Starting phenix.real_space_refine on Tue Jul 29 02:14:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8j12_35912/07_2025/8j12_35912.cif Found real_map, /net/cci-nas-00/data/ceres_data/8j12_35912/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8j12_35912/07_2025/8j12_35912.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8j12_35912/07_2025/8j12_35912.map" model { file = "/net/cci-nas-00/data/ceres_data/8j12_35912/07_2025/8j12_35912.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8j12_35912/07_2025/8j12_35912.cif" } resolution = 3.08 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 6.43, per 1000 atoms: 0.60 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: 2.42 Conformation dependent library (CDL) restraints added in 845.6 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 502 " pdb="ZN ZN A 502 " - pdb=" SG CYS A 375 " pdb="ZN ZN A 502 " - pdb=" SG CYS A 394 " pdb="ZN ZN A 502 " - pdb=" SG CYS A 391 " pdb="ZN ZN A 502 " - pdb=" SG CYS A 372 " pdb=" ZN B 502 " pdb="ZN ZN B 502 " - pdb=" SG CYS B 394 " pdb="ZN ZN B 502 " - pdb=" SG CYS B 375 " pdb="ZN ZN B 502 " - pdb=" SG CYS B 372 " pdb="ZN ZN B 502 " - pdb=" SG CYS B 391 " Number of angles added : 12 1594 Ramachandran restraints generated. 797 Oldfield, 0 Emsley, 797 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1516 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 9 sheets defined 49.1% alpha, 18.2% beta 76 base pairs and 119 stacking pairs defined. Time for finding SS restraints: 4.46 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: 4.89 Time building geometry restraints manager: 2.90 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: 0.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.420 Check model and map are aligned: 0.080 Set scattering table: 0.090 Process input model: 32.290 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.050 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:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.150 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (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 TRP 0.011 0.001 TRP A 43 HIS 0.003 0.001 HIS A 238 PHE 0.008 0.001 PHE A 209 TYR 0.016 0.001 TYR A 351 ARG 0.002 0.000 ARG A 298 Details of bonding type rmsd hydrogen bonds : bond 0.14816 ( 540) hydrogen bonds : angle 5.60407 ( 1366) metal coordination : bond 0.06498 ( 8) metal coordination : angle 33.85833 ( 12) covalent geometry : bond 0.00292 (11302) covalent geometry : angle 0.44623 (16162) *********************** 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 : 0.815 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: 0.3524 time to fit residues: 111.0436 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 : 0.810 ------------------------------------------------------------------------------- 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 82 optimal weight: 5.9990 chunk 74 optimal weight: 3.9990 chunk 41 optimal weight: 7.9990 chunk 25 optimal weight: 10.0000 chunk 50 optimal weight: 4.9990 chunk 39 optimal weight: 0.6980 chunk 76 optimal weight: 10.0000 chunk 29 optimal weight: 6.9990 chunk 46 optimal weight: 5.9990 chunk 57 optimal weight: 5.9990 chunk 88 optimal weight: 10.0000 overall best weight: 4.3388 ------------------------------------------------------------------------------- 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 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 = 0.3575 r_free = 0.3575 target = 0.115617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.095719 restraints weight = 17437.900| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 1.70 r_work: 0.3142 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3005 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.1543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.048 11310 Z= 0.317 Angle : 0.763 33.911 16174 Z= 0.346 Chirality : 0.043 0.199 1894 Planarity : 0.005 0.058 1352 Dihedral : 21.588 87.449 3754 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 4.27 % Allowed : 15.53 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.30), residues: 797 helix: 2.32 (0.26), residues: 365 sheet: -0.84 (0.44), residues: 137 loop : -1.12 (0.35), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 43 HIS 0.005 0.001 HIS A 303 PHE 0.028 0.002 PHE B 389 TYR 0.019 0.002 TYR A 351 ARG 0.008 0.001 ARG B 255 Details of bonding type rmsd hydrogen bonds : bond 0.06138 ( 540) hydrogen bonds : angle 4.10693 ( 1366) metal coordination : bond 0.01918 ( 8) metal coordination : angle 16.12889 ( 12) covalent geometry : bond 0.00689 (11302) covalent geometry : angle 0.62457 (16162) *********************** 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 218 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 188 time to evaluate : 0.968 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 GLU cc_start: 0.7936 (mm-30) cc_final: 0.7708 (mm-30) REVERT: A 82 LYS cc_start: 0.8677 (ttmt) cc_final: 0.8429 (ttmt) REVERT: A 130 GLU cc_start: 0.8328 (mp0) cc_final: 0.7840 (mp0) REVERT: A 145 SER cc_start: 0.8691 (m) cc_final: 0.8479 (p) REVERT: A 244 LYS cc_start: 0.8813 (pttt) cc_final: 0.8611 (ptpp) REVERT: A 262 ILE cc_start: 0.8446 (mt) cc_final: 0.8214 (mm) REVERT: A 285 LYS cc_start: 0.8388 (tttt) cc_final: 0.8153 (tttm) REVERT: A 344 ASP cc_start: 0.7830 (OUTLIER) cc_final: 0.7428 (m-30) REVERT: B 11 LYS cc_start: 0.8591 (pttt) cc_final: 0.8378 (pttp) REVERT: B 100 ASP cc_start: 0.7937 (m-30) cc_final: 0.7694 (m-30) REVERT: B 135 ASN cc_start: 0.8440 (t0) cc_final: 0.8221 (t0) REVERT: B 174 LYS cc_start: 0.8506 (tttt) cc_final: 0.7729 (tppp) REVERT: B 178 ASP cc_start: 0.7976 (m-30) cc_final: 0.7387 (m-30) REVERT: B 200 LYS cc_start: 0.8607 (mttt) cc_final: 0.8342 (mttp) REVERT: B 221 ILE cc_start: 0.8046 (mp) cc_final: 0.7575 (mm) REVERT: B 289 GLN cc_start: 0.7932 (mm-40) cc_final: 0.7556 (mm-40) REVERT: B 316 GLU cc_start: 0.8109 (mm-30) cc_final: 0.7873 (mm-30) REVERT: B 320 THR cc_start: 0.8011 (p) cc_final: 0.7797 (p) REVERT: B 417 ILE cc_start: 0.8955 (OUTLIER) cc_final: 0.8754 (tt) outliers start: 30 outliers final: 19 residues processed: 207 average time/residue: 0.3386 time to fit residues: 89.7762 Evaluate side-chains 195 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 174 time to evaluate : 0.924 ------------------------------------------------------------------------------- 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 252 ASN Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 344 ASP Chi-restraints excluded: chain A residue 361 ILE Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain B residue 114 MET Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 217 ASP Chi-restraints excluded: chain B residue 224 ILE Chi-restraints excluded: chain B residue 233 TYR Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 318 CYS Chi-restraints excluded: chain B residue 350 ILE Chi-restraints excluded: chain B residue 401 ASP Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain B residue 417 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 61 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 chunk 21 optimal weight: 9.9990 chunk 70 optimal weight: 0.9980 chunk 78 optimal weight: 10.0000 chunk 67 optimal weight: 8.9990 chunk 5 optimal weight: 6.9990 chunk 80 optimal weight: 5.9990 chunk 29 optimal weight: 0.9980 chunk 24 optimal weight: 3.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 366 GLN B 26 GLN B 407 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.118870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.098816 restraints weight = 17770.770| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 1.69 r_work: 0.3195 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3060 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.1695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 11310 Z= 0.147 Angle : 0.516 9.280 16174 Z= 0.277 Chirality : 0.037 0.198 1894 Planarity : 0.003 0.041 1352 Dihedral : 21.444 88.114 3749 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 3.56 % Allowed : 19.09 % Favored : 77.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.30), residues: 797 helix: 2.70 (0.25), residues: 365 sheet: -0.78 (0.40), residues: 156 loop : -1.19 (0.37), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 43 HIS 0.003 0.001 HIS A 238 PHE 0.027 0.002 PHE B 389 TYR 0.018 0.001 TYR B 202 ARG 0.008 0.000 ARG B 255 Details of bonding type rmsd hydrogen bonds : bond 0.04640 ( 540) hydrogen bonds : angle 3.73539 ( 1366) metal coordination : bond 0.00869 ( 8) metal coordination : angle 4.22129 ( 12) covalent geometry : bond 0.00315 (11302) covalent geometry : angle 0.50309 (16162) *********************** 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 201 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 176 time to evaluate : 0.825 Fit side-chains revert: symmetry clash REVERT: A 30 GLU cc_start: 0.7864 (mm-30) cc_final: 0.7652 (mm-30) REVERT: A 55 ASN cc_start: 0.8186 (t0) cc_final: 0.7966 (t0) REVERT: A 82 LYS cc_start: 0.8618 (ttmt) cc_final: 0.8408 (ttmt) REVERT: A 130 GLU cc_start: 0.8298 (mp0) cc_final: 0.8001 (mp0) REVERT: A 258 GLU cc_start: 0.7667 (mt-10) cc_final: 0.7356 (mt-10) REVERT: A 262 ILE cc_start: 0.8496 (mt) cc_final: 0.8277 (mm) REVERT: A 285 LYS cc_start: 0.8375 (tttt) cc_final: 0.8172 (tttm) REVERT: A 299 ASP cc_start: 0.8185 (t0) cc_final: 0.7926 (m-30) REVERT: A 344 ASP cc_start: 0.7838 (OUTLIER) cc_final: 0.7547 (t0) REVERT: B 11 LYS cc_start: 0.8534 (pttt) cc_final: 0.8329 (pttp) REVERT: B 100 ASP cc_start: 0.7904 (m-30) cc_final: 0.7699 (m-30) REVERT: B 133 SER cc_start: 0.9156 (t) cc_final: 0.8649 (p) REVERT: B 174 LYS cc_start: 0.8458 (tttt) cc_final: 0.7749 (tppp) REVERT: B 178 ASP cc_start: 0.7980 (m-30) cc_final: 0.7361 (m-30) REVERT: B 200 LYS cc_start: 0.8509 (mttt) cc_final: 0.8267 (mttp) REVERT: B 221 ILE cc_start: 0.8003 (mp) cc_final: 0.7627 (mm) REVERT: B 300 THR cc_start: 0.8741 (m) cc_final: 0.8335 (p) REVERT: B 417 ILE cc_start: 0.8658 (OUTLIER) cc_final: 0.8436 (tt) outliers start: 25 outliers final: 17 residues processed: 188 average time/residue: 0.3281 time to fit residues: 79.8601 Evaluate side-chains 190 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 171 time to evaluate : 0.896 ------------------------------------------------------------------------------- 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 344 ASP Chi-restraints excluded: chain A residue 361 ILE Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain B residue 210 GLU Chi-restraints excluded: chain B residue 217 ASP Chi-restraints excluded: chain B residue 224 ILE Chi-restraints excluded: chain B residue 233 TYR Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 263 SER 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 Chi-restraints excluded: chain B residue 417 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 41 optimal weight: 5.9990 chunk 47 optimal weight: 7.9990 chunk 16 optimal weight: 0.6980 chunk 2 optimal weight: 6.9990 chunk 95 optimal weight: 20.0000 chunk 18 optimal weight: 0.7980 chunk 72 optimal weight: 3.9990 chunk 29 optimal weight: 6.9990 chunk 57 optimal weight: 6.9990 chunk 67 optimal weight: 9.9990 chunk 69 optimal weight: 3.9990 overall best weight: 3.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 366 GLN B 366 GLN B 407 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.115268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.095376 restraints weight = 17231.248| |-----------------------------------------------------------------------------| r_work (start): 0.3251 rms_B_bonded: 1.75 r_work: 0.3127 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2988 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.1891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 11310 Z= 0.235 Angle : 0.563 7.626 16174 Z= 0.300 Chirality : 0.040 0.194 1894 Planarity : 0.004 0.061 1352 Dihedral : 21.483 90.511 3749 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 4.13 % Allowed : 20.37 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.30), residues: 797 helix: 2.57 (0.26), residues: 364 sheet: -0.79 (0.39), residues: 156 loop : -1.26 (0.37), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 43 HIS 0.003 0.001 HIS A 56 PHE 0.019 0.002 PHE B 389 TYR 0.018 0.002 TYR A 351 ARG 0.010 0.000 ARG B 255 Details of bonding type rmsd hydrogen bonds : bond 0.05255 ( 540) hydrogen bonds : angle 3.78055 ( 1366) metal coordination : bond 0.00972 ( 8) metal coordination : angle 4.16936 ( 12) covalent geometry : bond 0.00512 (11302) covalent geometry : angle 0.55121 (16162) *********************** 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 198 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 169 time to evaluate : 0.899 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 16 ASP cc_start: 0.8153 (m-30) cc_final: 0.7866 (t0) REVERT: A 30 GLU cc_start: 0.7864 (mm-30) cc_final: 0.7498 (mm-30) REVERT: A 55 ASN cc_start: 0.8291 (t0) cc_final: 0.8000 (t0) REVERT: A 82 LYS cc_start: 0.8673 (ttmt) cc_final: 0.8379 (ttmt) REVERT: A 130 GLU cc_start: 0.8382 (mp0) cc_final: 0.7987 (mp0) REVERT: A 262 ILE cc_start: 0.8349 (mt) cc_final: 0.8053 (mm) REVERT: A 285 LYS cc_start: 0.8361 (tttt) cc_final: 0.8124 (tttm) REVERT: A 299 ASP cc_start: 0.8064 (t0) cc_final: 0.7838 (m-30) REVERT: A 344 ASP cc_start: 0.7819 (OUTLIER) cc_final: 0.7347 (m-30) REVERT: B 11 LYS cc_start: 0.8762 (pttt) cc_final: 0.8334 (pttp) REVERT: B 166 ILE cc_start: 0.8953 (OUTLIER) cc_final: 0.8547 (mt) REVERT: B 174 LYS cc_start: 0.8474 (tttt) cc_final: 0.7726 (tppp) REVERT: B 178 ASP cc_start: 0.8117 (m-30) cc_final: 0.7470 (m-30) REVERT: B 200 LYS cc_start: 0.8521 (mttt) cc_final: 0.8264 (mttp) REVERT: B 221 ILE cc_start: 0.8186 (mp) cc_final: 0.7734 (mm) REVERT: B 251 GLU cc_start: 0.7517 (tt0) cc_final: 0.7294 (mt-10) REVERT: B 255 ARG cc_start: 0.7882 (mtm-85) cc_final: 0.7671 (mtm-85) REVERT: B 417 ILE cc_start: 0.8702 (OUTLIER) cc_final: 0.8483 (tt) outliers start: 29 outliers final: 20 residues processed: 182 average time/residue: 0.3212 time to fit residues: 75.1655 Evaluate side-chains 190 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 167 time to evaluate : 0.947 ------------------------------------------------------------------------------- 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 160 LYS Chi-restraints excluded: chain A residue 252 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 166 ILE Chi-restraints excluded: chain B residue 210 GLU Chi-restraints excluded: chain B residue 217 ASP Chi-restraints excluded: chain B residue 233 TYR Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 318 CYS Chi-restraints excluded: chain B residue 350 ILE Chi-restraints excluded: chain B residue 359 LYS Chi-restraints excluded: chain B residue 363 ILE Chi-restraints excluded: chain B residue 401 ASP Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain B residue 417 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 46 optimal weight: 4.9990 chunk 86 optimal weight: 10.0000 chunk 83 optimal weight: 7.9990 chunk 47 optimal weight: 6.9990 chunk 75 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 60 optimal weight: 5.9990 chunk 59 optimal weight: 0.9990 chunk 49 optimal weight: 5.9990 chunk 19 optimal weight: 4.9990 chunk 96 optimal weight: 7.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 366 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.115243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.095288 restraints weight = 17259.640| |-----------------------------------------------------------------------------| r_work (start): 0.3246 rms_B_bonded: 1.76 r_work: 0.3122 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2982 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.2038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 11310 Z= 0.242 Angle : 0.565 7.125 16174 Z= 0.303 Chirality : 0.040 0.194 1894 Planarity : 0.004 0.061 1352 Dihedral : 21.467 91.683 3747 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 5.70 % Allowed : 19.23 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.30), residues: 797 helix: 2.52 (0.25), residues: 365 sheet: -0.70 (0.39), residues: 155 loop : -1.29 (0.36), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 43 HIS 0.003 0.001 HIS A 56 PHE 0.034 0.002 PHE B 389 TYR 0.018 0.002 TYR A 351 ARG 0.008 0.001 ARG A 298 Details of bonding type rmsd hydrogen bonds : bond 0.05195 ( 540) hydrogen bonds : angle 3.76836 ( 1366) metal coordination : bond 0.00877 ( 8) metal coordination : angle 3.55454 ( 12) covalent geometry : bond 0.00526 (11302) covalent geometry : angle 0.55698 (16162) *********************** 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 215 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 175 time to evaluate : 0.913 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 ASP cc_start: 0.8213 (m-30) cc_final: 0.7939 (t0) REVERT: A 30 GLU cc_start: 0.7871 (mm-30) cc_final: 0.7559 (mm-30) REVERT: A 55 ASN cc_start: 0.8314 (t0) cc_final: 0.8003 (t0) REVERT: A 82 LYS cc_start: 0.8744 (ttmt) cc_final: 0.8401 (ttmm) REVERT: A 130 GLU cc_start: 0.8373 (mp0) cc_final: 0.8010 (mp0) REVERT: A 258 GLU cc_start: 0.7661 (mt-10) cc_final: 0.7251 (mt-10) REVERT: A 262 ILE cc_start: 0.8349 (mt) cc_final: 0.8056 (mm) REVERT: A 285 LYS cc_start: 0.8358 (tttt) cc_final: 0.8101 (tttm) REVERT: A 311 ASP cc_start: 0.8240 (m-30) cc_final: 0.7945 (m-30) REVERT: A 344 ASP cc_start: 0.7821 (OUTLIER) cc_final: 0.7358 (m-30) REVERT: B 11 LYS cc_start: 0.8749 (pttt) cc_final: 0.8368 (pttp) REVERT: B 133 SER cc_start: 0.9084 (t) cc_final: 0.8542 (p) REVERT: B 166 ILE cc_start: 0.8935 (OUTLIER) cc_final: 0.8642 (mt) REVERT: B 174 LYS cc_start: 0.8490 (tttt) cc_final: 0.7762 (tppp) REVERT: B 178 ASP cc_start: 0.8119 (m-30) cc_final: 0.7573 (m-30) REVERT: B 200 LYS cc_start: 0.8514 (mttt) cc_final: 0.8248 (mttp) REVERT: B 221 ILE cc_start: 0.8212 (mp) cc_final: 0.7750 (mm) REVERT: B 300 THR cc_start: 0.8666 (m) cc_final: 0.8218 (p) REVERT: B 417 ILE cc_start: 0.8715 (OUTLIER) cc_final: 0.8497 (tt) outliers start: 40 outliers final: 29 residues processed: 198 average time/residue: 0.3298 time to fit residues: 84.0279 Evaluate side-chains 202 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 170 time to evaluate : 0.946 ------------------------------------------------------------------------------- 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 133 SER Chi-restraints excluded: chain A residue 160 LYS Chi-restraints excluded: chain A residue 252 ASN Chi-restraints excluded: chain A residue 254 ARG Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 344 ASP Chi-restraints excluded: chain A residue 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 114 MET Chi-restraints excluded: chain B residue 128 ILE 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 359 LYS Chi-restraints excluded: chain B residue 363 ILE Chi-restraints excluded: chain B residue 401 ASP Chi-restraints excluded: chain B residue 413 ILE Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain B residue 417 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 97 optimal weight: 7.9990 chunk 87 optimal weight: 10.0000 chunk 37 optimal weight: 3.9990 chunk 88 optimal weight: 7.9990 chunk 34 optimal weight: 0.8980 chunk 4 optimal weight: 3.9990 chunk 92 optimal weight: 8.9990 chunk 16 optimal weight: 8.9990 chunk 80 optimal weight: 5.9990 chunk 46 optimal weight: 2.9990 chunk 66 optimal weight: 0.7980 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3564 r_free = 0.3564 target = 0.116025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.096084 restraints weight = 17411.090| |-----------------------------------------------------------------------------| r_work (start): 0.3263 rms_B_bonded: 1.76 r_work: 0.3140 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3001 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.2117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 11310 Z= 0.202 Angle : 0.544 6.162 16174 Z= 0.293 Chirality : 0.039 0.194 1894 Planarity : 0.004 0.053 1352 Dihedral : 21.458 91.999 3747 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 4.70 % Allowed : 20.23 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.30), residues: 797 helix: 2.61 (0.26), residues: 365 sheet: -0.68 (0.38), residues: 156 loop : -1.19 (0.37), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 43 HIS 0.002 0.001 HIS A 56 PHE 0.025 0.002 PHE B 389 TYR 0.017 0.002 TYR A 351 ARG 0.005 0.000 ARG B 255 Details of bonding type rmsd hydrogen bonds : bond 0.04922 ( 540) hydrogen bonds : angle 3.72181 ( 1366) metal coordination : bond 0.00697 ( 8) metal coordination : angle 3.13702 ( 12) covalent geometry : bond 0.00439 (11302) covalent geometry : angle 0.53778 (16162) *********************** 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 204 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 171 time to evaluate : 0.812 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 ASP cc_start: 0.8195 (m-30) cc_final: 0.7936 (t0) REVERT: A 30 GLU cc_start: 0.7843 (mm-30) cc_final: 0.7507 (mm-30) REVERT: A 55 ASN cc_start: 0.8263 (t0) cc_final: 0.7954 (t0) REVERT: A 82 LYS cc_start: 0.8720 (ttmt) cc_final: 0.8456 (ttmt) REVERT: A 130 GLU cc_start: 0.8366 (mp0) cc_final: 0.7996 (mp0) REVERT: A 258 GLU cc_start: 0.7649 (mt-10) cc_final: 0.7206 (mt-10) REVERT: A 262 ILE cc_start: 0.8352 (mt) cc_final: 0.8057 (mm) REVERT: A 285 LYS cc_start: 0.8345 (tttt) cc_final: 0.8077 (tttm) REVERT: A 311 ASP cc_start: 0.8243 (m-30) cc_final: 0.7959 (m-30) REVERT: A 344 ASP cc_start: 0.7812 (OUTLIER) cc_final: 0.7335 (m-30) REVERT: B 11 LYS cc_start: 0.8691 (pttt) cc_final: 0.8359 (pttp) REVERT: B 133 SER cc_start: 0.9040 (t) cc_final: 0.8507 (p) REVERT: B 166 ILE cc_start: 0.8901 (OUTLIER) cc_final: 0.8654 (mt) REVERT: B 174 LYS cc_start: 0.8496 (tttt) cc_final: 0.7803 (tppp) REVERT: B 178 ASP cc_start: 0.8115 (m-30) cc_final: 0.7570 (m-30) REVERT: B 200 LYS cc_start: 0.8530 (mttt) cc_final: 0.8262 (mttm) REVERT: B 221 ILE cc_start: 0.8232 (mp) cc_final: 0.7781 (mt) REVERT: B 300 THR cc_start: 0.8648 (m) cc_final: 0.8206 (p) REVERT: B 369 SER cc_start: 0.8406 (m) cc_final: 0.8087 (p) REVERT: B 417 ILE cc_start: 0.8703 (OUTLIER) cc_final: 0.8489 (tt) outliers start: 33 outliers final: 25 residues processed: 189 average time/residue: 0.3171 time to fit residues: 77.3575 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 : 0.805 ------------------------------------------------------------------------------- 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 160 LYS 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 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 114 MET Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 166 ILE Chi-restraints excluded: chain B residue 210 GLU Chi-restraints excluded: chain B residue 217 ASP Chi-restraints excluded: chain B residue 224 ILE Chi-restraints excluded: chain B residue 233 TYR Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 318 CYS Chi-restraints excluded: chain B residue 350 ILE Chi-restraints excluded: chain B residue 359 LYS Chi-restraints excluded: chain B residue 363 ILE Chi-restraints excluded: chain B residue 401 ASP Chi-restraints excluded: chain B residue 413 ILE Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain B residue 417 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 33 optimal weight: 9.9990 chunk 82 optimal weight: 5.9990 chunk 17 optimal weight: 0.7980 chunk 19 optimal weight: 10.0000 chunk 91 optimal weight: 10.0000 chunk 12 optimal weight: 5.9990 chunk 85 optimal weight: 8.9990 chunk 74 optimal weight: 0.8980 chunk 25 optimal weight: 7.9990 chunk 92 optimal weight: 10.0000 chunk 55 optimal weight: 0.5980 overall best weight: 2.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.115490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.095527 restraints weight = 17600.267| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 1.76 r_work: 0.3130 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2991 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.2190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 11310 Z= 0.222 Angle : 0.562 7.939 16174 Z= 0.303 Chirality : 0.039 0.191 1894 Planarity : 0.004 0.055 1352 Dihedral : 21.456 92.649 3747 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 4.99 % Allowed : 21.23 % Favored : 73.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.29), residues: 797 helix: 2.44 (0.25), residues: 365 sheet: -0.58 (0.39), residues: 154 loop : -1.29 (0.36), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 43 HIS 0.002 0.001 HIS A 238 PHE 0.022 0.002 PHE B 389 TYR 0.020 0.002 TYR A 233 ARG 0.006 0.000 ARG A 254 Details of bonding type rmsd hydrogen bonds : bond 0.05080 ( 540) hydrogen bonds : angle 3.76037 ( 1366) metal coordination : bond 0.00742 ( 8) metal coordination : angle 3.15722 ( 12) covalent geometry : bond 0.00487 (11302) covalent geometry : angle 0.55608 (16162) *********************** 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 204 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 169 time to evaluate : 1.235 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 30 GLU cc_start: 0.7852 (mm-30) cc_final: 0.7520 (mm-30) REVERT: A 55 ASN cc_start: 0.8222 (t0) cc_final: 0.7930 (t0) REVERT: A 82 LYS cc_start: 0.8689 (ttmt) cc_final: 0.8383 (ttmm) REVERT: A 130 GLU cc_start: 0.8351 (mp0) cc_final: 0.8007 (mp0) REVERT: A 254 ARG cc_start: 0.6881 (tpm170) cc_final: 0.6276 (tpm170) REVERT: A 258 GLU cc_start: 0.7589 (mt-10) cc_final: 0.7164 (mt-10) REVERT: A 262 ILE cc_start: 0.8338 (mt) cc_final: 0.8044 (mm) REVERT: A 285 LYS cc_start: 0.8353 (tttt) cc_final: 0.8076 (tttm) REVERT: A 311 ASP cc_start: 0.8244 (m-30) cc_final: 0.7963 (m-30) REVERT: A 344 ASP cc_start: 0.7821 (OUTLIER) cc_final: 0.7335 (m-30) REVERT: B 11 LYS cc_start: 0.8758 (pttt) cc_final: 0.8387 (pttp) REVERT: B 29 GLN cc_start: 0.8469 (tt0) cc_final: 0.8210 (tm-30) REVERT: B 166 ILE cc_start: 0.8941 (OUTLIER) cc_final: 0.8634 (mt) REVERT: B 174 LYS cc_start: 0.8508 (tttt) cc_final: 0.7833 (tppp) REVERT: B 178 ASP cc_start: 0.8129 (m-30) cc_final: 0.7595 (m-30) REVERT: B 200 LYS cc_start: 0.8525 (mttt) cc_final: 0.8274 (mttp) REVERT: B 221 ILE cc_start: 0.8246 (mp) cc_final: 0.7787 (mt) REVERT: B 255 ARG cc_start: 0.8073 (mtm-85) cc_final: 0.7698 (mtm-85) REVERT: B 300 THR cc_start: 0.8644 (m) cc_final: 0.8204 (p) REVERT: B 369 SER cc_start: 0.8417 (m) cc_final: 0.8111 (p) REVERT: B 417 ILE cc_start: 0.8703 (OUTLIER) cc_final: 0.8454 (tt) outliers start: 35 outliers final: 27 residues processed: 189 average time/residue: 0.3342 time to fit residues: 82.0289 Evaluate side-chains 195 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 165 time to evaluate : 0.858 ------------------------------------------------------------------------------- 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 133 SER Chi-restraints excluded: chain A residue 160 LYS 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 326 LEU 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 B residue 10 VAL Chi-restraints excluded: chain B residue 39 THR Chi-restraints excluded: chain B residue 114 MET Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 166 ILE Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 210 GLU Chi-restraints excluded: chain B residue 217 ASP Chi-restraints excluded: chain B residue 224 ILE Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 318 CYS Chi-restraints excluded: chain B residue 350 ILE Chi-restraints excluded: chain B residue 363 ILE Chi-restraints excluded: chain B residue 401 ASP Chi-restraints excluded: chain B residue 413 ILE Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain B residue 417 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 59 optimal weight: 1.9990 chunk 80 optimal weight: 5.9990 chunk 31 optimal weight: 0.8980 chunk 24 optimal weight: 4.9990 chunk 79 optimal weight: 0.4980 chunk 76 optimal weight: 1.9990 chunk 67 optimal weight: 0.9980 chunk 70 optimal weight: 4.9990 chunk 77 optimal weight: 20.0000 chunk 6 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.118871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.099013 restraints weight = 17407.424| |-----------------------------------------------------------------------------| r_work (start): 0.3315 rms_B_bonded: 1.75 r_work: 0.3192 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3053 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.2335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 11310 Z= 0.125 Angle : 0.498 7.233 16174 Z= 0.271 Chirality : 0.036 0.183 1894 Planarity : 0.003 0.035 1352 Dihedral : 21.394 92.287 3745 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 4.84 % Allowed : 21.23 % Favored : 73.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.33 (0.30), residues: 797 helix: 2.80 (0.25), residues: 367 sheet: -0.29 (0.40), residues: 148 loop : -1.10 (0.36), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 43 HIS 0.002 0.001 HIS A 139 PHE 0.019 0.001 PHE B 389 TYR 0.016 0.001 TYR A 351 ARG 0.004 0.000 ARG A 254 Details of bonding type rmsd hydrogen bonds : bond 0.04327 ( 540) hydrogen bonds : angle 3.57191 ( 1366) metal coordination : bond 0.00348 ( 8) metal coordination : angle 2.02307 ( 12) covalent geometry : bond 0.00266 (11302) covalent geometry : angle 0.49540 (16162) *********************** 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 203 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 169 time to evaluate : 0.921 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 GLU cc_start: 0.7774 (mm-30) cc_final: 0.7447 (mm-30) REVERT: A 55 ASN cc_start: 0.8235 (t0) cc_final: 0.7891 (t0) REVERT: A 82 LYS cc_start: 0.8651 (ttmt) cc_final: 0.8358 (ttmt) REVERT: A 130 GLU cc_start: 0.8309 (mp0) cc_final: 0.7951 (mp0) REVERT: A 254 ARG cc_start: 0.6866 (tpm170) cc_final: 0.6340 (tpm170) REVERT: A 258 GLU cc_start: 0.7669 (mt-10) cc_final: 0.7165 (mt-10) REVERT: A 262 ILE cc_start: 0.8350 (mt) cc_final: 0.8065 (mm) REVERT: A 285 LYS cc_start: 0.8229 (tttt) cc_final: 0.7944 (tttm) REVERT: A 298 ARG cc_start: 0.7884 (mtt180) cc_final: 0.7441 (mtt180) REVERT: A 344 ASP cc_start: 0.7760 (OUTLIER) cc_final: 0.7262 (m-30) REVERT: A 421 ILE cc_start: 0.7036 (mm) cc_final: 0.6798 (tp) REVERT: B 11 LYS cc_start: 0.8582 (pttt) cc_final: 0.8326 (pttp) REVERT: B 133 SER cc_start: 0.9046 (t) cc_final: 0.8514 (p) REVERT: B 166 ILE cc_start: 0.8842 (OUTLIER) cc_final: 0.8624 (mt) REVERT: B 174 LYS cc_start: 0.8409 (tttt) cc_final: 0.7810 (tppp) REVERT: B 178 ASP cc_start: 0.8118 (m-30) cc_final: 0.7573 (m-30) REVERT: B 200 LYS cc_start: 0.8464 (mttt) cc_final: 0.8220 (mttm) REVERT: B 221 ILE cc_start: 0.8187 (mp) cc_final: 0.7793 (mt) REVERT: B 255 ARG cc_start: 0.8000 (mtm-85) cc_final: 0.7619 (mtm-85) REVERT: B 300 THR cc_start: 0.8561 (m) cc_final: 0.8162 (p) REVERT: B 369 SER cc_start: 0.8367 (m) cc_final: 0.8129 (p) REVERT: B 417 ILE cc_start: 0.8678 (OUTLIER) cc_final: 0.8423 (tt) outliers start: 34 outliers final: 24 residues processed: 189 average time/residue: 0.3183 time to fit residues: 77.4660 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 : 0.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 MET Chi-restraints excluded: chain A residue 59 TYR Chi-restraints excluded: chain A residue 133 SER Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 344 ASP Chi-restraints excluded: chain A residue 359 LYS Chi-restraints excluded: chain A residue 361 ILE Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain B residue 39 THR Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 166 ILE Chi-restraints excluded: chain B residue 210 GLU Chi-restraints excluded: chain B residue 217 ASP Chi-restraints excluded: chain B residue 224 ILE Chi-restraints excluded: chain B residue 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 401 ASP Chi-restraints excluded: chain B residue 413 ILE Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain B residue 417 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 70 optimal weight: 6.9990 chunk 3 optimal weight: 6.9990 chunk 40 optimal weight: 5.9990 chunk 53 optimal weight: 0.9990 chunk 60 optimal weight: 0.9980 chunk 1 optimal weight: 4.9990 chunk 42 optimal weight: 4.9990 chunk 85 optimal weight: 10.0000 chunk 90 optimal weight: 8.9990 chunk 87 optimal weight: 10.0000 chunk 43 optimal weight: 0.6980 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.116317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.096338 restraints weight = 17458.925| |-----------------------------------------------------------------------------| r_work (start): 0.3268 rms_B_bonded: 1.76 r_work: 0.3144 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3005 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.2339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 11310 Z= 0.204 Angle : 0.548 8.242 16174 Z= 0.294 Chirality : 0.038 0.177 1894 Planarity : 0.004 0.034 1352 Dihedral : 21.416 93.654 3745 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 4.42 % Allowed : 21.51 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.30), residues: 797 helix: 2.64 (0.25), residues: 366 sheet: -0.29 (0.40), residues: 149 loop : -1.18 (0.36), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 43 HIS 0.002 0.001 HIS A 139 PHE 0.012 0.001 PHE A 209 TYR 0.017 0.002 TYR A 351 ARG 0.005 0.000 ARG A 254 Details of bonding type rmsd hydrogen bonds : bond 0.04888 ( 540) hydrogen bonds : angle 3.67723 ( 1366) metal coordination : bond 0.00655 ( 8) metal coordination : angle 2.66085 ( 12) covalent geometry : bond 0.00446 (11302) covalent geometry : angle 0.54296 (16162) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1594 Ramachandran restraints generated. 797 Oldfield, 0 Emsley, 797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1594 Ramachandran restraints generated. 797 Oldfield, 0 Emsley, 797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 170 time to evaluate : 0.810 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 GLU cc_start: 0.7799 (mm-30) cc_final: 0.7499 (mm-30) REVERT: A 55 ASN cc_start: 0.8244 (t0) cc_final: 0.7904 (t0) REVERT: A 82 LYS cc_start: 0.8631 (ttmt) cc_final: 0.8352 (ttmt) REVERT: A 130 GLU cc_start: 0.8327 (mp0) cc_final: 0.7939 (mp0) REVERT: A 254 ARG cc_start: 0.6824 (tpm170) cc_final: 0.6532 (tpm170) REVERT: A 258 GLU cc_start: 0.7551 (mt-10) cc_final: 0.7152 (mt-10) REVERT: A 262 ILE cc_start: 0.8304 (mt) cc_final: 0.7993 (mm) REVERT: A 285 LYS cc_start: 0.8391 (tttt) cc_final: 0.8122 (tttm) REVERT: A 311 ASP cc_start: 0.8260 (m-30) cc_final: 0.7952 (m-30) REVERT: A 344 ASP cc_start: 0.7806 (OUTLIER) cc_final: 0.7316 (m-30) REVERT: B 11 LYS cc_start: 0.8703 (pttt) cc_final: 0.8449 (pttp) REVERT: B 133 SER cc_start: 0.9052 (t) cc_final: 0.8533 (p) REVERT: B 174 LYS cc_start: 0.8479 (tttt) cc_final: 0.7878 (tppp) REVERT: B 178 ASP cc_start: 0.8140 (m-30) cc_final: 0.7627 (m-30) REVERT: B 200 LYS cc_start: 0.8506 (mttt) cc_final: 0.8253 (mttm) REVERT: B 221 ILE cc_start: 0.8196 (mp) cc_final: 0.7793 (mt) REVERT: B 255 ARG cc_start: 0.8029 (mtm-85) cc_final: 0.7638 (mtm-85) REVERT: B 300 THR cc_start: 0.8639 (m) cc_final: 0.8209 (p) REVERT: B 369 SER cc_start: 0.8447 (m) cc_final: 0.8136 (p) REVERT: B 417 ILE cc_start: 0.8695 (OUTLIER) cc_final: 0.8452 (tt) outliers start: 31 outliers final: 23 residues processed: 187 average time/residue: 0.3204 time to fit residues: 77.4085 Evaluate side-chains 194 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 169 time to evaluate : 0.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 MET Chi-restraints excluded: chain A residue 59 TYR Chi-restraints excluded: chain A residue 133 SER Chi-restraints excluded: chain A residue 244 LYS Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 344 ASP Chi-restraints excluded: chain A residue 359 LYS Chi-restraints excluded: chain A residue 361 ILE Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain B residue 39 THR Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 210 GLU Chi-restraints excluded: chain B residue 217 ASP Chi-restraints excluded: chain B residue 224 ILE Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 350 ILE Chi-restraints excluded: chain B residue 363 ILE Chi-restraints excluded: chain B residue 401 ASP Chi-restraints excluded: chain B residue 413 ILE Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain B residue 417 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 4 optimal weight: 3.9990 chunk 48 optimal weight: 0.0040 chunk 65 optimal weight: 2.9990 chunk 11 optimal weight: 0.9980 chunk 93 optimal weight: 7.9990 chunk 3 optimal weight: 3.9990 chunk 7 optimal weight: 0.6980 chunk 13 optimal weight: 0.9980 chunk 22 optimal weight: 7.9990 chunk 92 optimal weight: 8.9990 chunk 74 optimal weight: 0.5980 overall best weight: 0.6592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 289 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.120646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.100826 restraints weight = 17385.570| |-----------------------------------------------------------------------------| r_work (start): 0.3339 rms_B_bonded: 1.74 r_work: 0.3218 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3081 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.2628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 11310 Z= 0.110 Angle : 0.497 8.405 16174 Z= 0.268 Chirality : 0.035 0.167 1894 Planarity : 0.003 0.033 1352 Dihedral : 21.348 92.440 3745 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 2.28 % Allowed : 23.79 % Favored : 73.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.52 (0.30), residues: 797 helix: 2.89 (0.25), residues: 367 sheet: -0.10 (0.41), residues: 148 loop : -0.98 (0.37), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 17 HIS 0.002 0.001 HIS A 139 PHE 0.023 0.001 PHE B 389 TYR 0.015 0.001 TYR A 351 ARG 0.005 0.000 ARG A 254 Details of bonding type rmsd hydrogen bonds : bond 0.04142 ( 540) hydrogen bonds : angle 3.49439 ( 1366) metal coordination : bond 0.00280 ( 8) metal coordination : angle 1.55870 ( 12) covalent geometry : bond 0.00232 (11302) covalent geometry : angle 0.49501 (16162) ********************** 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 189 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 173 time to evaluate : 0.922 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 GLU cc_start: 0.7778 (mm-30) cc_final: 0.7474 (mm-30) REVERT: A 55 ASN cc_start: 0.8219 (t0) cc_final: 0.7852 (t0) REVERT: A 82 LYS cc_start: 0.8624 (ttmt) cc_final: 0.8340 (ttmt) REVERT: A 130 GLU cc_start: 0.8241 (mp0) cc_final: 0.7927 (mp0) REVERT: A 244 LYS cc_start: 0.8451 (OUTLIER) cc_final: 0.8110 (mmtm) REVERT: A 262 ILE cc_start: 0.8254 (mt) cc_final: 0.7966 (mm) REVERT: A 285 LYS cc_start: 0.8178 (tttt) cc_final: 0.7899 (tttm) REVERT: A 343 TYR cc_start: 0.8087 (t80) cc_final: 0.7490 (t80) REVERT: A 344 ASP cc_start: 0.7663 (t0) cc_final: 0.7177 (m-30) REVERT: A 347 GLN cc_start: 0.7881 (tt0) cc_final: 0.7654 (mt0) REVERT: A 421 ILE cc_start: 0.7116 (mm) cc_final: 0.6888 (tp) REVERT: B 11 LYS cc_start: 0.8676 (pttt) cc_final: 0.8370 (pttp) REVERT: B 133 SER cc_start: 0.9025 (t) cc_final: 0.8496 (p) REVERT: B 174 LYS cc_start: 0.8346 (tttt) cc_final: 0.7857 (tppp) REVERT: B 178 ASP cc_start: 0.8127 (m-30) cc_final: 0.7593 (m-30) REVERT: B 200 LYS cc_start: 0.8433 (mttt) cc_final: 0.8195 (mttm) REVERT: B 255 ARG cc_start: 0.7978 (mtm-85) cc_final: 0.7582 (mtm-85) REVERT: B 300 THR cc_start: 0.8530 (m) cc_final: 0.8151 (p) REVERT: B 311 ASP cc_start: 0.8130 (m-30) cc_final: 0.7920 (m-30) REVERT: B 369 SER cc_start: 0.8386 (m) cc_final: 0.8078 (p) REVERT: B 417 ILE cc_start: 0.8660 (OUTLIER) cc_final: 0.8407 (tt) outliers start: 16 outliers final: 12 residues processed: 182 average time/residue: 0.3281 time to fit residues: 76.4604 Evaluate side-chains 181 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 167 time to evaluate : 0.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 MET Chi-restraints excluded: chain A residue 59 TYR Chi-restraints excluded: chain A residue 244 LYS 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 359 LYS Chi-restraints excluded: chain A residue 361 ILE Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 217 ASP Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 401 ASP Chi-restraints excluded: chain B residue 417 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 59 optimal weight: 6.9990 chunk 73 optimal weight: 5.9990 chunk 46 optimal weight: 3.9990 chunk 35 optimal weight: 0.9990 chunk 52 optimal weight: 3.9990 chunk 38 optimal weight: 20.0000 chunk 0 optimal weight: 8.9990 chunk 54 optimal weight: 0.0270 chunk 77 optimal weight: 30.0000 chunk 44 optimal weight: 6.9990 chunk 91 optimal weight: 10.0000 overall best weight: 3.0046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 ASN B 338 GLN B 366 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.115714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.095697 restraints weight = 17391.695| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 1.75 r_work: 0.3133 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2993 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.2489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 11310 Z= 0.233 Angle : 0.585 12.480 16174 Z= 0.311 Chirality : 0.039 0.161 1894 Planarity : 0.004 0.056 1352 Dihedral : 21.407 94.061 3743 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 2.56 % Allowed : 23.22 % Favored : 74.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.30), residues: 797 helix: 2.56 (0.26), residues: 367 sheet: -0.15 (0.42), residues: 139 loop : -1.16 (0.36), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 43 HIS 0.003 0.001 HIS A 139 PHE 0.020 0.002 PHE B 389 TYR 0.018 0.002 TYR A 351 ARG 0.013 0.001 ARG A 254 Details of bonding type rmsd hydrogen bonds : bond 0.05182 ( 540) hydrogen bonds : angle 3.70370 ( 1366) metal coordination : bond 0.00745 ( 8) metal coordination : angle 2.68027 ( 12) covalent geometry : bond 0.00509 (11302) covalent geometry : angle 0.58073 (16162) =============================================================================== Job complete usr+sys time: 6841.53 seconds wall clock time: 118 minutes 33.09 seconds (7113.09 seconds total)