265 (mttm) REVERT: B 300 THR cc_start: 0.8663 (m) cc_final: 0.8226 (p) REVERT: B 369 SER cc_start: 0.8270 (m) cc_final: 0.7925 (p) REVERT: B 417 ILE cc_start: 0.8711 (OUTLIER) cc_final: 0.8489 (tt) outliers start: 31 outliers final: 25 residues processed: 188 average time/residue: 0.1084 time to fit residues: 26.5180 Evaluate side-chains 195 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 168 time to evaluate : 0.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 GLU Chi-restraints excluded: chain A residue 46 MET Chi-restraints excluded: chain A residue 138 ASN Chi-restraints excluded: chain A residue 252 ASN Chi-restraints excluded: chain A residue 291 ARG Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 344 ASP Chi-restraints excluded: chain A residue 361 ILE Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain B residue 114 MET Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 210 GLU Chi-restraints excluded: chain B residue 217 ASP Chi-restraints excluded: chain B residue 224 ILE Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 318 CYS Chi-restraints excluded: chain B residue 350 ILE Chi-restraints excluded: chain B residue 359 LYS Chi-restraints excluded: chain B residue 363 ILE Chi-restraints excluded: chain B residue 401 ASP Chi-restraints excluded: chain B residue 413 ILE Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain B residue 417 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 2 optimal weight: 4.9990 chunk 12 optimal weight: 4.9990 chunk 33 optimal weight: 5.9990 chunk 84 optimal weight: 6.9990 chunk 59 optimal weight: 1.9990 chunk 43 optimal weight: 7.9990 chunk 35 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 32 optimal weight: 5.9990 chunk 64 optimal weight: 2.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 407 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.117132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.096876 restraints weight = 17886.741| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 1.74 r_work: 0.3161 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3024 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.2512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 11310 Z= 0.263 Angle : 0.882 12.408 16174 Z= 0.395 Chirality : 0.070 0.764 1894 Planarity : 0.004 0.054 1352 Dihedral : 18.971 175.233 3209 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 4.84 % Allowed : 19.94 % Favored : 75.21 % 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: 1.04 (0.30), residues: 797 helix: 2.55 (0.26), residues: 366 sheet: -0.38 (0.39), residues: 148 loop : -1.25 (0.36), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 25 TYR 0.018 0.002 TYR A 351 PHE 0.027 0.002 PHE B 389 TRP 0.010 0.002 TRP B 43 HIS 0.003 0.001 HIS A 238 Details of bonding type rmsd/Z covalent geometry : bond 0.00569 / 0.26 (11302) covalent geometry : angle 0.87554 / 0.39 (16162) hydrogen bonds : bond 0.05978 / 4.19 ( 540) hydrogen bonds : angle 3.74144 / 2.70 ( 1366) metal coordination : bond 0.00948 / 0.56 ( 8) metal coordination : angle 3.98622 / 2.69 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1594 Ramachandran restraints generated. 797 Oldfield, 0 Emsley, 797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1594 Ramachandran restraints generated. 797 Oldfield, 0 Emsley, 797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 170 time to evaluate : 0.201 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 130 GLU cc_start: 0.8329 (mp0) cc_final: 0.7958 (mp0) REVERT: A 254 ARG cc_start: 0.7024 (ttt180) cc_final: 0.6765 (ttt180) REVERT: A 258 GLU cc_start: 0.7438 (mt-10) cc_final: 0.7170 (mt-10) REVERT: A 262 ILE cc_start: 0.8389 (mt) cc_final: 0.8103 (mm) REVERT: A 280 ARG cc_start: 0.8233 (ttm110) cc_final: 0.7966 (ttm110) REVERT: A 285 LYS cc_start: 0.8423 (tttt) cc_final: 0.8189 (tttm) REVERT: A 311 ASP cc_start: 0.8117 (m-30) cc_final: 0.7844 (m-30) REVERT: A 344 ASP cc_start: 0.7878 (OUTLIER) cc_final: 0.7424 (m-30) REVERT: B 178 ASP cc_start: 0.8071 (m-30) cc_final: 0.7469 (m-30) REVERT: B 200 LYS cc_start: 0.8521 (mttt) cc_final: 0.8263 (mttp) REVERT: B 300 THR cc_start: 0.8699 (m) cc_final: 0.8271 (p) REVERT: B 366 GLN cc_start: 0.7982 (mm-40) cc_final: 0.7623 (mm-40) REVERT: B 369 SER cc_start: 0.8330 (m) cc_final: 0.7991 (p) REVERT: B 417 ILE cc_start: 0.8727 (OUTLIER) cc_final: 0.8507 (tt) outliers start: 34 outliers final: 27 residues processed: 187 average time/residue: 0.1027 time to fit residues: 25.2278 Evaluate side-chains 199 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 170 time to evaluate : 0.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 GLU Chi-restraints excluded: chain A residue 46 MET Chi-restraints excluded: chain A residue 138 ASN Chi-restraints excluded: chain A residue 147 SER Chi-restraints excluded: chain A residue 252 ASN Chi-restraints excluded: chain A residue 291 ARG Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 344 ASP Chi-restraints excluded: chain A residue 359 LYS Chi-restraints excluded: chain A residue 361 ILE Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain B residue 114 MET Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 210 GLU Chi-restraints excluded: chain B residue 217 ASP Chi-restraints excluded: chain B residue 224 ILE Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 318 CYS Chi-restraints excluded: chain B residue 350 ILE Chi-restraints excluded: chain B residue 359 LYS Chi-restraints excluded: chain B residue 363 ILE Chi-restraints excluded: chain B residue 401 ASP Chi-restraints excluded: chain B residue 413 ILE Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain B residue 417 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 54 optimal weight: 5.9990 chunk 31 optimal weight: 0.5980 chunk 86 optimal weight: 6.9990 chunk 22 optimal weight: 5.9990 chunk 38 optimal weight: 0.1980 chunk 46 optimal weight: 5.9990 chunk 91 optimal weight: 8.9990 chunk 3 optimal weight: 2.9990 chunk 10 optimal weight: 4.9990 chunk 89 optimal weight: 6.9990 chunk 27 optimal weight: 0.2980 overall best weight: 1.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 366 GLN ** B 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 407 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.119093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.098872 restraints weight = 17999.876| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 1.76 r_work: 0.3195 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3058 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.2556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 11310 Z= 0.174 Angle : 0.829 11.656 16174 Z= 0.371 Chirality : 0.067 0.692 1894 Planarity : 0.004 0.054 1352 Dihedral : 18.904 177.345 3209 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 4.13 % Allowed : 20.94 % Favored : 74.93 % 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: 1.23 (0.30), residues: 797 helix: 2.72 (0.26), residues: 366 sheet: -0.31 (0.40), residues: 148 loop : -1.18 (0.36), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 392 TYR 0.017 0.001 TYR A 351 PHE 0.025 0.002 PHE B 389 TRP 0.008 0.001 TRP A 43 HIS 0.002 0.001 HIS A 303 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.17 (11302) covalent geometry : angle 0.82346 / 0.37 (16162) hydrogen bonds : bond 0.05438 / 3.86 ( 540) hydrogen bonds : angle 3.67100 / 2.65 ( 1366) metal coordination : bond 0.00642 / 0.37 ( 8) metal coordination : angle 3.54180 / 2.48 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1594 Ramachandran restraints generated. 797 Oldfield, 0 Emsley, 797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1594 Ramachandran restraints generated. 797 Oldfield, 0 Emsley, 797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 172 time to evaluate : 0.180 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 130 GLU cc_start: 0.8300 (mp0) cc_final: 0.7945 (mp0) REVERT: A 244 LYS cc_start: 0.8659 (mtmm) cc_final: 0.8438 (ttmm) REVERT: A 254 ARG cc_start: 0.6992 (ttt180) cc_final: 0.6726 (ttt180) REVERT: A 258 GLU cc_start: 0.7437 (mt-10) cc_final: 0.7148 (mt-10) REVERT: A 262 ILE cc_start: 0.8434 (mt) cc_final: 0.8155 (mm) REVERT: A 280 ARG cc_start: 0.8175 (ttm110) cc_final: 0.7876 (ttm110) REVERT: A 285 LYS cc_start: 0.8392 (tttt) cc_final: 0.8024 (tttm) REVERT: A 344 ASP cc_start: 0.7837 (OUTLIER) cc_final: 0.7374 (m-30) REVERT: B 133 SER cc_start: 0.9030 (t) cc_final: 0.8471 (p) REVERT: B 135 ASN cc_start: 0.8523 (t0) cc_final: 0.8106 (t0) REVERT: B 178 ASP cc_start: 0.8062 (m-30) cc_final: 0.7444 (m-30) REVERT: B 200 LYS cc_start: 0.8502 (mttt) cc_final: 0.8234 (mttp) REVERT: B 300 THR cc_start: 0.8661 (m) cc_final: 0.8234 (p) REVERT: B 417 ILE cc_start: 0.8719 (OUTLIER) cc_final: 0.8509 (tt) outliers start: 29 outliers final: 27 residues processed: 187 average time/residue: 0.1248 time to fit residues: 30.3083 Evaluate side-chains 199 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 170 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 GLU Chi-restraints excluded: chain A residue 46 MET Chi-restraints excluded: chain A residue 59 TYR Chi-restraints excluded: chain A residue 138 ASN Chi-restraints excluded: chain A residue 252 ASN Chi-restraints excluded: chain A residue 291 ARG Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 344 ASP Chi-restraints excluded: chain A residue 359 LYS Chi-restraints excluded: chain A residue 361 ILE Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain B residue 114 MET Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 210 GLU Chi-restraints excluded: chain B residue 217 ASP Chi-restraints excluded: chain B residue 224 ILE Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 318 CYS Chi-restraints excluded: chain B residue 350 ILE Chi-restraints excluded: chain B residue 359 LYS Chi-restraints excluded: chain B residue 363 ILE Chi-restraints excluded: chain B residue 401 ASP Chi-restraints excluded: chain B residue 413 ILE Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain B residue 417 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 3 optimal weight: 4.9990 chunk 31 optimal weight: 3.9990 chunk 87 optimal weight: 7.9990 chunk 57 optimal weight: 0.9980 chunk 50 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 27 optimal weight: 5.9990 chunk 46 optimal weight: 5.9990 chunk 95 optimal weight: 10.0000 chunk 72 optimal weight: 0.0170 chunk 56 optimal weight: 3.9990 overall best weight: 2.0024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 407 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.119101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.099061 restraints weight = 17946.014| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 1.69 r_work: 0.3202 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3068 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.2614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 11310 Z= 0.186 Angle : 0.831 12.218 16174 Z= 0.373 Chirality : 0.066 0.678 1894 Planarity : 0.004 0.053 1352 Dihedral : 18.895 177.275 3209 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 4.27 % Allowed : 21.65 % Favored : 74.07 % 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: 1.19 (0.30), residues: 797 helix: 2.73 (0.26), residues: 366 sheet: -0.28 (0.40), residues: 145 loop : -1.28 (0.35), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 392 TYR 0.017 0.001 TYR A 351 PHE 0.040 0.002 PHE B 389 TRP 0.009 0.001 TRP A 43 HIS 0.003 0.001 HIS A 303 Details of bonding type rmsd/Z covalent geometry : bond 0.00396 / 0.19 (11302) covalent geometry : angle 0.82647 / 0.37 (16162) hydrogen bonds : bond 0.05483 / 3.88 ( 540) hydrogen bonds : angle 3.66901 / 2.65 ( 1366) metal coordination : bond 0.00604 / 0.34 ( 8) metal coordination : angle 3.38339 / 2.33 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1594 Ramachandran restraints generated. 797 Oldfield, 0 Emsley, 797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1594 Ramachandran restraints generated. 797 Oldfield, 0 Emsley, 797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 172 time to evaluate : 0.226 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 130 GLU cc_start: 0.8257 (mp0) cc_final: 0.7912 (mp0) REVERT: A 254 ARG cc_start: 0.6985 (ttt180) cc_final: 0.6719 (ttt180) REVERT: A 258 GLU cc_start: 0.7520 (mt-10) cc_final: 0.7205 (mt-10) REVERT: A 262 ILE cc_start: 0.8442 (mt) cc_final: 0.8177 (mm) REVERT: A 285 LYS cc_start: 0.8385 (tttt) cc_final: 0.8125 (tttm) REVERT: A 344 ASP cc_start: 0.7824 (OUTLIER) cc_final: 0.7365 (m-30) REVERT: B 133 SER cc_start: 0.9025 (t) cc_final: 0.8466 (p) REVERT: B 135 ASN cc_start: 0.8523 (t0) cc_final: 0.8136 (t0) REVERT: B 178 ASP cc_start: 0.8017 (m-30) cc_final: 0.7411 (m-30) REVERT: B 200 LYS cc_start: 0.8504 (mttt) cc_final: 0.8241 (mttm) REVERT: B 254 ARG cc_start: 0.8109 (ttm-80) cc_final: 0.7603 (mtp85) REVERT: B 300 THR cc_start: 0.8673 (m) cc_final: 0.8254 (p) REVERT: B 359 LYS cc_start: 0.8502 (OUTLIER) cc_final: 0.8114 (tmmt) REVERT: B 366 GLN cc_start: 0.7750 (mm-40) cc_final: 0.7516 (mm-40) REVERT: B 369 SER cc_start: 0.8265 (m) cc_final: 0.7943 (p) REVERT: B 417 ILE cc_start: 0.8704 (OUTLIER) cc_final: 0.8448 (tt) outliers start: 30 outliers final: 27 residues processed: 187 average time/residue: 0.1221 time to fit residues: 29.4737 Evaluate side-chains 201 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 171 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 GLU Chi-restraints excluded: chain A residue 46 MET Chi-restraints excluded: chain A residue 59 TYR Chi-restraints excluded: chain A residue 138 ASN Chi-restraints excluded: chain A residue 252 ASN Chi-restraints excluded: chain A residue 291 ARG Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 344 ASP Chi-restraints excluded: chain A residue 359 LYS Chi-restraints excluded: chain A residue 361 ILE Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain B residue 114 MET Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 210 GLU Chi-restraints excluded: chain B residue 217 ASP Chi-restraints excluded: chain B residue 224 ILE Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 318 CYS Chi-restraints excluded: chain B residue 350 ILE Chi-restraints excluded: chain B residue 359 LYS Chi-restraints excluded: chain B residue 362 LYS Chi-restraints excluded: chain B residue 363 ILE Chi-restraints excluded: chain B residue 401 ASP Chi-restraints excluded: chain B residue 413 ILE Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain B residue 417 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 28 optimal weight: 7.9990 chunk 93 optimal weight: 6.9990 chunk 4 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 70 optimal weight: 5.9990 chunk 32 optimal weight: 7.9990 chunk 57 optimal weight: 5.9990 chunk 11 optimal weight: 5.9990 chunk 53 optimal weight: 3.9990 chunk 79 optimal weight: 0.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 407 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.118347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.098074 restraints weight = 18056.984| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 1.76 r_work: 0.3179 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3041 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.2650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 11310 Z= 0.229 Angle : 0.855 12.597 16174 Z= 0.384 Chirality : 0.067 0.700 1894 Planarity : 0.004 0.050 1352 Dihedral : 18.942 176.439 3209 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 4.56 % Allowed : 21.94 % Favored : 73.50 % 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 (0.29), residues: 797 helix: 2.64 (0.25), residues: 367 sheet: -0.31 (0.40), residues: 146 loop : -1.34 (0.35), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 280 TYR 0.017 0.002 TYR A 351 PHE 0.038 0.002 PHE B 389 TRP 0.010 0.002 TRP A 43 HIS 0.003 0.001 HIS A 303 Details of bonding type rmsd/Z covalent geometry : bond 0.00493 / 0.23 (11302) covalent geometry : angle 0.85018 / 0.38 (16162) hydrogen bonds : bond 0.05700 / 4.01 ( 540) hydrogen bonds : angle 3.68851 / 2.66 ( 1366) metal coordination : bond 0.00766 / 0.45 ( 8) metal coordination : angle 3.40630 / 2.27 ( 12) =============================================================================== Job complete usr+sys time: 2457.60 seconds wall clock time: 42 minutes 41.13 seconds (2561.13 seconds total)