Starting phenix.real_space_refine on Sat Oct 11 02:23:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8j12_35912/10_2025/8j12_35912.cif Found real_map, /net/cci-nas-00/data/ceres_data/8j12_35912/10_2025/8j12_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 { model { file = "/net/cci-nas-00/data/ceres_data/8j12_35912/10_2025/8j12_35912.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8j12_35912/10_2025/8j12_35912.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8j12_35912/10_2025/8j12_35912.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8j12_35912/10_2025/8j12_35912.map" } resolution = 3.08 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.008 sd= 0.070 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 194 5.49 5 Mg 7 5.21 5 S 32 5.16 5 C 6014 2.51 5 N 1933 2.21 5 O 2522 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/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: 3.23, per 1000 atoms: 0.30 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 433.2 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 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: 1.31 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: 2.24 Time building geometry restraints manager: 1.31 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=" C4' DT E -3 " pdb=" C3' DT E -3 " ideal model delta sigma weight residual 1.523 1.504 0.019 2.00e-02 2.50e+03 8.76e-01 bond pdb=" C LYS B 285 " pdb=" N PRO B 286 " ideal model delta sigma weight residual 1.334 1.355 -0.021 2.34e-02 1.83e+03 8.15e-01 bond pdb=" CA ILE B 378 " pdb=" CB ILE B 378 " ideal model delta sigma weight residual 1.527 1.538 -0.011 1.31e-02 5.83e+03 7.65e-01 bond pdb=" C4' DC D 18 " pdb=" O4' DC D 18 " ideal model delta sigma weight residual 1.450 1.434 0.016 2.00e-02 2.50e+03 6.78e-01 bond pdb=" O4' DT D 14 " pdb=" C1' DT D 14 " ideal model delta sigma weight residual 1.414 1.398 0.016 2.00e-02 2.50e+03 6.68e-01 ... (remaining 11297 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.00: 15569 1.00 - 2.00: 474 2.00 - 3.01: 97 3.01 - 4.01: 17 4.01 - 5.01: 5 Bond angle restraints: 16162 Sorted by residual: angle pdb=" C2' A C-114 " pdb=" C1' A C-114 " pdb=" N9 A C-114 " ideal model delta sigma weight residual 112.00 115.43 -3.43 1.50e+00 4.44e-01 5.24e+00 angle pdb=" C2' G C-166 " pdb=" C1' G C-166 " pdb=" N9 G C-166 " ideal model delta sigma weight residual 112.00 115.02 -3.02 1.50e+00 4.44e-01 4.06e+00 angle pdb=" CA TYR A 351 " pdb=" CB TYR A 351 " pdb=" CG TYR A 351 " ideal model delta sigma weight residual 113.90 117.45 -3.55 1.80e+00 3.09e-01 3.90e+00 angle pdb=" C2' C C -72 " pdb=" C1' C C -72 " pdb=" N1 C C -72 " ideal model delta sigma weight residual 112.00 114.92 -2.92 1.50e+00 4.44e-01 3.79e+00 angle pdb=" N ILE B 378 " pdb=" CA ILE B 378 " pdb=" C ILE B 378 " ideal model delta sigma weight residual 106.55 109.32 -2.77 1.45e+00 4.76e-01 3.64e+00 ... (remaining 16157 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.74: 5735 17.74 - 35.47: 646 35.47 - 53.21: 290 53.21 - 70.94: 204 70.94 - 88.68: 41 Dihedral angle restraints: 6916 sinusoidal: 4549 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 6913 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 1516 0.039 - 0.079: 279 0.079 - 0.118: 86 0.118 - 0.158: 12 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=" 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 chirality pdb=" C1' G C-166 " pdb=" O4' G C-166 " pdb=" C2' G C-166 " pdb=" N9 G C-166 " both_signs ideal model delta sigma weight residual False 2.46 2.31 0.15 2.00e-01 2.50e+01 5.51e-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: 0.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 14.160 Find NCS groups from input model: 0.220 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:1.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 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 : 0.003 0.102 11310 Z= 0.151 Angle : 1.024 61.226 16174 Z= 0.301 Chirality : 0.036 0.197 1894 Planarity : 0.003 0.033 1352 Dihedral : 19.900 88.680 5400 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 aren 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 covalent geometry : bond 0.00292 (11302) covalent geometry : angle 0.44623 (16162) hydrogen bonds : bond 0.14816 ( 540) hydrogen bonds : angle 5.60407 ( 1366) metal coordination : bond 0.06498 ( 8) metal coordination : angle 33.85833 ( 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 : 0.323 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: 0.7271 (m-30) cc_final: 0.6753 (m-30) outliers start: 15 outliers final: 5 residues processed: 246 average time/residue: 0.1481 time to fit residues: 46.9123 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 : 0.315 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: A 56 HIS A 194 HIS ** A 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 322 GLN A 366 GLN A 370 GLN ** A 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 26 GLN B 252 ASN B 303 HIS ** B 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 407 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.116809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.096597 restraints weight = 17698.774| |-----------------------------------------------------------------------------| r_work (start): 0.3284 rms_B_bonded: 1.71 r_work: 0.3156 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3021 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.1435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 11310 Z= 0.241 Angle : 0.621 17.596 16174 Z= 0.313 Chirality : 0.040 0.196 1894 Planarity : 0.004 0.052 1352 Dihedral : 21.541 87.483 3754 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 3.70 % Allowed : 16.10 % Favored : 80.20 % 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 aren not related in a simple way. whole: 0.98 (0.30), residues: 797 helix: 2.51 (0.26), residues: 365 sheet: -0.73 (0.43), residues: 147 loop : -1.06 (0.36), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 255 TYR 0.017 0.002 TYR A 351 PHE 0.026 0.002 PHE B 389 TRP 0.011 0.002 TRP A 43 HIS 0.005 0.001 HIS A 56 Details of bonding type rmsd covalent geometry : bond 0.00521 (11302) covalent geometry : angle 0.56785 (16162) hydrogen bonds : bond 0.05557 ( 540) hydrogen bonds : angle 3.99663 ( 1366) metal coordination : bond 0.01466 ( 8) metal coordination : angle 9.22950 ( 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 213 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 187 time to evaluate : 0.385 Fit side-chains revert: symmetry clash REVERT: A 30 GLU cc_start: 0.7941 (mm-30) cc_final: 0.7697 (mm-30) REVERT: A 82 LYS cc_start: 0.8639 (ttmt) cc_final: 0.8408 (ttmt) REVERT: A 130 GLU cc_start: 0.8304 (mp0) cc_final: 0.7805 (mp0) REVERT: A 262 ILE cc_start: 0.8442 (mt) cc_final: 0.8209 (mm) REVERT: A 344 ASP cc_start: 0.7803 (OUTLIER) cc_final: 0.7439 (m-30) REVERT: B 11 LYS cc_start: 0.8561 (pttt) cc_final: 0.8347 (pttp) REVERT: B 100 ASP cc_start: 0.7898 (m-30) cc_final: 0.7647 (m-30) REVERT: B 133 SER cc_start: 0.9109 (t) cc_final: 0.8672 (p) REVERT: B 174 LYS cc_start: 0.8490 (tttt) cc_final: 0.7714 (tppp) REVERT: B 178 ASP cc_start: 0.8005 (m-30) cc_final: 0.7408 (m-30) REVERT: B 200 LYS cc_start: 0.8604 (mttt) cc_final: 0.8337 (mttm) REVERT: B 221 ILE cc_start: 0.8008 (mp) cc_final: 0.7586 (mm) REVERT: B 234 MET cc_start: 0.8762 (mtm) cc_final: 0.8546 (mtp) REVERT: B 251 GLU cc_start: 0.7842 (tt0) cc_final: 0.7633 (tt0) REVERT: B 300 THR cc_start: 0.8746 (m) cc_final: 0.8326 (p) REVERT: B 320 THR cc_start: 0.7991 (p) cc_final: 0.7777 (p) outliers start: 26 outliers final: 14 residues processed: 202 average time/residue: 0.1590 time to fit residues: 41.4384 Evaluate side-chains 190 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 175 time to evaluate : 0.331 ------------------------------------------------------------------------------- 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 103 LYS Chi-restraints excluded: chain A residue 138 ASN Chi-restraints excluded: chain A residue 344 ASP Chi-restraints excluded: chain A residue 361 ILE Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain B residue 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 401 ASP Chi-restraints excluded: chain B residue 416 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 2 optimal weight: 1.9990 chunk 18 optimal weight: 6.9990 chunk 56 optimal weight: 3.9990 chunk 64 optimal weight: 0.9990 chunk 93 optimal weight: 7.9990 chunk 58 optimal weight: 4.9990 chunk 86 optimal weight: 10.0000 chunk 53 optimal weight: 0.9990 chunk 4 optimal weight: 4.9990 chunk 16 optimal weight: 4.9990 chunk 19 optimal weight: 0.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 366 GLN A 370 GLN ** B 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 407 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.118849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.098884 restraints weight = 17582.767| |-----------------------------------------------------------------------------| r_work (start): 0.3317 rms_B_bonded: 1.68 r_work: 0.3194 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3057 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.1698 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= 0.158 Angle : 0.515 8.497 16174 Z= 0.277 Chirality : 0.037 0.197 1894 Planarity : 0.004 0.058 1352 Dihedral : 21.441 88.549 3749 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 3.56 % Allowed : 18.23 % Favored : 78.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.12 (0.30), residues: 797 helix: 2.75 (0.25), residues: 365 sheet: -0.71 (0.40), residues: 156 loop : -1.18 (0.37), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 255 TYR 0.018 0.001 TYR B 202 PHE 0.026 0.002 PHE B 389 TRP 0.009 0.001 TRP A 43 HIS 0.002 0.001 HIS A 238 Details of bonding type rmsd covalent geometry : bond 0.00338 (11302) covalent geometry : angle 0.50335 (16162) hydrogen bonds : bond 0.04672 ( 540) hydrogen bonds : angle 3.71098 ( 1366) metal coordination : bond 0.00886 ( 8) metal coordination : angle 3.98339 ( 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 199 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 174 time to evaluate : 0.380 Fit side-chains revert: symmetry clash REVERT: A 30 GLU cc_start: 0.7848 (mm-30) cc_final: 0.7617 (mm-30) REVERT: A 55 ASN cc_start: 0.8183 (t0) cc_final: 0.7967 (t0) REVERT: A 82 LYS cc_start: 0.8592 (ttmt) cc_final: 0.8375 (ttmt) REVERT: A 130 GLU cc_start: 0.8248 (mp0) cc_final: 0.7962 (mp0) REVERT: A 258 GLU cc_start: 0.7692 (mt-10) cc_final: 0.7451 (mt-10) REVERT: A 262 ILE cc_start: 0.8498 (mt) cc_final: 0.8272 (mm) REVERT: A 344 ASP cc_start: 0.7856 (OUTLIER) cc_final: 0.7564 (t0) REVERT: B 11 LYS cc_start: 0.8529 (pttt) cc_final: 0.8212 (pttp) REVERT: B 100 ASP cc_start: 0.7883 (m-30) cc_final: 0.7679 (m-30) REVERT: B 133 SER cc_start: 0.9157 (t) cc_final: 0.8651 (p) REVERT: B 166 ILE cc_start: 0.8901 (OUTLIER) cc_final: 0.8611 (mt) REVERT: B 174 LYS cc_start: 0.8454 (tttt) cc_final: 0.7738 (tppp) REVERT: B 178 ASP cc_start: 0.7991 (m-30) cc_final: 0.7369 (m-30) REVERT: B 200 LYS cc_start: 0.8529 (mttt) cc_final: 0.8274 (mttm) REVERT: B 221 ILE cc_start: 0.7989 (mp) cc_final: 0.7590 (mm) REVERT: B 300 THR cc_start: 0.8739 (m) cc_final: 0.8322 (p) outliers start: 25 outliers final: 19 residues processed: 187 average time/residue: 0.1452 time to fit residues: 35.1377 Evaluate side-chains 190 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 169 time to evaluate : 0.259 ------------------------------------------------------------------------------- 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 344 ASP Chi-restraints excluded: chain A residue 361 ILE Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain B residue 114 MET Chi-restraints excluded: chain B residue 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 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 401 ASP Chi-restraints excluded: chain B residue 413 ILE Chi-restraints excluded: chain B residue 416 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: 0.9990 chunk 43 optimal weight: 4.9990 chunk 63 optimal weight: 7.9990 chunk 66 optimal weight: 0.9990 chunk 37 optimal weight: 8.9990 chunk 6 optimal weight: 5.9990 chunk 72 optimal weight: 0.7980 chunk 97 optimal weight: 8.9990 chunk 76 optimal weight: 6.9990 chunk 34 optimal weight: 0.9980 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 366 GLN A 370 GLN B 366 GLN ** B 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.118136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.098076 restraints weight = 17751.274| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 1.72 r_work: 0.3181 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3045 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.1922 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= 0.155 Angle : 0.502 5.177 16174 Z= 0.272 Chirality : 0.037 0.192 1894 Planarity : 0.003 0.032 1352 Dihedral : 21.421 90.453 3749 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 3.85 % Allowed : 20.51 % Favored : 75.64 % 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 aren not related in a simple way. whole: 1.30 (0.30), residues: 797 helix: 2.89 (0.25), residues: 365 sheet: -0.55 (0.39), residues: 156 loop : -1.11 (0.37), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 255 TYR 0.016 0.001 TYR A 351 PHE 0.019 0.001 PHE B 389 TRP 0.008 0.001 TRP A 43 HIS 0.003 0.001 HIS A 303 Details of bonding type rmsd covalent geometry : bond 0.00333 (11302) covalent geometry : angle 0.49541 (16162) hydrogen bonds : bond 0.04504 ( 540) hydrogen bonds : angle 3.62596 ( 1366) metal coordination : bond 0.00726 ( 8) metal coordination : angle 3.11882 ( 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 200 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 173 time to evaluate : 0.218 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 ASP cc_start: 0.8106 (m-30) cc_final: 0.7808 (t0) REVERT: A 30 GLU cc_start: 0.7800 (mm-30) cc_final: 0.7512 (mm-30) REVERT: A 55 ASN cc_start: 0.8223 (t0) cc_final: 0.7940 (t0) REVERT: A 82 LYS cc_start: 0.8619 (ttmt) cc_final: 0.8340 (ttmt) REVERT: A 130 GLU cc_start: 0.8318 (mp0) cc_final: 0.7966 (mp0) REVERT: A 217 ASP cc_start: 0.8105 (t0) cc_final: 0.7889 (t0) REVERT: A 262 ILE cc_start: 0.8352 (mt) cc_final: 0.8085 (mm) REVERT: A 344 ASP cc_start: 0.7826 (OUTLIER) cc_final: 0.7326 (m-30) REVERT: B 11 LYS cc_start: 0.8662 (pttt) cc_final: 0.8395 (pttp) REVERT: B 100 ASP cc_start: 0.7959 (m-30) cc_final: 0.7744 (m-30) REVERT: B 133 SER cc_start: 0.9086 (t) cc_final: 0.8570 (p) REVERT: B 174 LYS cc_start: 0.8385 (tttt) cc_final: 0.7680 (tppp) REVERT: B 178 ASP cc_start: 0.8138 (m-30) cc_final: 0.7491 (m-30) REVERT: B 200 LYS cc_start: 0.8479 (mttt) cc_final: 0.8228 (mttm) REVERT: B 221 ILE cc_start: 0.8169 (mp) cc_final: 0.7744 (mm) REVERT: B 234 MET cc_start: 0.8645 (mtp) cc_final: 0.8350 (mtm) REVERT: B 300 THR cc_start: 0.8649 (m) cc_final: 0.8207 (p) REVERT: B 369 SER cc_start: 0.8468 (m) cc_final: 0.8104 (p) outliers start: 27 outliers final: 19 residues processed: 185 average time/residue: 0.1600 time to fit residues: 38.1305 Evaluate side-chains 190 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 170 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 341 THR Chi-restraints excluded: chain A residue 344 ASP Chi-restraints excluded: chain A residue 361 ILE Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain B residue 114 MET Chi-restraints excluded: chain B residue 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 236 PHE Chi-restraints excluded: chain B residue 251 GLU 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 401 ASP Chi-restraints excluded: chain B residue 416 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 19 optimal weight: 6.9990 chunk 12 optimal weight: 0.9990 chunk 52 optimal weight: 5.9990 chunk 5 optimal weight: 2.9990 chunk 66 optimal weight: 0.9980 chunk 38 optimal weight: 9.9990 chunk 61 optimal weight: 2.9990 chunk 7 optimal weight: 5.9990 chunk 46 optimal weight: 0.8980 chunk 33 optimal weight: 10.0000 chunk 54 optimal weight: 0.9980 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 366 GLN B 366 GLN 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 = 0.118849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.098818 restraints weight = 17512.726| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 1.70 r_work: 0.3195 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3060 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.2022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11310 Z= 0.135 Angle : 0.485 4.950 16174 Z= 0.264 Chirality : 0.036 0.188 1894 Planarity : 0.003 0.037 1352 Dihedral : 21.394 91.181 3747 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 4.13 % Allowed : 19.66 % Favored : 76.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.40 (0.30), residues: 797 helix: 2.95 (0.25), residues: 365 sheet: -0.48 (0.39), residues: 156 loop : -1.05 (0.37), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 255 TYR 0.016 0.001 TYR A 351 PHE 0.029 0.001 PHE B 389 TRP 0.007 0.001 TRP B 43 HIS 0.002 0.001 HIS A 303 Details of bonding type rmsd covalent geometry : bond 0.00288 (11302) covalent geometry : angle 0.47990 (16162) hydrogen bonds : bond 0.04313 ( 540) hydrogen bonds : angle 3.54241 ( 1366) metal coordination : bond 0.00547 ( 8) metal coordination : angle 2.56061 ( 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 198 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 169 time to evaluate : 0.326 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 16 ASP cc_start: 0.8114 (m-30) cc_final: 0.7834 (t0) REVERT: A 30 GLU cc_start: 0.7777 (mm-30) cc_final: 0.7492 (mm-30) REVERT: A 55 ASN cc_start: 0.8227 (t0) cc_final: 0.7919 (t0) REVERT: A 82 LYS cc_start: 0.8601 (ttmt) cc_final: 0.8324 (ttmt) REVERT: A 130 GLU cc_start: 0.8280 (mp0) cc_final: 0.7938 (mp0) REVERT: A 258 GLU cc_start: 0.7536 (mt-10) cc_final: 0.7116 (mt-10) REVERT: A 262 ILE cc_start: 0.8398 (mt) cc_final: 0.8136 (mm) REVERT: A 344 ASP cc_start: 0.7797 (OUTLIER) cc_final: 0.7291 (m-30) REVERT: B 11 LYS cc_start: 0.8652 (pttt) cc_final: 0.8267 (pttp) REVERT: B 100 ASP cc_start: 0.8029 (m-30) cc_final: 0.7817 (m-30) REVERT: B 133 SER cc_start: 0.9072 (t) cc_final: 0.8541 (p) REVERT: B 166 ILE cc_start: 0.8919 (OUTLIER) cc_final: 0.8626 (mt) REVERT: B 174 LYS cc_start: 0.8361 (tttt) cc_final: 0.7692 (tppp) REVERT: B 178 ASP cc_start: 0.8124 (m-30) cc_final: 0.7557 (m-30) REVERT: B 200 LYS cc_start: 0.8468 (mttt) cc_final: 0.8214 (mttp) REVERT: B 255 ARG cc_start: 0.8024 (mtm-85) cc_final: 0.7652 (mtm-85) REVERT: B 300 THR cc_start: 0.8572 (m) cc_final: 0.8135 (p) REVERT: B 369 SER cc_start: 0.8376 (m) cc_final: 0.8056 (p) outliers start: 29 outliers final: 19 residues processed: 185 average time/residue: 0.1516 time to fit residues: 36.3050 Evaluate side-chains 190 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 169 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 MET Chi-restraints excluded: chain A residue 138 ASN Chi-restraints excluded: chain A residue 252 ASN Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 344 ASP Chi-restraints excluded: chain A residue 361 ILE Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain B residue 39 THR Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain B residue 166 ILE Chi-restraints excluded: chain B residue 217 ASP Chi-restraints excluded: chain B residue 233 TYR Chi-restraints excluded: chain B residue 236 PHE 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 363 ILE Chi-restraints excluded: chain B residue 373 SER 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: 0.0980 chunk 89 optimal weight: 10.0000 chunk 19 optimal weight: 9.9990 chunk 69 optimal weight: 5.9990 chunk 58 optimal weight: 6.9990 chunk 36 optimal weight: 7.9990 chunk 26 optimal weight: 7.9990 chunk 71 optimal weight: 4.9990 chunk 95 optimal weight: 20.0000 chunk 97 optimal weight: 5.9990 overall best weight: 4.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 366 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.113892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.094009 restraints weight = 17345.712| |-----------------------------------------------------------------------------| r_work (start): 0.3227 rms_B_bonded: 1.77 r_work: 0.3102 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2963 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.2121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.047 11310 Z= 0.309 Angle : 0.611 5.850 16174 Z= 0.325 Chirality : 0.043 0.183 1894 Planarity : 0.005 0.086 1352 Dihedral : 21.506 93.639 3747 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 4.70 % Allowed : 19.80 % Favored : 75.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.94 (0.29), residues: 797 helix: 2.55 (0.25), residues: 365 sheet: -0.66 (0.40), residues: 145 loop : -1.27 (0.35), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 298 TYR 0.023 0.002 TYR A 233 PHE 0.034 0.002 PHE B 389 TRP 0.013 0.002 TRP B 43 HIS 0.004 0.001 HIS A 56 Details of bonding type rmsd covalent geometry : bond 0.00674 (11302) covalent geometry : angle 0.60359 (16162) hydrogen bonds : bond 0.05772 ( 540) hydrogen bonds : angle 3.82194 ( 1366) metal coordination : bond 0.01053 ( 8) metal coordination : angle 3.64554 ( 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 205 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 172 time to evaluate : 0.319 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 16 ASP cc_start: 0.8235 (m-30) cc_final: 0.7946 (t0) REVERT: A 30 GLU cc_start: 0.7870 (mm-30) cc_final: 0.7539 (mm-30) REVERT: A 55 ASN cc_start: 0.8333 (t0) cc_final: 0.8027 (t0) REVERT: A 61 LYS cc_start: 0.8976 (mmmt) cc_final: 0.8532 (mmmm) REVERT: A 82 LYS cc_start: 0.8655 (ttmt) cc_final: 0.8376 (ttmt) REVERT: A 130 GLU cc_start: 0.8398 (mp0) cc_final: 0.8045 (mp0) REVERT: A 234 MET cc_start: 0.9035 (mtm) cc_final: 0.8657 (mtm) REVERT: A 258 GLU cc_start: 0.7587 (mt-10) cc_final: 0.7126 (mt-10) REVERT: A 262 ILE cc_start: 0.8365 (mt) cc_final: 0.8082 (mm) REVERT: A 311 ASP cc_start: 0.8250 (m-30) cc_final: 0.7960 (m-30) REVERT: A 344 ASP cc_start: 0.7832 (OUTLIER) cc_final: 0.7334 (m-30) REVERT: B 11 LYS cc_start: 0.8782 (pttt) cc_final: 0.8400 (pttp) REVERT: B 100 ASP cc_start: 0.7912 (m-30) cc_final: 0.7696 (m-30) REVERT: B 166 ILE cc_start: 0.8970 (OUTLIER) cc_final: 0.8706 (mt) REVERT: B 174 LYS cc_start: 0.8530 (tttt) cc_final: 0.7793 (tppp) REVERT: B 178 ASP cc_start: 0.8121 (m-30) cc_final: 0.7584 (m-30) REVERT: B 200 LYS cc_start: 0.8554 (mttt) cc_final: 0.8283 (mttp) REVERT: B 221 ILE cc_start: 0.8245 (mp) cc_final: 0.7776 (mt) REVERT: B 251 GLU cc_start: 0.7768 (OUTLIER) cc_final: 0.7529 (tt0) REVERT: B 255 ARG cc_start: 0.8135 (mtm-85) cc_final: 0.7730 (mtm-85) REVERT: B 300 THR cc_start: 0.8686 (m) cc_final: 0.8232 (p) REVERT: B 316 GLU cc_start: 0.7965 (mm-30) cc_final: 0.7721 (mm-30) REVERT: B 369 SER cc_start: 0.8419 (m) cc_final: 0.8121 (p) outliers start: 33 outliers final: 25 residues processed: 191 average time/residue: 0.1574 time to fit residues: 38.7444 Evaluate side-chains 198 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 170 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 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 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 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 233 TYR Chi-restraints excluded: chain B residue 251 GLU 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 363 ILE Chi-restraints excluded: chain B residue 373 SER 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: 7.9990 chunk 6 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 chunk 24 optimal weight: 0.0270 chunk 30 optimal weight: 4.9990 chunk 72 optimal weight: 6.9990 chunk 31 optimal weight: 0.7980 chunk 96 optimal weight: 7.9990 chunk 86 optimal weight: 7.9990 chunk 62 optimal weight: 0.0980 overall best weight: 0.7840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.119499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.099557 restraints weight = 17460.353| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 1.76 r_work: 0.3198 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3061 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.2272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 11310 Z= 0.113 Angle : 0.482 6.452 16174 Z= 0.264 Chirality : 0.035 0.182 1894 Planarity : 0.003 0.059 1352 Dihedral : 21.382 92.361 3747 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 2.71 % Allowed : 23.22 % Favored : 74.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.40 (0.30), residues: 797 helix: 2.91 (0.25), residues: 366 sheet: -0.26 (0.40), residues: 148 loop : -1.15 (0.36), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 254 TYR 0.015 0.001 TYR A 351 PHE 0.025 0.001 PHE B 389 TRP 0.008 0.001 TRP B 17 HIS 0.001 0.000 HIS B 238 Details of bonding type rmsd covalent geometry : bond 0.00237 (11302) covalent geometry : angle 0.47926 (16162) hydrogen bonds : bond 0.04176 ( 540) hydrogen bonds : angle 3.51163 ( 1366) metal coordination : bond 0.00323 ( 8) metal coordination : angle 1.93678 ( 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 187 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 168 time to evaluate : 0.323 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 GLU cc_start: 0.7803 (mm-30) cc_final: 0.7493 (mm-30) REVERT: A 55 ASN cc_start: 0.8207 (t0) cc_final: 0.7860 (t0) REVERT: A 82 LYS cc_start: 0.8626 (ttmt) cc_final: 0.8319 (ttmt) REVERT: A 130 GLU cc_start: 0.8289 (mp0) cc_final: 0.7936 (mp0) REVERT: A 258 GLU cc_start: 0.7485 (mt-10) cc_final: 0.7042 (mt-10) REVERT: A 262 ILE cc_start: 0.8360 (mt) cc_final: 0.8095 (mm) REVERT: A 344 ASP cc_start: 0.7725 (t0) cc_final: 0.7217 (m-30) REVERT: B 11 LYS cc_start: 0.8559 (pttt) cc_final: 0.8350 (pttp) REVERT: B 29 GLN cc_start: 0.8430 (tt0) cc_final: 0.8190 (tm-30) REVERT: B 100 ASP cc_start: 0.7969 (m-30) cc_final: 0.7742 (m-30) REVERT: B 133 SER cc_start: 0.9088 (t) cc_final: 0.8530 (p) REVERT: B 174 LYS cc_start: 0.8409 (tttt) cc_final: 0.7784 (tppp) REVERT: B 178 ASP cc_start: 0.8120 (m-30) cc_final: 0.7571 (m-30) REVERT: B 200 LYS cc_start: 0.8475 (mttt) cc_final: 0.8203 (mttm) REVERT: B 255 ARG cc_start: 0.8031 (mtm-85) cc_final: 0.7607 (mtm-85) REVERT: B 300 THR cc_start: 0.8556 (m) cc_final: 0.8156 (p) REVERT: B 369 SER cc_start: 0.8356 (m) cc_final: 0.8112 (p) REVERT: B 377 ASN cc_start: 0.8286 (t0) cc_final: 0.7902 (p0) outliers start: 19 outliers final: 17 residues processed: 182 average time/residue: 0.1559 time to fit residues: 36.5805 Evaluate side-chains 183 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 166 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 MET Chi-restraints excluded: chain A residue 138 ASN Chi-restraints excluded: chain A residue 252 ASN Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 361 ILE Chi-restraints excluded: chain B residue 39 THR Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain B residue 166 ILE Chi-restraints excluded: chain B residue 217 ASP Chi-restraints excluded: chain B residue 251 GLU Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 318 CYS 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: 3.9990 chunk 12 optimal weight: 0.9980 chunk 33 optimal weight: 0.9980 chunk 84 optimal weight: 8.9990 chunk 59 optimal weight: 4.9990 chunk 43 optimal weight: 0.0060 chunk 35 optimal weight: 7.9990 chunk 61 optimal weight: 2.9990 chunk 0 optimal weight: 8.9990 chunk 32 optimal weight: 2.9990 chunk 64 optimal weight: 3.9990 overall best weight: 1.6000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 366 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.118232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.098285 restraints weight = 17308.558| |-----------------------------------------------------------------------------| r_work (start): 0.3299 rms_B_bonded: 1.74 r_work: 0.3177 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3040 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.2303 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= 0.147 Angle : 0.496 6.765 16174 Z= 0.270 Chirality : 0.036 0.170 1894 Planarity : 0.004 0.053 1352 Dihedral : 21.363 93.580 3745 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.99 % Allowed : 21.37 % Favored : 75.64 % 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 aren not related in a simple way. whole: 1.44 (0.30), residues: 797 helix: 2.93 (0.25), residues: 366 sheet: -0.13 (0.41), residues: 148 loop : -1.18 (0.35), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 298 TYR 0.016 0.001 TYR A 351 PHE 0.008 0.001 PHE A 209 TRP 0.008 0.001 TRP A 43 HIS 0.002 0.001 HIS A 56 Details of bonding type rmsd covalent geometry : bond 0.00317 (11302) covalent geometry : angle 0.49323 (16162) hydrogen bonds : bond 0.04370 ( 540) hydrogen bonds : angle 3.52393 ( 1366) metal coordination : bond 0.00479 ( 8) metal coordination : angle 2.08259 ( 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 189 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 168 time to evaluate : 0.334 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 GLU cc_start: 0.7787 (mm-30) cc_final: 0.7489 (mm-30) REVERT: A 55 ASN cc_start: 0.8236 (t0) cc_final: 0.7889 (t0) REVERT: A 82 LYS cc_start: 0.8619 (ttmt) cc_final: 0.8304 (ttmt) REVERT: A 130 GLU cc_start: 0.8278 (mp0) cc_final: 0.7918 (mp0) REVERT: A 258 GLU cc_start: 0.7489 (mt-10) cc_final: 0.7087 (mt-10) REVERT: A 262 ILE cc_start: 0.8380 (mt) cc_final: 0.8109 (mm) REVERT: A 344 ASP cc_start: 0.7764 (t0) cc_final: 0.7493 (t0) REVERT: B 11 LYS cc_start: 0.8610 (pttt) cc_final: 0.8388 (pttp) REVERT: B 29 GLN cc_start: 0.8454 (tt0) cc_final: 0.8178 (tm-30) REVERT: B 133 SER cc_start: 0.9095 (t) cc_final: 0.8552 (p) REVERT: B 174 LYS cc_start: 0.8407 (tttt) cc_final: 0.7836 (tppp) REVERT: B 178 ASP cc_start: 0.8123 (m-30) cc_final: 0.7582 (m-30) REVERT: B 200 LYS cc_start: 0.8493 (mttt) cc_final: 0.8219 (mttm) REVERT: B 255 ARG cc_start: 0.8051 (mtm-85) cc_final: 0.7648 (mtm-85) REVERT: B 300 THR cc_start: 0.8556 (m) cc_final: 0.8131 (p) REVERT: B 369 SER cc_start: 0.8447 (m) cc_final: 0.8109 (p) outliers start: 21 outliers final: 19 residues processed: 181 average time/residue: 0.1675 time to fit residues: 39.2620 Evaluate side-chains 185 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 166 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 MET Chi-restraints excluded: chain A residue 133 SER 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 324 GLU Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 361 ILE Chi-restraints excluded: chain B residue 39 THR Chi-restraints excluded: chain B residue 94 THR 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 257 VAL Chi-restraints excluded: chain B residue 318 CYS Chi-restraints excluded: chain B residue 363 ILE Chi-restraints excluded: chain B residue 373 SER Chi-restraints excluded: chain B residue 401 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 54 optimal weight: 7.9990 chunk 31 optimal weight: 4.9990 chunk 86 optimal weight: 10.0000 chunk 22 optimal weight: 7.9990 chunk 38 optimal weight: 9.9990 chunk 46 optimal weight: 3.9990 chunk 91 optimal weight: 10.0000 chunk 3 optimal weight: 6.9990 chunk 10 optimal weight: 4.9990 chunk 89 optimal weight: 8.9990 chunk 27 optimal weight: 7.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.112408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.092514 restraints weight = 17477.805| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 1.81 r_work: 0.3077 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2938 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.2434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.077 11310 Z= 0.410 Angle : 0.712 7.316 16174 Z= 0.373 Chirality : 0.047 0.192 1894 Planarity : 0.005 0.079 1352 Dihedral : 21.605 94.735 3743 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 3.85 % Allowed : 20.80 % 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 aren not related in a simple way. whole: 0.66 (0.29), residues: 797 helix: 2.17 (0.25), residues: 365 sheet: -0.39 (0.42), residues: 143 loop : -1.43 (0.34), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 101 TYR 0.021 0.003 TYR A 351 PHE 0.021 0.003 PHE B 389 TRP 0.016 0.003 TRP B 43 HIS 0.004 0.001 HIS A 56 Details of bonding type rmsd covalent geometry : bond 0.00894 (11302) covalent geometry : angle 0.70389 (16162) hydrogen bonds : bond 0.06628 ( 540) hydrogen bonds : angle 3.97502 ( 1366) metal coordination : bond 0.01430 ( 8) metal coordination : angle 4.07958 ( 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 197 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 170 time to evaluate : 0.319 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 GLU cc_start: 0.7912 (mm-30) cc_final: 0.7607 (mm-30) REVERT: A 61 LYS cc_start: 0.8981 (mmmt) cc_final: 0.8534 (mmmm) REVERT: A 82 LYS cc_start: 0.8618 (ttmt) cc_final: 0.8361 (ttmm) REVERT: A 130 GLU cc_start: 0.8410 (mp0) cc_final: 0.8048 (mp0) REVERT: A 258 GLU cc_start: 0.7527 (mt-10) cc_final: 0.7135 (mt-10) REVERT: A 262 ILE cc_start: 0.8350 (mt) cc_final: 0.8056 (mm) REVERT: A 293 LYS cc_start: 0.8629 (mttp) cc_final: 0.8421 (mttm) REVERT: A 311 ASP cc_start: 0.8284 (m-30) cc_final: 0.8033 (m-30) REVERT: A 344 ASP cc_start: 0.7846 (OUTLIER) cc_final: 0.7327 (m-30) REVERT: B 11 LYS cc_start: 0.8884 (pttt) cc_final: 0.8600 (ptmm) REVERT: B 29 GLN cc_start: 0.8442 (tt0) cc_final: 0.8239 (tm-30) REVERT: B 100 ASP cc_start: 0.7929 (m-30) cc_final: 0.7703 (m-30) REVERT: B 174 LYS cc_start: 0.8606 (tttt) cc_final: 0.7845 (tppp) REVERT: B 178 ASP cc_start: 0.8124 (m-30) cc_final: 0.7590 (m-30) REVERT: B 200 LYS cc_start: 0.8563 (mttt) cc_final: 0.8305 (mttp) REVERT: B 221 ILE cc_start: 0.8246 (mp) cc_final: 0.7801 (mt) REVERT: B 251 GLU cc_start: 0.7836 (tt0) cc_final: 0.7605 (tt0) REVERT: B 255 ARG cc_start: 0.8170 (mtm-85) cc_final: 0.7770 (mtm-85) REVERT: B 300 THR cc_start: 0.8705 (m) cc_final: 0.8256 (p) outliers start: 27 outliers final: 24 residues processed: 185 average time/residue: 0.1650 time to fit residues: 39.2612 Evaluate side-chains 192 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 167 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 MET Chi-restraints excluded: chain A residue 138 ASN Chi-restraints excluded: chain A residue 252 ASN Chi-restraints excluded: chain A residue 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 361 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 128 ILE Chi-restraints excluded: chain B residue 137 MET 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 257 VAL Chi-restraints excluded: chain B residue 318 CYS Chi-restraints excluded: chain B residue 350 ILE Chi-restraints excluded: chain B residue 363 ILE Chi-restraints excluded: chain B residue 373 SER 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: 0.9980 chunk 31 optimal weight: 0.5980 chunk 87 optimal weight: 8.9990 chunk 57 optimal weight: 3.9990 chunk 50 optimal weight: 0.7980 chunk 55 optimal weight: 0.9980 chunk 27 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 chunk 95 optimal weight: 20.0000 chunk 72 optimal weight: 0.9990 chunk 56 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 26 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.118970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.099099 restraints weight = 17397.802| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 1.76 r_work: 0.3187 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3050 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.2432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11310 Z= 0.123 Angle : 0.517 9.467 16174 Z= 0.282 Chirality : 0.036 0.190 1894 Planarity : 0.004 0.064 1352 Dihedral : 21.383 91.969 3743 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 2.56 % Allowed : 22.36 % Favored : 75.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.25 (0.30), residues: 797 helix: 2.73 (0.25), residues: 366 sheet: -0.13 (0.41), residues: 148 loop : -1.25 (0.35), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 25 TYR 0.016 0.001 TYR A 351 PHE 0.022 0.001 PHE B 389 TRP 0.008 0.001 TRP A 17 HIS 0.002 0.001 HIS B 303 Details of bonding type rmsd covalent geometry : bond 0.00262 (11302) covalent geometry : angle 0.51473 (16162) hydrogen bonds : bond 0.04428 ( 540) hydrogen bonds : angle 3.59129 ( 1366) metal coordination : bond 0.00306 ( 8) metal coordination : angle 1.84494 ( 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 185 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 167 time to evaluate : 0.329 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 GLU cc_start: 0.7802 (mm-30) cc_final: 0.7495 (mm-30) REVERT: A 82 LYS cc_start: 0.8641 (ttmt) cc_final: 0.8341 (ttmt) REVERT: A 130 GLU cc_start: 0.8305 (mp0) cc_final: 0.7975 (mp0) REVERT: A 258 GLU cc_start: 0.7472 (mt-10) cc_final: 0.7030 (mt-10) REVERT: A 262 ILE cc_start: 0.8375 (mt) cc_final: 0.8112 (mm) REVERT: A 311 ASP cc_start: 0.8204 (m-30) cc_final: 0.7923 (m-30) REVERT: A 344 ASP cc_start: 0.7588 (t0) cc_final: 0.7268 (t0) REVERT: B 11 LYS cc_start: 0.8548 (pttt) cc_final: 0.8339 (pttp) REVERT: B 100 ASP cc_start: 0.8014 (m-30) cc_final: 0.7706 (m-30) REVERT: B 133 SER cc_start: 0.9096 (t) cc_final: 0.8510 (p) REVERT: B 174 LYS cc_start: 0.8393 (tttt) cc_final: 0.7709 (tppp) REVERT: B 178 ASP cc_start: 0.8100 (m-30) cc_final: 0.7552 (m-30) REVERT: B 200 LYS cc_start: 0.8461 (mttt) cc_final: 0.8189 (mttm) REVERT: B 221 ILE cc_start: 0.8179 (mp) cc_final: 0.7780 (mm) REVERT: B 222 MET cc_start: 0.8122 (ttp) cc_final: 0.7879 (ttm) REVERT: B 255 ARG cc_start: 0.8054 (mtm-85) cc_final: 0.7630 (mtm-85) REVERT: B 300 THR cc_start: 0.8554 (m) cc_final: 0.8167 (p) REVERT: B 369 SER cc_start: 0.8467 (m) cc_final: 0.8190 (p) REVERT: B 377 ASN cc_start: 0.8295 (t0) cc_final: 0.7960 (p0) outliers start: 18 outliers final: 17 residues processed: 180 average time/residue: 0.1614 time to fit residues: 37.5151 Evaluate side-chains 182 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 165 time to evaluate : 0.407 ------------------------------------------------------------------------------- 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 252 ASN Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 361 ILE Chi-restraints excluded: chain B residue 39 THR Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain B residue 166 ILE Chi-restraints excluded: chain B residue 187 VAL 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 363 ILE Chi-restraints excluded: chain B residue 401 ASP 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: 7.9990 chunk 70 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 57 optimal weight: 8.9990 chunk 11 optimal weight: 5.9990 chunk 53 optimal weight: 5.9990 chunk 79 optimal weight: 3.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 403 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.115019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.095098 restraints weight = 17472.248| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 1.77 r_work: 0.3117 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2977 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.2430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.038 11310 Z= 0.256 Angle : 0.601 8.817 16174 Z= 0.319 Chirality : 0.041 0.185 1894 Planarity : 0.005 0.070 1352 Dihedral : 21.447 93.326 3743 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 2.71 % Allowed : 22.79 % Favored : 74.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.07 (0.29), residues: 797 helix: 2.55 (0.25), residues: 365 sheet: -0.15 (0.43), residues: 138 loop : -1.29 (0.34), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 101 TYR 0.017 0.002 TYR A 351 PHE 0.014 0.002 PHE A 209 TRP 0.012 0.002 TRP B 43 HIS 0.004 0.001 HIS A 303 Details of bonding type rmsd covalent geometry : bond 0.00555 (11302) covalent geometry : angle 0.59402 (16162) hydrogen bonds : bond 0.05405 ( 540) hydrogen bonds : angle 3.74294 ( 1366) metal coordination : bond 0.00889 ( 8) metal coordination : angle 3.34954 ( 12) =============================================================================== Job complete usr+sys time: 3437.98 seconds wall clock time: 59 minutes 30.24 seconds (3570.24 seconds total)