Starting phenix.real_space_refine on Thu Jul 2 23:27:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8j12_35912/07_2026/8j12_35912.cif Found real_map, /net/cci-nas-00/data/ceres_data/8j12_35912/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8j12_35912/07_2026/8j12_35912.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8j12_35912/07_2026/8j12_35912.map" model { file = "/net/cci-nas-00/data/ceres_data/8j12_35912/07_2026/8j12_35912.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8j12_35912/07_2026/8j12_35912.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8j12_35912/07_2026/8j12_35912.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8j12_35912/07_2026/8j12_35912.cif" } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/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: {'RNA': 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: 2.22, per 1000 atoms: 0.21 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: 0.91 Conformation dependent library (CDL) restraints added in 247.0 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: 1.20 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: 1.91 Time building geometry restraints manager: 1.14 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 - 1.00: 15428 1.00 - 2.00: 556 2.00 - 3.01: 156 3.01 - 4.01: 17 4.01 - 5.01: 5 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: 5554 17.74 - 35.47: 563 35.47 - 53.21: 201 53.21 - 70.94: 53 70.94 - 88.68: 9 Dihedral angle restraints: 6380 sinusoidal: 4013 harmonic: 2367 Sorted by residual: dihedral pdb=" O4' A C -92 " pdb=" C1' A C -92 " pdb=" N9 A C -92 " pdb=" C4 A C -92 " ideal model delta sinusoidal sigma weight residual -106.00 -167.76 61.76 1 1.70e+01 3.46e-03 1.75e+01 dihedral pdb=" O4' C C-103 " pdb=" C1' C C-103 " pdb=" N1 C C-103 " pdb=" C2 C C-103 " ideal model delta sinusoidal sigma weight residual -128.00 -75.45 -52.55 1 1.70e+01 3.46e-03 1.30e+01 dihedral pdb=" CA LEU B 337 " pdb=" C LEU B 337 " pdb=" N GLN B 338 " pdb=" CA GLN B 338 " ideal model delta harmonic sigma weight residual -180.00 -163.60 -16.40 0 5.00e+00 4.00e-02 1.08e+01 ... (remaining 6377 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 1485 0.039 - 0.079: 289 0.079 - 0.118: 104 0.118 - 0.158: 15 0.158 - 0.197: 1 Chirality restraints: 1894 Sorted by residual: chirality pdb=" C1' A C-114 " pdb=" O4' A C-114 " pdb=" C2' A C-114 " pdb=" N9 A C-114 " both_signs ideal model delta sigma weight residual False 2.46 2.26 0.20 2.00e-01 2.50e+01 9.74e-01 chirality pdb=" C3' DC D 10 " pdb=" C4' DC D 10 " pdb=" O3' DC D 10 " pdb=" C2' DC D 10 " both_signs ideal model delta sigma weight residual False -2.73 -2.58 -0.15 2.00e-01 2.50e+01 5.85e-01 chirality pdb=" C1' A C -91 " pdb=" O4' A C -91 " pdb=" C2' A C -91 " pdb=" N9 A C -91 " both_signs ideal model delta sigma weight residual False 2.46 2.31 0.15 2.00e-01 2.50e+01 5.55e-01 ... (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: 0.210 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: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.680 Find NCS groups from input model: 0.180 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:1.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.380 ------------------------------------------------------------------------------- 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= 0.251 Angle : 1.042 61.226 16174 Z= 0.384 Chirality : 0.038 0.197 1894 Planarity : 0.003 0.033 1352 Dihedral : 15.434 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 0.00344 / 0.24 (11302) covalent geometry : angle 0.48516 / 0.34 (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 : 0.295 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: 0.1372 time to fit residues: 43.7765 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 : 0.301 ------------------------------------------------------------------------------- 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: 8.9990 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 ** 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 = 0.3597 r_free = 0.3597 target = 0.117222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.097133 restraints weight = 17531.828| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 1.69 r_work: 0.3164 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3025 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.1179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 11310 Z= 0.242 Angle : 0.902 53.979 16174 Z= 0.347 Chirality : 0.041 0.196 1894 Planarity : 0.005 0.064 1352 Dihedral : 15.939 85.711 3218 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 3.85 % Allowed : 15.81 % 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: 0.97 (0.30), residues: 797 helix: 2.48 (0.26), residues: 365 sheet: -0.64 (0.43), residues: 147 loop : -1.11 (0.36), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 255 TYR 0.015 0.002 TYR B 342 PHE 0.026 0.002 PHE B 389 TRP 0.012 0.002 TRP A 43 HIS 0.004 0.001 HIS A 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00513 / 0.24 (11302) covalent geometry : angle 0.58609 / 0.32 (16162) hydrogen bonds : bond 0.05853 / 3.88 ( 540) hydrogen bonds : angle 4.26620 / 3.07 ( 1366) metal coordination : bond 0.01748 / 1.07 ( 8) metal coordination : angle 25.17582 / 13.86 ( 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 215 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 188 time to evaluate : 0.228 Fit side-chains revert: symmetry clash REVERT: A 82 LYS cc_start: 0.8651 (ttmt) cc_final: 0.8424 (ttmt) REVERT: A 130 GLU cc_start: 0.8338 (mp0) cc_final: 0.7862 (mp0) REVERT: A 145 SER cc_start: 0.8653 (m) cc_final: 0.8419 (p) REVERT: A 262 ILE cc_start: 0.8435 (mt) cc_final: 0.8198 (mm) REVERT: A 299 ASP cc_start: 0.8158 (t0) cc_final: 0.7955 (m-30) REVERT: A 311 ASP cc_start: 0.8118 (m-30) cc_final: 0.7836 (m-30) REVERT: A 344 ASP cc_start: 0.7836 (OUTLIER) cc_final: 0.7468 (m-30) REVERT: B 100 ASP cc_start: 0.7891 (m-30) cc_final: 0.7636 (m-30) REVERT: B 133 SER cc_start: 0.9087 (t) cc_final: 0.8640 (p) REVERT: B 137 MET cc_start: 0.6800 (mmt) cc_final: 0.6539 (mmt) REVERT: B 200 LYS cc_start: 0.8609 (mttt) cc_final: 0.8361 (mttp) REVERT: B 221 ILE cc_start: 0.8023 (mp) cc_final: 0.7712 (mm) REVERT: B 244 LYS cc_start: 0.8673 (pttt) cc_final: 0.8417 (pttm) REVERT: B 289 GLN cc_start: 0.7946 (mm-40) cc_final: 0.7594 (mm-40) REVERT: B 316 GLU cc_start: 0.8139 (mm-30) cc_final: 0.7908 (mm-30) REVERT: B 417 ILE cc_start: 0.8989 (OUTLIER) cc_final: 0.8775 (tt) outliers start: 27 outliers final: 14 residues processed: 204 average time/residue: 0.1330 time to fit residues: 35.2440 Evaluate side-chains 202 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 186 time to evaluate : 0.315 ------------------------------------------------------------------------------- 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 329 ILE Chi-restraints excluded: chain A residue 344 ASP Chi-restraints excluded: chain A residue 361 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: 0.9990 chunk 18 optimal weight: 6.9990 chunk 56 optimal weight: 5.9990 chunk 64 optimal weight: 1.9990 chunk 93 optimal weight: 7.9990 chunk 58 optimal weight: 5.9990 chunk 86 optimal weight: 10.0000 chunk 53 optimal weight: 0.9990 chunk 4 optimal weight: 4.9990 chunk 16 optimal weight: 0.9990 chunk 19 optimal weight: 7.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 366 GLN ** B 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 403 ASN B 407 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.118339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.098156 restraints weight = 17557.995| |-----------------------------------------------------------------------------| r_work (start): 0.3310 rms_B_bonded: 1.71 r_work: 0.3184 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3046 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 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 : 0.004 0.044 11310 Z= 0.172 Angle : 0.603 19.668 16174 Z= 0.301 Chirality : 0.039 0.196 1894 Planarity : 0.004 0.047 1352 Dihedral : 15.882 86.787 3213 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 3.13 % Allowed : 17.81 % Favored : 79.06 % 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: 1.06 (0.30), residues: 797 helix: 2.64 (0.25), residues: 365 sheet: -0.72 (0.42), residues: 146 loop : -1.12 (0.35), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 136 TYR 0.017 0.001 TYR A 351 PHE 0.024 0.002 PHE B 389 TRP 0.010 0.002 TRP A 43 HIS 0.002 0.001 HIS A 238 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.17 (11302) covalent geometry : angle 0.53177 / 0.30 (16162) hydrogen bonds : bond 0.05117 / 3.39 ( 540) hydrogen bonds : angle 3.90760 / 2.83 ( 1366) metal coordination : bond 0.01272 / 0.75 ( 8) metal coordination : angle 10.42639 / 6.76 ( 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 206 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 184 time to evaluate : 0.303 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 126 ASP cc_start: 0.8234 (t70) cc_final: 0.8024 (t0) REVERT: A 130 GLU cc_start: 0.8273 (mp0) cc_final: 0.7994 (mp0) REVERT: A 244 LYS cc_start: 0.8574 (ptpp) cc_final: 0.8360 (mtmm) REVERT: A 262 ILE cc_start: 0.8466 (mt) cc_final: 0.8241 (mm) REVERT: A 285 LYS cc_start: 0.8374 (tttt) cc_final: 0.8055 (tttm) REVERT: A 344 ASP cc_start: 0.7836 (OUTLIER) cc_final: 0.7498 (m-30) REVERT: B 133 SER cc_start: 0.9069 (t) cc_final: 0.8609 (p) REVERT: B 178 ASP cc_start: 0.8021 (m-30) cc_final: 0.7418 (m-30) REVERT: B 200 LYS cc_start: 0.8499 (mttt) cc_final: 0.8241 (mttm) REVERT: B 221 ILE cc_start: 0.7973 (mp) cc_final: 0.7695 (mt) REVERT: B 244 LYS cc_start: 0.8702 (pttt) cc_final: 0.8391 (pttm) REVERT: B 289 GLN cc_start: 0.7801 (mm-40) cc_final: 0.7471 (mm-40) REVERT: B 417 ILE cc_start: 0.8968 (OUTLIER) cc_final: 0.8762 (tt) outliers start: 22 outliers final: 17 residues processed: 195 average time/residue: 0.1242 time to fit residues: 31.6986 Evaluate side-chains 193 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 174 time to evaluate : 0.234 ------------------------------------------------------------------------------- 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 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 355 GLU Chi-restraints excluded: chain A residue 361 ILE Chi-restraints excluded: chain A residue 388 ILE 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 92 optimal weight: 10.0000 chunk 73 optimal weight: 2.9990 chunk 43 optimal weight: 4.9990 chunk 63 optimal weight: 9.9990 chunk 66 optimal weight: 0.9990 chunk 37 optimal weight: 0.9990 chunk 6 optimal weight: 5.9990 chunk 72 optimal weight: 0.7980 chunk 97 optimal weight: 8.9990 chunk 76 optimal weight: 8.9990 chunk 34 optimal weight: 0.8980 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 366 GLN B 26 GLN ** B 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 366 GLN B 407 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.119221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.098956 restraints weight = 17890.618| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 1.73 r_work: 0.3196 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3057 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.1669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 11310 Z= 0.138 Angle : 0.522 15.465 16174 Z= 0.282 Chirality : 0.037 0.196 1894 Planarity : 0.003 0.032 1352 Dihedral : 15.835 87.712 3213 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 4.13 % Allowed : 17.95 % Favored : 77.92 % 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: 1.20 (0.30), residues: 797 helix: 2.83 (0.25), residues: 365 sheet: -0.67 (0.39), residues: 156 loop : -1.15 (0.37), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 255 TYR 0.017 0.001 TYR B 202 PHE 0.016 0.001 PHE B 389 TRP 0.008 0.001 TRP A 43 HIS 0.005 0.001 HIS A 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.14 (11302) covalent geometry : angle 0.50013 / 0.28 (16162) hydrogen bonds : bond 0.04672 / 3.10 ( 540) hydrogen bonds : angle 3.70592 / 2.68 ( 1366) metal coordination : bond 0.00906 / 0.52 ( 8) metal coordination : angle 5.56885 / 4.34 ( 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 204 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 175 time to evaluate : 0.303 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 ASP cc_start: 0.8148 (m-30) cc_final: 0.7880 (t0) REVERT: A 126 ASP cc_start: 0.8200 (t70) cc_final: 0.7986 (t0) REVERT: A 130 GLU cc_start: 0.8250 (mp0) cc_final: 0.7989 (mp0) REVERT: A 244 LYS cc_start: 0.8584 (ptpp) cc_final: 0.8366 (mtmm) REVERT: A 258 GLU cc_start: 0.7651 (mt-10) cc_final: 0.7448 (mt-10) REVERT: A 262 ILE cc_start: 0.8485 (mt) cc_final: 0.8257 (mm) REVERT: A 344 ASP cc_start: 0.7804 (OUTLIER) cc_final: 0.7354 (m-30) REVERT: B 11 LYS cc_start: 0.8673 (pttt) cc_final: 0.8462 (pttp) REVERT: B 133 SER cc_start: 0.9044 (t) cc_final: 0.8583 (p) REVERT: B 244 LYS cc_start: 0.8682 (pttt) cc_final: 0.8402 (pttm) REVERT: B 255 ARG cc_start: 0.8008 (mtm-85) cc_final: 0.7636 (mtm-85) REVERT: B 289 GLN cc_start: 0.7740 (mm-40) cc_final: 0.7425 (mm-40) REVERT: B 417 ILE cc_start: 0.8949 (OUTLIER) cc_final: 0.8697 (tt) outliers start: 29 outliers final: 23 residues processed: 187 average time/residue: 0.1316 time to fit residues: 32.2462 Evaluate side-chains 198 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 173 time to evaluate : 0.205 ------------------------------------------------------------------------------- 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 110 LEU Chi-restraints excluded: chain A residue 138 ASN Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 344 ASP Chi-restraints excluded: chain A residue 355 GLU Chi-restraints excluded: chain A residue 361 ILE Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 421 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 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 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: 2.9990 chunk 52 optimal weight: 6.9990 chunk 5 optimal weight: 2.9990 chunk 66 optimal weight: 4.9990 chunk 38 optimal weight: 5.9990 chunk 61 optimal weight: 6.9990 chunk 7 optimal weight: 5.9990 chunk 46 optimal weight: 5.9990 chunk 33 optimal weight: 8.9990 chunk 54 optimal weight: 0.5980 overall best weight: 3.5188 ------------------------------------------------------------------------------- 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 366 GLN B 407 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.116381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.096101 restraints weight = 17714.785| |-----------------------------------------------------------------------------| r_work (start): 0.3279 rms_B_bonded: 1.73 r_work: 0.3153 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3016 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.1783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 11310 Z= 0.259 Angle : 0.579 12.302 16174 Z= 0.310 Chirality : 0.041 0.196 1894 Planarity : 0.004 0.054 1352 Dihedral : 15.921 89.053 3213 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 4.56 % Allowed : 19.09 % Favored : 76.35 % 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: 0.98 (0.30), residues: 797 helix: 2.62 (0.25), residues: 365 sheet: -0.74 (0.39), residues: 156 loop : -1.25 (0.36), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 298 TYR 0.017 0.002 TYR A 351 PHE 0.033 0.002 PHE B 389 TRP 0.011 0.002 TRP B 43 HIS 0.003 0.001 HIS A 238 Details of bonding type rmsd/Z covalent geometry : bond 0.00552 / 0.26 (11302) covalent geometry : angle 0.56254 / 0.31 (16162) hydrogen bonds : bond 0.05352 / 3.54 ( 540) hydrogen bonds : angle 3.77369 / 2.72 ( 1366) metal coordination : bond 0.01109 / 0.66 ( 8) metal coordination : angle 4.98680 / 3.64 ( 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 201 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 169 time to evaluate : 0.297 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 ASP cc_start: 0.8167 (m-30) cc_final: 0.7916 (t0) REVERT: A 130 GLU cc_start: 0.8261 (mp0) cc_final: 0.7965 (mp0) REVERT: A 244 LYS cc_start: 0.8587 (ptpp) cc_final: 0.8371 (mtmm) REVERT: A 258 GLU cc_start: 0.7788 (mt-10) cc_final: 0.7483 (mt-10) REVERT: A 262 ILE cc_start: 0.8473 (mt) cc_final: 0.8210 (mm) REVERT: A 344 ASP cc_start: 0.7863 (OUTLIER) cc_final: 0.7440 (m-30) REVERT: B 11 LYS cc_start: 0.8762 (pttt) cc_final: 0.8531 (pttp) REVERT: B 224 ILE cc_start: 0.7687 (OUTLIER) cc_final: 0.7484 (tt) REVERT: B 255 ARG cc_start: 0.8043 (mtm-85) cc_final: 0.7705 (mtm-85) REVERT: B 289 GLN cc_start: 0.7716 (mm-40) cc_final: 0.7393 (mm-40) REVERT: B 366 GLN cc_start: 0.7951 (tp40) cc_final: 0.7549 (tm-30) outliers start: 32 outliers final: 27 residues processed: 187 average time/residue: 0.1387 time to fit residues: 33.7020 Evaluate side-chains 195 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 166 time to evaluate : 0.299 ------------------------------------------------------------------------------- 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 110 LEU 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 355 GLU Chi-restraints excluded: chain A residue 361 ILE Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain B residue 16 ASP Chi-restraints excluded: chain B residue 39 THR 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 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 6 optimal weight: 3.9990 chunk 12 optimal weight: 0.1980 chunk 89 optimal weight: 10.0000 chunk 19 optimal weight: 5.9990 chunk 69 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 36 optimal weight: 7.9990 chunk 26 optimal weight: 3.9990 chunk 71 optimal weight: 4.9990 chunk 95 optimal weight: 20.0000 chunk 97 optimal weight: 5.9990 overall best weight: 2.8388 ------------------------------------------------------------------------------- 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 = 0.3604 r_free = 0.3604 target = 0.117530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.097564 restraints weight = 17643.692| |-----------------------------------------------------------------------------| r_work (start): 0.3293 rms_B_bonded: 1.67 r_work: 0.3167 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3031 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.1839 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= 0.212 Angle : 0.551 10.313 16174 Z= 0.298 Chirality : 0.040 0.195 1894 Planarity : 0.004 0.070 1352 Dihedral : 15.927 89.831 3213 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 4.56 % Allowed : 19.52 % Favored : 75.93 % 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: 0.99 (0.29), residues: 797 helix: 2.63 (0.25), residues: 365 sheet: -0.70 (0.38), residues: 156 loop : -1.26 (0.36), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 298 TYR 0.017 0.002 TYR A 351 PHE 0.034 0.002 PHE B 389 TRP 0.010 0.001 TRP B 43 HIS 0.003 0.001 HIS A 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00448 / 0.21 (11302) covalent geometry : angle 0.53814 / 0.30 (16162) hydrogen bonds : bond 0.05073 / 3.36 ( 540) hydrogen bonds : angle 3.74315 / 2.71 ( 1366) metal coordination : bond 0.00922 / 0.54 ( 8) metal coordination : angle 4.36242 / 3.13 ( 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 198 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 166 time to evaluate : 0.303 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 16 ASP cc_start: 0.8198 (m-30) cc_final: 0.7959 (t0) REVERT: A 130 GLU cc_start: 0.8245 (mp0) cc_final: 0.7927 (mp0) REVERT: A 262 ILE cc_start: 0.8487 (mt) cc_final: 0.8243 (mm) REVERT: A 344 ASP cc_start: 0.7825 (OUTLIER) cc_final: 0.7400 (m-30) REVERT: B 11 LYS cc_start: 0.8728 (pttt) cc_final: 0.8517 (pttp) REVERT: B 133 SER cc_start: 0.9046 (t) cc_final: 0.8588 (p) REVERT: B 254 ARG cc_start: 0.8096 (ttp-110) cc_final: 0.7603 (mtp85) REVERT: B 255 ARG cc_start: 0.8081 (mtm-85) cc_final: 0.7684 (mtm-85) REVERT: B 289 GLN cc_start: 0.7675 (mm-40) cc_final: 0.7383 (mm-40) REVERT: B 300 THR cc_start: 0.8764 (m) cc_final: 0.8355 (p) outliers start: 32 outliers final: 27 residues processed: 184 average time/residue: 0.1241 time to fit residues: 29.9512 Evaluate side-chains 194 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 166 time to evaluate : 0.282 ------------------------------------------------------------------------------- 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 110 LEU 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 341 THR Chi-restraints excluded: chain A residue 344 ASP Chi-restraints excluded: chain A residue 355 GLU Chi-restraints excluded: chain A residue 361 ILE Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 421 ILE Chi-restraints excluded: chain B residue 39 THR 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 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 363 ILE Chi-restraints excluded: chain B residue 401 ASP Chi-restraints excluded: chain B residue 416 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 88 optimal weight: 10.0000 chunk 39 optimal weight: 6.9990 chunk 6 optimal weight: 6.9990 chunk 17 optimal weight: 0.9990 chunk 24 optimal weight: 0.2980 chunk 30 optimal weight: 1.9990 chunk 72 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 96 optimal weight: 7.9990 chunk 86 optimal weight: 7.9990 chunk 62 optimal weight: 0.0270 overall best weight: 1.0644 ------------------------------------------------------------------------------- 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 366 GLN B 407 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.118695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.098592 restraints weight = 17637.784| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 1.77 r_work: 0.3186 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3048 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.1916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11310 Z= 0.126 Angle : 0.519 12.297 16174 Z= 0.281 Chirality : 0.037 0.194 1894 Planarity : 0.004 0.068 1352 Dihedral : 15.849 90.204 3211 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 4.84 % Allowed : 19.80 % Favored : 75.36 % 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: 1.31 (0.30), residues: 797 helix: 2.90 (0.25), residues: 365 sheet: -0.50 (0.39), residues: 148 loop : -1.13 (0.36), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 392 TYR 0.017 0.001 TYR A 351 PHE 0.033 0.002 PHE B 389 TRP 0.007 0.001 TRP A 43 HIS 0.002 0.001 HIS A 238 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.13 (11302) covalent geometry : angle 0.50344 / 0.28 (16162) hydrogen bonds : bond 0.04465 / 2.97 ( 540) hydrogen bonds : angle 3.60590 / 2.61 ( 1366) metal coordination : bond 0.00657 / 0.39 ( 8) metal coordination : angle 4.63143 / 3.61 ( 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 207 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 173 time to evaluate : 0.288 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 ASP cc_start: 0.8149 (m-30) cc_final: 0.7870 (t0) REVERT: A 130 GLU cc_start: 0.8308 (mp0) cc_final: 0.7978 (mp0) REVERT: A 258 GLU cc_start: 0.7492 (mt-10) cc_final: 0.7072 (mt-10) REVERT: A 262 ILE cc_start: 0.8394 (mt) cc_final: 0.8107 (mm) REVERT: A 344 ASP cc_start: 0.7812 (OUTLIER) cc_final: 0.7333 (m-30) REVERT: B 11 LYS cc_start: 0.8691 (pttt) cc_final: 0.8429 (pttp) REVERT: B 133 SER cc_start: 0.9034 (t) cc_final: 0.8539 (p) REVERT: B 254 ARG cc_start: 0.8017 (ttp-110) cc_final: 0.7518 (mtp85) REVERT: B 255 ARG cc_start: 0.8037 (mtm-85) cc_final: 0.7594 (mtm-85) REVERT: B 300 THR cc_start: 0.8660 (m) cc_final: 0.8218 (p) REVERT: B 366 GLN cc_start: 0.7943 (tp40) cc_final: 0.7438 (tm-30) REVERT: B 369 SER cc_start: 0.8242 (m) cc_final: 0.7872 (p) outliers start: 34 outliers final: 28 residues processed: 190 average time/residue: 0.1138 time to fit residues: 28.4405 Evaluate side-chains 205 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 176 time to evaluate : 0.209 ------------------------------------------------------------------------------- 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 110 LEU 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 324 GLU Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 344 ASP Chi-restraints excluded: chain A residue 355 GLU 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 128 ILE 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 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 416 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 2 optimal weight: 6.9990 chunk 12 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 84 optimal weight: 8.9990 chunk 59 optimal weight: 6.9990 chunk 43 optimal weight: 5.9990 chunk 35 optimal weight: 5.9990 chunk 61 optimal weight: 5.9990 chunk 0 optimal weight: 7.9990 chunk 32 optimal weight: 6.9990 chunk 64 optimal weight: 4.9990 overall best weight: 3.9788 ------------------------------------------------------------------------------- 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 = 0.3578 r_free = 0.3578 target = 0.115819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.095847 restraints weight = 17660.440| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 1.69 r_work: 0.3150 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3014 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.1968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 11310 Z= 0.284 Angle : 0.603 9.360 16174 Z= 0.322 Chirality : 0.042 0.192 1894 Planarity : 0.004 0.085 1352 Dihedral : 15.949 91.343 3209 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 4.84 % Allowed : 20.23 % 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: 0.98 (0.29), residues: 797 helix: 2.57 (0.25), residues: 365 sheet: -0.55 (0.39), residues: 148 loop : -1.29 (0.36), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 298 TYR 0.018 0.002 TYR A 351 PHE 0.046 0.002 PHE B 389 TRP 0.011 0.002 TRP B 43 HIS 0.003 0.001 HIS A 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00612 / 0.28 (11302) covalent geometry : angle 0.59149 / 0.32 (16162) hydrogen bonds : bond 0.05491 / 3.64 ( 540) hydrogen bonds : angle 3.74799 / 2.71 ( 1366) metal coordination : bond 0.01130 / 0.70 ( 8) metal coordination : angle 4.30167 / 2.94 ( 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 206 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 172 time to evaluate : 0.305 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 ASP cc_start: 0.8240 (m-30) cc_final: 0.8015 (t0) REVERT: A 30 GLU cc_start: 0.7900 (OUTLIER) cc_final: 0.7402 (mp0) REVERT: A 130 GLU cc_start: 0.8273 (mp0) cc_final: 0.7967 (mp0) REVERT: A 258 GLU cc_start: 0.7598 (mt-10) cc_final: 0.7197 (mt-10) REVERT: A 262 ILE cc_start: 0.8491 (mt) cc_final: 0.8230 (mm) REVERT: A 344 ASP cc_start: 0.7862 (OUTLIER) cc_final: 0.7434 (m-30) REVERT: B 11 LYS cc_start: 0.8662 (pttt) cc_final: 0.8290 (pttp) REVERT: B 166 ILE cc_start: 0.8993 (OUTLIER) cc_final: 0.8703 (mt) REVERT: B 255 ARG cc_start: 0.8091 (mtm-85) cc_final: 0.7717 (mtm-85) REVERT: B 289 GLN cc_start: 0.7628 (mm-40) cc_final: 0.7332 (mm-40) outliers start: 34 outliers final: 31 residues processed: 187 average time/residue: 0.1393 time to fit residues: 34.0165 Evaluate side-chains 203 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 169 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 0 SER Chi-restraints excluded: chain A residue 30 GLU 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 233 TYR 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 324 GLU 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 355 GLU 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 128 ILE 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 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 416 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 54 optimal weight: 0.8980 chunk 31 optimal weight: 0.8980 chunk 86 optimal weight: 8.9990 chunk 22 optimal weight: 5.9990 chunk 38 optimal weight: 10.0000 chunk 46 optimal weight: 0.8980 chunk 91 optimal weight: 10.0000 chunk 3 optimal weight: 3.9990 chunk 10 optimal weight: 0.9990 chunk 89 optimal weight: 8.9990 chunk 27 optimal weight: 4.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- 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 = 0.3595 r_free = 0.3595 target = 0.117652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.097547 restraints weight = 17675.643| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 1.77 r_work: 0.3170 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3031 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.1984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11310 Z= 0.148 Angle : 0.525 8.667 16174 Z= 0.286 Chirality : 0.038 0.191 1894 Planarity : 0.004 0.076 1352 Dihedral : 15.870 91.492 3209 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 4.70 % Allowed : 21.08 % Favored : 74.22 % 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: 1.20 (0.30), residues: 797 helix: 2.78 (0.25), residues: 365 sheet: -0.48 (0.39), residues: 148 loop : -1.19 (0.36), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 298 TYR 0.018 0.001 TYR A 351 PHE 0.037 0.002 PHE B 389 TRP 0.008 0.001 TRP B 43 HIS 0.002 0.001 HIS A 303 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.15 (11302) covalent geometry : angle 0.51597 / 0.29 (16162) hydrogen bonds : bond 0.04647 / 3.08 ( 540) hydrogen bonds : angle 3.63593 / 2.64 ( 1366) metal coordination : bond 0.00624 / 0.35 ( 8) metal coordination : angle 3.66358 / 2.62 ( 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 205 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 172 time to evaluate : 0.349 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 ASP cc_start: 0.8175 (m-30) cc_final: 0.7904 (t0) REVERT: A 30 GLU cc_start: 0.7847 (OUTLIER) cc_final: 0.7358 (mp0) REVERT: A 130 GLU cc_start: 0.8324 (mp0) cc_final: 0.7975 (mp0) REVERT: A 258 GLU cc_start: 0.7482 (mt-10) cc_final: 0.7022 (mt-10) REVERT: A 262 ILE cc_start: 0.8377 (mt) cc_final: 0.8086 (mm) REVERT: A 344 ASP cc_start: 0.7861 (OUTLIER) cc_final: 0.7349 (m-30) REVERT: B 11 LYS cc_start: 0.8730 (pttt) cc_final: 0.8465 (pttp) REVERT: B 133 SER cc_start: 0.9040 (t) cc_final: 0.8503 (p) REVERT: B 255 ARG cc_start: 0.8056 (mtm-85) cc_final: 0.7663 (mtm-85) REVERT: B 300 THR cc_start: 0.8667 (m) cc_final: 0.8223 (p) outliers start: 33 outliers final: 29 residues processed: 187 average time/residue: 0.1305 time to fit residues: 32.0934 Evaluate side-chains 202 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 171 time to evaluate : 0.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 0 SER Chi-restraints excluded: chain A residue 30 GLU 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 252 ASN Chi-restraints excluded: chain A residue 291 ARG 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 355 GLU 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 128 ILE 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 416 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 3 optimal weight: 5.9990 chunk 31 optimal weight: 0.6980 chunk 87 optimal weight: 10.0000 chunk 57 optimal weight: 0.3980 chunk 50 optimal weight: 3.9990 chunk 55 optimal weight: 1.9990 chunk 27 optimal weight: 7.9990 chunk 46 optimal weight: 4.9990 chunk 95 optimal weight: 20.0000 chunk 72 optimal weight: 0.8980 chunk 56 optimal weight: 1.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- 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 = 0.3612 r_free = 0.3612 target = 0.118764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.098664 restraints weight = 17566.252| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 1.77 r_work: 0.3189 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3050 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.2067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11310 Z= 0.131 Angle : 0.518 9.270 16174 Z= 0.282 Chirality : 0.037 0.190 1894 Planarity : 0.004 0.085 1352 Dihedral : 15.817 91.917 3209 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 4.70 % Allowed : 21.51 % Favored : 73.79 % 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: 2.80 (0.25), residues: 366 sheet: -0.37 (0.39), residues: 148 loop : -1.26 (0.36), residues: 283 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 0.034 0.002 PHE B 389 TRP 0.008 0.001 TRP A 43 HIS 0.002 0.000 HIS A 303 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.13 (11302) covalent geometry : angle 0.51154 / 0.28 (16162) hydrogen bonds : bond 0.04422 / 2.94 ( 540) hydrogen bonds : angle 3.57531 / 2.60 ( 1366) metal coordination : bond 0.00492 / 0.27 ( 8) metal coordination : angle 3.11520 / 2.21 ( 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 207 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 174 time to evaluate : 0.250 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 GLU cc_start: 0.7823 (OUTLIER) cc_final: 0.7337 (mp0) REVERT: A 130 GLU cc_start: 0.8273 (mp0) cc_final: 0.7952 (mp0) REVERT: A 258 GLU cc_start: 0.7513 (mt-10) cc_final: 0.7004 (mt-10) REVERT: A 262 ILE cc_start: 0.8404 (mt) cc_final: 0.8126 (mm) REVERT: A 344 ASP cc_start: 0.7831 (OUTLIER) cc_final: 0.7319 (m-30) REVERT: B 11 LYS cc_start: 0.8696 (pttt) cc_final: 0.8398 (pttp) REVERT: B 133 SER cc_start: 0.9018 (t) cc_final: 0.8511 (p) REVERT: B 255 ARG cc_start: 0.8040 (mtm-85) cc_final: 0.7651 (mtm-85) REVERT: B 300 THR cc_start: 0.8595 (m) cc_final: 0.8162 (p) REVERT: B 359 LYS cc_start: 0.8477 (OUTLIER) cc_final: 0.8236 (tmmt) REVERT: B 366 GLN cc_start: 0.7869 (mm-40) cc_final: 0.7233 (tm-30) REVERT: B 369 SER cc_start: 0.8310 (m) cc_final: 0.8013 (p) outliers start: 33 outliers final: 26 residues processed: 189 average time/residue: 0.1257 time to fit residues: 30.9556 Evaluate side-chains 203 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 174 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 0 SER Chi-restraints excluded: chain A residue 30 GLU 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 233 TYR 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 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 355 GLU 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 128 ILE 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 416 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 28 optimal weight: 6.9990 chunk 93 optimal weight: 8.9990 chunk 4 optimal weight: 4.9990 chunk 51 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 70 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 57 optimal weight: 0.6980 chunk 11 optimal weight: 0.9990 chunk 53 optimal weight: 0.7980 chunk 79 optimal weight: 7.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 29 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 = 0.3612 r_free = 0.3612 target = 0.118756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.098598 restraints weight = 17658.636| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 1.77 r_work: 0.3187 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3048 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.2142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11310 Z= 0.144 Angle : 0.533 7.903 16174 Z= 0.291 Chirality : 0.037 0.187 1894 Planarity : 0.004 0.098 1352 Dihedral : 15.806 92.344 3209 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 4.84 % Allowed : 20.51 % Favored : 74.64 % 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: 1.28 (0.30), residues: 797 helix: 2.81 (0.25), residues: 366 sheet: -0.22 (0.40), residues: 147 loop : -1.27 (0.36), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 298 TYR 0.017 0.001 TYR A 351 PHE 0.033 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 0.00297 / 0.14 (11302) covalent geometry : angle 0.52709 / 0.29 (16162) hydrogen bonds : bond 0.04501 / 2.98 ( 540) hydrogen bonds : angle 3.59559 / 2.61 ( 1366) metal coordination : bond 0.00517 / 0.29 ( 8) metal coordination : angle 2.96886 / 2.05 ( 12) =============================================================================== Job complete usr+sys time: 2783.10 seconds wall clock time: 48 minutes 18.65 seconds (2898.65 seconds total)