Starting phenix.real_space_refine on Sun Apr 7 14:09:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j12_35912/04_2024/8j12_35912.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j12_35912/04_2024/8j12_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j12_35912/04_2024/8j12_35912.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j12_35912/04_2024/8j12_35912.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j12_35912/04_2024/8j12_35912.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j12_35912/04_2024/8j12_35912.pdb" } 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 Residue "A TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 379": "OD1" <-> "OD2" Residue "B ASP 401": "OD1" <-> "OD2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/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: 6.41, 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 - 3.50 Amino acid : False - 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: 5.73 Conformation dependent library (CDL) restraints added in 1.2 seconds 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: 3.98 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: 5.20 Time building geometry restraints manager: 5.99 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: 99.73 - 106.59: 1255 106.59 - 113.45: 6322 113.45 - 120.30: 4223 120.30 - 127.16: 3892 127.16 - 134.02: 470 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 2.440 nonbonded pdb=" O ILE B 416 " pdb=" OG SER B 420 " model vdw 2.234 2.440 nonbonded pdb=" OH TYR A 76 " pdb=" OP2 DT E -3 " model vdw 2.241 2.440 nonbonded pdb=" O LEU A 337 " pdb=" OH TYR A 342 " model vdw 2.244 2.440 nonbonded pdb=" O2' C C-103 " pdb=" OP2 U C -5 " model vdw 2.264 2.440 ... (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 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: 0.010 Extract box with map and model: 1.110 Check model and map are aligned: 0.160 Set scattering table: 0.100 Process input model: 38.140 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.040 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:3.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.300 ------------------------------------------------------------------------------- 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 0.031 11302 Z= 0.180 Angle : 0.446 5.012 16162 Z= 0.250 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 *********************** 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 fitting. rotamer outliers: 15 poor density : 232 time to evaluate : 0.884 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: 0.3468 time to fit residues: 108.3783 Evaluate side-chains 191 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 185 time to evaluate : 1.008 ------------------------------------------------------------------------------- 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: 4.9990 chunk 41 optimal weight: 7.9990 chunk 25 optimal weight: 10.0000 chunk 50 optimal weight: 4.9990 chunk 39 optimal weight: 0.4980 chunk 76 optimal weight: 0.0040 chunk 29 optimal weight: 4.9990 chunk 46 optimal weight: 5.9990 chunk 57 optimal weight: 9.9990 chunk 88 optimal weight: 10.0000 overall best weight: 3.0998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 HIS A 366 GLN A 370 GLN B 26 GLN ** B 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 407 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.1321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 11302 Z= 0.313 Angle : 0.550 6.868 16162 Z= 0.300 Chirality : 0.039 0.196 1894 Planarity : 0.004 0.051 1352 Dihedral : 21.552 87.369 3754 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 4.13 % Allowed : 16.38 % Favored : 79.49 % 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: 0.98 (0.30), residues: 797 helix: 2.50 (0.26), residues: 365 sheet: -0.73 (0.43), residues: 147 loop : -1.06 (0.36), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 43 HIS 0.005 0.001 HIS A 56 PHE 0.027 0.002 PHE B 389 TYR 0.017 0.002 TYR A 351 ARG 0.007 0.001 ARG B 255 *********************** 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 fitting. rotamer outliers: 29 poor density : 189 time to evaluate : 1.010 Fit side-chains revert: symmetry clash REVERT: A 8 GLU cc_start: 0.7853 (tt0) cc_final: 0.7649 (tt0) REVERT: A 30 GLU cc_start: 0.7731 (mm-30) cc_final: 0.7420 (mm-30) REVERT: A 82 LYS cc_start: 0.8518 (ttmt) cc_final: 0.8255 (ttmt) REVERT: A 130 GLU cc_start: 0.8305 (mp0) cc_final: 0.7712 (mp0) REVERT: A 145 SER cc_start: 0.8797 (m) cc_final: 0.8525 (p) REVERT: A 258 GLU cc_start: 0.7195 (mt-10) cc_final: 0.6972 (mt-10) REVERT: A 262 ILE cc_start: 0.8368 (mt) cc_final: 0.8096 (mm) REVERT: A 298 ARG cc_start: 0.7771 (mtt180) cc_final: 0.7555 (mtt180) REVERT: A 301 THR cc_start: 0.7966 (m) cc_final: 0.7731 (p) REVERT: A 344 ASP cc_start: 0.7897 (OUTLIER) cc_final: 0.7491 (m-30) REVERT: B 11 LYS cc_start: 0.8835 (pttt) cc_final: 0.8579 (pttp) REVERT: B 90 ASN cc_start: 0.8909 (OUTLIER) cc_final: 0.8660 (m-40) REVERT: B 100 ASP cc_start: 0.7990 (m-30) cc_final: 0.7701 (m-30) REVERT: B 123 ILE cc_start: 0.7995 (OUTLIER) cc_final: 0.7787 (tp) REVERT: B 133 SER cc_start: 0.9137 (t) cc_final: 0.8657 (p) REVERT: B 174 LYS cc_start: 0.8307 (tttt) cc_final: 0.7492 (tppp) REVERT: B 178 ASP cc_start: 0.8034 (m-30) cc_final: 0.7376 (m-30) REVERT: B 200 LYS cc_start: 0.8516 (mttt) cc_final: 0.8167 (mttm) REVERT: B 221 ILE cc_start: 0.8271 (mp) cc_final: 0.7758 (mm) REVERT: B 234 MET cc_start: 0.8849 (mtm) cc_final: 0.8605 (mtp) REVERT: B 289 GLN cc_start: 0.7985 (mm-40) cc_final: 0.7567 (mm-40) REVERT: B 320 THR cc_start: 0.8158 (p) cc_final: 0.7929 (p) outliers start: 29 outliers final: 16 residues processed: 208 average time/residue: 0.3489 time to fit residues: 94.6723 Evaluate side-chains 192 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 173 time to evaluate : 0.987 ------------------------------------------------------------------------------- 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 90 ASN Chi-restraints excluded: chain A residue 138 ASN Chi-restraints excluded: chain A residue 344 ASP Chi-restraints excluded: chain A residue 361 ILE Chi-restraints excluded: chain B residue 90 ASN Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 217 ASP Chi-restraints excluded: chain B residue 224 ILE Chi-restraints excluded: chain B residue 233 TYR Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 318 CYS Chi-restraints excluded: chain B residue 350 ILE Chi-restraints excluded: chain B residue 401 ASP Chi-restraints excluded: chain B residue 414 ASP Chi-restraints excluded: chain B residue 416 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 49 optimal weight: 8.9990 chunk 27 optimal weight: 6.9990 chunk 74 optimal weight: 2.9990 chunk 60 optimal weight: 3.9990 chunk 24 optimal weight: 4.9990 chunk 89 optimal weight: 10.0000 chunk 96 optimal weight: 8.9990 chunk 79 optimal weight: 0.8980 chunk 88 optimal weight: 10.0000 chunk 30 optimal weight: 2.9990 chunk 71 optimal weight: 0.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 ASN A 366 GLN A 370 GLN B 26 GLN ** B 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 366 GLN B 407 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.1606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 11302 Z= 0.253 Angle : 0.507 5.172 16162 Z= 0.278 Chirality : 0.038 0.197 1894 Planarity : 0.003 0.034 1352 Dihedral : 21.444 89.497 3749 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 4.27 % Allowed : 19.23 % Favored : 76.50 % 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: 1.02 (0.30), residues: 797 helix: 2.65 (0.25), residues: 365 sheet: -0.72 (0.40), residues: 156 loop : -1.21 (0.37), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 43 HIS 0.003 0.001 HIS A 303 PHE 0.016 0.001 PHE B 389 TYR 0.019 0.002 TYR B 202 ARG 0.004 0.000 ARG B 255 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1594 Ramachandran restraints generated. 797 Oldfield, 0 Emsley, 797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1594 Ramachandran restraints generated. 797 Oldfield, 0 Emsley, 797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 169 time to evaluate : 1.979 Fit side-chains revert: symmetry clash REVERT: A 8 GLU cc_start: 0.7838 (tt0) cc_final: 0.7637 (tt0) REVERT: A 30 GLU cc_start: 0.7711 (mm-30) cc_final: 0.7432 (mm-30) REVERT: A 82 LYS cc_start: 0.8511 (ttmt) cc_final: 0.8257 (ttmt) REVERT: A 130 GLU cc_start: 0.8267 (mp0) cc_final: 0.7858 (mp0) REVERT: A 145 SER cc_start: 0.8775 (m) cc_final: 0.8553 (p) REVERT: A 258 GLU cc_start: 0.7214 (mt-10) cc_final: 0.6983 (mt-10) REVERT: A 262 ILE cc_start: 0.8384 (mt) cc_final: 0.8104 (mm) REVERT: A 298 ARG cc_start: 0.7720 (mtt180) cc_final: 0.7431 (mtt180) REVERT: A 301 THR cc_start: 0.7968 (m) cc_final: 0.7734 (p) REVERT: A 344 ASP cc_start: 0.7947 (OUTLIER) cc_final: 0.7429 (m-30) REVERT: B 11 LYS cc_start: 0.8725 (pttt) cc_final: 0.8474 (pttp) REVERT: B 90 ASN cc_start: 0.8884 (OUTLIER) cc_final: 0.8617 (m-40) REVERT: B 100 ASP cc_start: 0.7963 (m-30) cc_final: 0.7758 (m-30) REVERT: B 174 LYS cc_start: 0.8323 (tttt) cc_final: 0.7540 (tppp) REVERT: B 178 ASP cc_start: 0.8041 (m-30) cc_final: 0.7377 (m-30) REVERT: B 200 LYS cc_start: 0.8478 (mttt) cc_final: 0.8168 (mttp) REVERT: B 234 MET cc_start: 0.8837 (mtm) cc_final: 0.8635 (mtp) REVERT: B 261 ARG cc_start: 0.8408 (tpp80) cc_final: 0.8191 (tpp80) outliers start: 30 outliers final: 20 residues processed: 184 average time/residue: 0.3324 time to fit residues: 80.1764 Evaluate side-chains 187 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 165 time to evaluate : 0.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 0 SER Chi-restraints excluded: chain A residue 46 MET Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 138 ASN Chi-restraints excluded: chain A residue 252 ASN Chi-restraints excluded: chain A residue 344 ASP Chi-restraints excluded: chain A residue 361 ILE Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain B residue 16 ASP Chi-restraints excluded: chain B residue 90 ASN Chi-restraints excluded: chain B residue 115 SER 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 88 optimal weight: 10.0000 chunk 67 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 9 optimal weight: 5.9990 chunk 42 optimal weight: 7.9990 chunk 59 optimal weight: 1.9990 chunk 89 optimal weight: 10.0000 chunk 94 optimal weight: 10.0000 chunk 84 optimal weight: 8.9990 chunk 25 optimal weight: 10.0000 chunk 78 optimal weight: 9.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 194 HIS A 366 GLN ** B 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 366 GLN B 407 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.1952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.054 11302 Z= 0.431 Angle : 0.604 5.246 16162 Z= 0.325 Chirality : 0.043 0.198 1894 Planarity : 0.004 0.039 1352 Dihedral : 21.539 92.254 3749 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 5.27 % Allowed : 21.08 % Favored : 73.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.76 (0.30), residues: 797 helix: 2.31 (0.26), residues: 365 sheet: -0.70 (0.39), residues: 160 loop : -1.27 (0.37), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 43 HIS 0.005 0.001 HIS A 194 PHE 0.034 0.002 PHE B 389 TYR 0.020 0.002 TYR A 351 ARG 0.005 0.001 ARG A 85 *********************** 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 201 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 164 time to evaluate : 1.256 Fit side-chains REVERT: A 8 GLU cc_start: 0.7881 (tt0) cc_final: 0.7676 (tt0) REVERT: A 16 ASP cc_start: 0.8078 (m-30) cc_final: 0.7775 (t0) REVERT: A 30 GLU cc_start: 0.7800 (mm-30) cc_final: 0.7458 (mm-30) REVERT: A 82 LYS cc_start: 0.8617 (ttmt) cc_final: 0.8408 (ttmt) REVERT: A 130 GLU cc_start: 0.8292 (mp0) cc_final: 0.7844 (mp0) REVERT: A 145 SER cc_start: 0.8808 (m) cc_final: 0.8575 (p) REVERT: A 258 GLU cc_start: 0.7239 (mt-10) cc_final: 0.7003 (mt-10) REVERT: A 262 ILE cc_start: 0.8373 (mt) cc_final: 0.8089 (mm) REVERT: A 301 THR cc_start: 0.8032 (m) cc_final: 0.7764 (p) REVERT: A 311 ASP cc_start: 0.8269 (m-30) cc_final: 0.7955 (m-30) REVERT: A 344 ASP cc_start: 0.7920 (OUTLIER) cc_final: 0.7414 (m-30) REVERT: B 11 LYS cc_start: 0.8817 (pttt) cc_final: 0.8402 (pttp) REVERT: B 100 ASP cc_start: 0.7995 (m-30) cc_final: 0.7704 (m-30) REVERT: B 166 ILE cc_start: 0.9066 (OUTLIER) cc_final: 0.8797 (mt) REVERT: B 174 LYS cc_start: 0.8414 (tttt) cc_final: 0.7587 (tppp) REVERT: B 178 ASP cc_start: 0.8040 (m-30) cc_final: 0.7411 (m-30) REVERT: B 200 LYS cc_start: 0.8505 (mttt) cc_final: 0.8199 (mttm) outliers start: 37 outliers final: 28 residues processed: 188 average time/residue: 0.3230 time to fit residues: 79.4700 Evaluate side-chains 193 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 163 time to evaluate : 0.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 0 SER Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 46 MET Chi-restraints excluded: chain A residue 90 ASN Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 138 ASN Chi-restraints excluded: chain A residue 252 ASN Chi-restraints excluded: chain A residue 291 ARG Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 344 ASP Chi-restraints excluded: chain A residue 361 ILE Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 394 CYS Chi-restraints excluded: chain B residue 16 ASP Chi-restraints excluded: chain B residue 39 THR Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain B residue 115 SER 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 363 ILE Chi-restraints excluded: chain B residue 401 ASP Chi-restraints excluded: chain B residue 416 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 53 optimal weight: 0.9980 chunk 1 optimal weight: 3.9990 chunk 70 optimal weight: 1.9990 chunk 39 optimal weight: 5.9990 chunk 80 optimal weight: 5.9990 chunk 65 optimal weight: 0.9990 chunk 0 optimal weight: 5.9990 chunk 48 optimal weight: 0.9990 chunk 85 optimal weight: 7.9990 chunk 23 optimal weight: 3.9990 chunk 31 optimal weight: 0.8980 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 407 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.1953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11302 Z= 0.167 Angle : 0.477 5.133 16162 Z= 0.262 Chirality : 0.036 0.192 1894 Planarity : 0.003 0.033 1352 Dihedral : 21.388 91.860 3749 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 5.56 % Allowed : 20.80 % Favored : 73.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.20 (0.30), residues: 797 helix: 2.81 (0.25), residues: 365 sheet: -0.55 (0.37), residues: 168 loop : -1.23 (0.38), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 17 HIS 0.002 0.001 HIS A 303 PHE 0.021 0.001 PHE B 389 TYR 0.013 0.001 TYR A 351 ARG 0.003 0.000 ARG A 85 *********************** 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 208 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 169 time to evaluate : 0.847 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 30 GLU cc_start: 0.7696 (mm-30) cc_final: 0.7403 (mm-30) REVERT: A 82 LYS cc_start: 0.8515 (ttmt) cc_final: 0.8228 (ttmt) REVERT: A 130 GLU cc_start: 0.8224 (mp0) cc_final: 0.7819 (mp0) REVERT: A 145 SER cc_start: 0.8748 (m) cc_final: 0.8546 (p) REVERT: A 258 GLU cc_start: 0.7215 (mt-10) cc_final: 0.6971 (mt-10) REVERT: A 262 ILE cc_start: 0.8388 (mt) cc_final: 0.8121 (mm) REVERT: A 311 ASP cc_start: 0.8200 (m-30) cc_final: 0.7861 (m-30) REVERT: A 344 ASP cc_start: 0.7859 (OUTLIER) cc_final: 0.7384 (m-30) REVERT: A 421 ILE cc_start: 0.7236 (mm) cc_final: 0.6994 (tp) REVERT: B 11 LYS cc_start: 0.8657 (pttt) cc_final: 0.8410 (pttp) REVERT: B 100 ASP cc_start: 0.8003 (m-30) cc_final: 0.7693 (m-30) REVERT: B 133 SER cc_start: 0.9101 (t) cc_final: 0.8557 (p) REVERT: B 174 LYS cc_start: 0.8330 (tttt) cc_final: 0.7598 (tppp) REVERT: B 178 ASP cc_start: 0.8018 (m-30) cc_final: 0.7400 (m-30) REVERT: B 200 LYS cc_start: 0.8430 (mttt) cc_final: 0.8135 (mttp) REVERT: B 221 ILE cc_start: 0.8260 (mp) cc_final: 0.7853 (mm) REVERT: B 300 THR cc_start: 0.8596 (m) cc_final: 0.8157 (p) REVERT: B 369 SER cc_start: 0.8328 (m) cc_final: 0.8111 (p) outliers start: 39 outliers final: 27 residues processed: 194 average time/residue: 0.3035 time to fit residues: 77.0200 Evaluate side-chains 196 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 168 time to evaluate : 0.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 46 MET Chi-restraints excluded: chain A residue 70 ASN Chi-restraints excluded: chain A residue 90 ASN Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 133 SER Chi-restraints excluded: chain A residue 138 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 A residue 394 CYS Chi-restraints excluded: chain B residue 16 ASP Chi-restraints excluded: chain B residue 39 THR Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 166 ILE Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 217 ASP Chi-restraints excluded: chain B residue 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 401 ASP Chi-restraints excluded: chain B residue 413 ILE Chi-restraints excluded: chain B residue 416 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 85 optimal weight: 10.0000 chunk 18 optimal weight: 6.9990 chunk 55 optimal weight: 2.9990 chunk 23 optimal weight: 9.9990 chunk 94 optimal weight: 10.0000 chunk 78 optimal weight: 10.0000 chunk 43 optimal weight: 5.9990 chunk 7 optimal weight: 5.9990 chunk 31 optimal weight: 0.8980 chunk 49 optimal weight: 5.9990 chunk 91 optimal weight: 10.0000 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 347 GLN B 90 ASN ** B 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 366 GLN ** B 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.2137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.055 11302 Z= 0.432 Angle : 0.605 5.452 16162 Z= 0.325 Chirality : 0.043 0.192 1894 Planarity : 0.004 0.045 1352 Dihedral : 21.496 93.974 3745 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 5.56 % Allowed : 22.22 % Favored : 72.22 % 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: 0.78 (0.30), residues: 797 helix: 2.40 (0.26), residues: 365 sheet: -0.70 (0.37), residues: 169 loop : -1.37 (0.38), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 43 HIS 0.003 0.001 HIS B 77 PHE 0.016 0.002 PHE A 209 TYR 0.022 0.002 TYR A 233 ARG 0.003 0.001 ARG A 85 *********************** 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 fitting. rotamer outliers: 39 poor density : 165 time to evaluate : 1.100 Fit side-chains revert: symmetry clash REVERT: A 30 GLU cc_start: 0.7790 (mm-30) cc_final: 0.7447 (mm-30) REVERT: A 82 LYS cc_start: 0.8574 (ttmt) cc_final: 0.8346 (ttmt) REVERT: A 130 GLU cc_start: 0.8250 (mp0) cc_final: 0.7779 (mp0) REVERT: A 145 SER cc_start: 0.8797 (m) cc_final: 0.8569 (p) REVERT: A 258 GLU cc_start: 0.7196 (mt-10) cc_final: 0.6954 (mt-10) REVERT: A 262 ILE cc_start: 0.8372 (mt) cc_final: 0.8091 (mm) REVERT: A 311 ASP cc_start: 0.8263 (m-30) cc_final: 0.7964 (m-30) REVERT: A 344 ASP cc_start: 0.7944 (OUTLIER) cc_final: 0.7430 (m-30) REVERT: B 11 LYS cc_start: 0.8922 (pttt) cc_final: 0.8580 (ptmm) REVERT: B 100 ASP cc_start: 0.7947 (m-30) cc_final: 0.7623 (m-30) REVERT: B 174 LYS cc_start: 0.8453 (tttt) cc_final: 0.7633 (tppp) REVERT: B 178 ASP cc_start: 0.8049 (m-30) cc_final: 0.7422 (m-30) REVERT: B 200 LYS cc_start: 0.8477 (mttt) cc_final: 0.8198 (mttp) REVERT: B 221 ILE cc_start: 0.8361 (mp) cc_final: 0.7962 (mt) REVERT: B 369 SER cc_start: 0.8452 (m) cc_final: 0.8192 (p) outliers start: 39 outliers final: 33 residues processed: 192 average time/residue: 0.3203 time to fit residues: 80.7708 Evaluate side-chains 197 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 163 time to evaluate : 0.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 0 SER Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 46 MET Chi-restraints excluded: chain A residue 90 ASN Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain A residue 133 SER Chi-restraints excluded: chain A residue 138 ASN Chi-restraints excluded: chain A residue 252 ASN Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 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 A residue 394 CYS Chi-restraints excluded: chain B residue 16 ASP Chi-restraints excluded: chain B residue 39 THR Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 166 ILE Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 210 GLU Chi-restraints excluded: chain B residue 217 ASP Chi-restraints excluded: chain B residue 233 TYR Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 312 MET 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 416 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 10 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 chunk 69 optimal weight: 0.8980 chunk 53 optimal weight: 0.9990 chunk 79 optimal weight: 5.9990 chunk 52 optimal weight: 2.9990 chunk 94 optimal weight: 10.0000 chunk 59 optimal weight: 2.9990 chunk 57 optimal weight: 9.9990 chunk 43 optimal weight: 3.9990 chunk 58 optimal weight: 3.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 403 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.2099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 11302 Z= 0.240 Angle : 0.511 6.889 16162 Z= 0.278 Chirality : 0.037 0.192 1894 Planarity : 0.003 0.035 1352 Dihedral : 21.407 93.151 3745 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 5.27 % Allowed : 21.94 % Favored : 72.79 % 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: 0.99 (0.30), residues: 797 helix: 2.61 (0.26), residues: 366 sheet: -0.59 (0.36), residues: 168 loop : -1.35 (0.37), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 43 HIS 0.002 0.001 HIS A 303 PHE 0.009 0.001 PHE A 209 TYR 0.015 0.001 TYR A 351 ARG 0.003 0.000 ARG B 254 *********************** 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 fitting. rotamer outliers: 37 poor density : 167 time to evaluate : 0.930 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 GLU cc_start: 0.7731 (mm-30) cc_final: 0.7394 (mm-30) REVERT: A 82 LYS cc_start: 0.8492 (ttmt) cc_final: 0.8230 (ttmt) REVERT: A 130 GLU cc_start: 0.8209 (mp0) cc_final: 0.7751 (mp0) REVERT: A 145 SER cc_start: 0.8764 (m) cc_final: 0.8559 (p) REVERT: A 258 GLU cc_start: 0.7181 (mt-10) cc_final: 0.6934 (mt-10) REVERT: A 262 ILE cc_start: 0.8376 (mt) cc_final: 0.8103 (mm) REVERT: A 311 ASP cc_start: 0.8247 (m-30) cc_final: 0.7935 (m-30) REVERT: A 344 ASP cc_start: 0.7875 (OUTLIER) cc_final: 0.7369 (m-30) REVERT: B 11 LYS cc_start: 0.8696 (pttt) cc_final: 0.8449 (pttp) REVERT: B 100 ASP cc_start: 0.7916 (m-30) cc_final: 0.7596 (m-30) REVERT: B 133 SER cc_start: 0.9109 (t) cc_final: 0.8549 (p) REVERT: B 174 LYS cc_start: 0.8394 (tttt) cc_final: 0.7626 (tppp) REVERT: B 178 ASP cc_start: 0.8027 (m-30) cc_final: 0.7425 (m-30) REVERT: B 200 LYS cc_start: 0.8441 (mttt) cc_final: 0.8161 (mttp) REVERT: B 221 ILE cc_start: 0.8322 (mp) cc_final: 0.7887 (mt) REVERT: B 300 THR cc_start: 0.8628 (m) cc_final: 0.8169 (p) REVERT: B 369 SER cc_start: 0.8390 (m) cc_final: 0.8137 (p) outliers start: 37 outliers final: 33 residues processed: 190 average time/residue: 0.3277 time to fit residues: 81.1706 Evaluate side-chains 199 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 165 time to evaluate : 1.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 46 MET Chi-restraints excluded: chain A residue 90 ASN Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain A residue 133 SER Chi-restraints excluded: chain A residue 138 ASN Chi-restraints excluded: chain A residue 244 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 A residue 394 CYS Chi-restraints excluded: chain B residue 16 ASP Chi-restraints excluded: chain B residue 39 THR Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain B residue 115 SER 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 312 MET 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 37 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 28 optimal weight: 5.9990 chunk 18 optimal weight: 0.0050 chunk 60 optimal weight: 5.9990 chunk 64 optimal weight: 2.9990 chunk 46 optimal weight: 4.9990 chunk 8 optimal weight: 0.9990 chunk 74 optimal weight: 0.0870 chunk 85 optimal weight: 8.9990 chunk 90 optimal weight: 10.0000 overall best weight: 1.2178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 366 GLN ** B 403 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.2150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11302 Z= 0.173 Angle : 0.483 7.239 16162 Z= 0.266 Chirality : 0.036 0.187 1894 Planarity : 0.003 0.029 1352 Dihedral : 21.388 93.191 3745 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 5.41 % Allowed : 22.08 % Favored : 72.51 % 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: 1.18 (0.30), residues: 797 helix: 2.74 (0.26), residues: 366 sheet: -0.43 (0.37), residues: 168 loop : -1.26 (0.38), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 43 HIS 0.002 0.000 HIS A 238 PHE 0.019 0.001 PHE B 389 TYR 0.015 0.001 TYR A 351 ARG 0.003 0.000 ARG B 254 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1594 Ramachandran restraints generated. 797 Oldfield, 0 Emsley, 797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1594 Ramachandran restraints generated. 797 Oldfield, 0 Emsley, 797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 166 time to evaluate : 0.944 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 GLU cc_start: 0.7694 (mm-30) cc_final: 0.7356 (mm-30) REVERT: A 82 LYS cc_start: 0.8487 (ttmt) cc_final: 0.8223 (ttmt) REVERT: A 130 GLU cc_start: 0.8189 (mp0) cc_final: 0.7750 (mp0) REVERT: A 258 GLU cc_start: 0.7137 (mt-10) cc_final: 0.6894 (mt-10) REVERT: A 262 ILE cc_start: 0.8378 (mt) cc_final: 0.8111 (mm) REVERT: A 311 ASP cc_start: 0.8195 (m-30) cc_final: 0.7852 (m-30) REVERT: A 344 ASP cc_start: 0.7829 (OUTLIER) cc_final: 0.7323 (m-30) REVERT: B 11 LYS cc_start: 0.8614 (pttt) cc_final: 0.8228 (pttp) REVERT: B 100 ASP cc_start: 0.7992 (m-30) cc_final: 0.7680 (m-30) REVERT: B 133 SER cc_start: 0.9105 (t) cc_final: 0.8553 (p) REVERT: B 166 ILE cc_start: 0.9009 (OUTLIER) cc_final: 0.8704 (mt) REVERT: B 174 LYS cc_start: 0.8346 (tttt) cc_final: 0.7629 (tppp) REVERT: B 178 ASP cc_start: 0.8001 (m-30) cc_final: 0.7486 (m-30) REVERT: B 200 LYS cc_start: 0.8420 (mttt) cc_final: 0.8143 (mttp) REVERT: B 221 ILE cc_start: 0.8306 (mp) cc_final: 0.7888 (mt) REVERT: B 300 THR cc_start: 0.8606 (m) cc_final: 0.8154 (p) REVERT: B 369 SER cc_start: 0.8368 (m) cc_final: 0.8083 (p) outliers start: 38 outliers final: 29 residues processed: 188 average time/residue: 0.3116 time to fit residues: 76.8240 Evaluate side-chains 197 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 166 time to evaluate : 1.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 46 MET Chi-restraints excluded: chain A residue 90 ASN Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 133 SER 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 A residue 394 CYS Chi-restraints excluded: chain B residue 16 ASP Chi-restraints excluded: chain B residue 39 THR Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain B residue 116 ILE 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 312 MET 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 82 optimal weight: 5.9990 chunk 88 optimal weight: 10.0000 chunk 90 optimal weight: 10.0000 chunk 52 optimal weight: 1.9990 chunk 38 optimal weight: 20.0000 chunk 69 optimal weight: 6.9990 chunk 27 optimal weight: 6.9990 chunk 79 optimal weight: 0.4980 chunk 83 optimal weight: 8.9990 chunk 87 optimal weight: 8.9990 chunk 57 optimal weight: 3.9990 overall best weight: 3.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 403 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.2254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 11302 Z= 0.390 Angle : 0.586 7.252 16162 Z= 0.314 Chirality : 0.041 0.187 1894 Planarity : 0.004 0.036 1352 Dihedral : 21.462 94.416 3745 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 4.70 % Allowed : 22.79 % Favored : 72.51 % 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: 0.89 (0.29), residues: 797 helix: 2.44 (0.25), residues: 366 sheet: -0.39 (0.37), residues: 166 loop : -1.43 (0.37), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 43 HIS 0.003 0.001 HIS A 238 PHE 0.021 0.002 PHE B 389 TYR 0.020 0.002 TYR A 351 ARG 0.003 0.001 ARG B 254 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1594 Ramachandran restraints generated. 797 Oldfield, 0 Emsley, 797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1594 Ramachandran restraints generated. 797 Oldfield, 0 Emsley, 797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 164 time to evaluate : 0.915 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 30 GLU cc_start: 0.7762 (mm-30) cc_final: 0.7419 (mm-30) REVERT: A 82 LYS cc_start: 0.8486 (ttmt) cc_final: 0.8242 (ttmt) REVERT: A 130 GLU cc_start: 0.8219 (mp0) cc_final: 0.7775 (mp0) REVERT: A 208 ASP cc_start: 0.7746 (m-30) cc_final: 0.7506 (m-30) REVERT: A 258 GLU cc_start: 0.7167 (mt-10) cc_final: 0.6917 (mt-10) REVERT: A 262 ILE cc_start: 0.8373 (mt) cc_final: 0.8095 (mm) REVERT: A 311 ASP cc_start: 0.8260 (m-30) cc_final: 0.7957 (m-30) REVERT: A 344 ASP cc_start: 0.7936 (OUTLIER) cc_final: 0.7429 (m-30) REVERT: B 11 LYS cc_start: 0.8748 (pttt) cc_final: 0.8262 (ptmm) REVERT: B 30 GLU cc_start: 0.7857 (tm-30) cc_final: 0.7618 (tm-30) REVERT: B 100 ASP cc_start: 0.7907 (m-30) cc_final: 0.7586 (m-30) REVERT: B 166 ILE cc_start: 0.9073 (OUTLIER) cc_final: 0.8636 (mt) REVERT: B 174 LYS cc_start: 0.8453 (tttt) cc_final: 0.7675 (tppp) REVERT: B 178 ASP cc_start: 0.8048 (m-30) cc_final: 0.7440 (m-30) REVERT: B 200 LYS cc_start: 0.8477 (mttt) cc_final: 0.8198 (mttp) REVERT: B 221 ILE cc_start: 0.8341 (mp) cc_final: 0.7992 (mt) REVERT: B 369 SER cc_start: 0.8447 (m) cc_final: 0.8176 (p) outliers start: 33 outliers final: 31 residues processed: 184 average time/residue: 0.3194 time to fit residues: 76.5162 Evaluate side-chains 195 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 162 time to evaluate : 0.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 46 MET Chi-restraints excluded: chain A residue 90 ASN Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 133 SER Chi-restraints excluded: chain A residue 244 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 A residue 394 CYS Chi-restraints excluded: chain B residue 16 ASP Chi-restraints excluded: chain B residue 39 THR Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 137 MET Chi-restraints excluded: chain B residue 166 ILE Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 210 GLU Chi-restraints excluded: chain B residue 217 ASP Chi-restraints excluded: chain B residue 224 ILE Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 312 MET 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 93 optimal weight: 7.9990 chunk 56 optimal weight: 4.9990 chunk 44 optimal weight: 1.9990 chunk 64 optimal weight: 0.9990 chunk 97 optimal weight: 7.9990 chunk 89 optimal weight: 8.9990 chunk 77 optimal weight: 0.2980 chunk 8 optimal weight: 0.6980 chunk 60 optimal weight: 4.9990 chunk 47 optimal weight: 0.8980 chunk 61 optimal weight: 0.8980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 252 ASN B 366 GLN B 407 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.2434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 11302 Z= 0.150 Angle : 0.476 8.746 16162 Z= 0.260 Chirality : 0.035 0.176 1894 Planarity : 0.003 0.031 1352 Dihedral : 21.361 92.636 3745 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 3.56 % Allowed : 23.65 % Favored : 72.79 % 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: 1.45 (0.30), residues: 797 helix: 2.91 (0.25), residues: 366 sheet: -0.13 (0.38), residues: 167 loop : -1.18 (0.38), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 43 HIS 0.002 0.001 HIS A 139 PHE 0.022 0.001 PHE B 389 TYR 0.012 0.001 TYR A 351 ARG 0.003 0.000 ARG A 291 ********************** 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 fitting. rotamer outliers: 25 poor density : 164 time to evaluate : 0.980 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 GLU cc_start: 0.7651 (mm-30) cc_final: 0.7355 (mm-30) REVERT: A 82 LYS cc_start: 0.8516 (ttmt) cc_final: 0.8232 (ttmt) REVERT: A 130 GLU cc_start: 0.8151 (mp0) cc_final: 0.7777 (mp0) REVERT: A 258 GLU cc_start: 0.7139 (mt-10) cc_final: 0.6890 (mt-10) REVERT: A 262 ILE cc_start: 0.8375 (mt) cc_final: 0.8118 (mm) REVERT: A 343 TYR cc_start: 0.8100 (t80) cc_final: 0.7703 (t80) REVERT: A 344 ASP cc_start: 0.7731 (t0) cc_final: 0.7253 (m-30) REVERT: B 100 ASP cc_start: 0.7937 (m-30) cc_final: 0.7395 (m-30) REVERT: B 133 SER cc_start: 0.9105 (t) cc_final: 0.8560 (p) REVERT: B 174 LYS cc_start: 0.8250 (tttt) cc_final: 0.7602 (tppp) REVERT: B 178 ASP cc_start: 0.7993 (m-30) cc_final: 0.7481 (m-30) REVERT: B 200 LYS cc_start: 0.8396 (mttt) cc_final: 0.8131 (mttp) REVERT: B 300 THR cc_start: 0.8597 (m) cc_final: 0.8189 (p) REVERT: B 369 SER cc_start: 0.8370 (m) cc_final: 0.8039 (p) REVERT: B 374 GLU cc_start: 0.7305 (mt-10) cc_final: 0.6906 (mt-10) outliers start: 25 outliers final: 19 residues processed: 181 average time/residue: 0.3074 time to fit residues: 72.8458 Evaluate side-chains 190 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 171 time to evaluate : 0.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 46 MET Chi-restraints excluded: chain A residue 90 ASN 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 361 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 166 ILE 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 82 optimal weight: 6.9990 chunk 23 optimal weight: 10.0000 chunk 71 optimal weight: 9.9990 chunk 11 optimal weight: 5.9990 chunk 21 optimal weight: 9.9990 chunk 77 optimal weight: 30.0000 chunk 32 optimal weight: 4.9990 chunk 79 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 14 optimal weight: 6.9990 chunk 68 optimal weight: 5.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 403 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.114361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.094699 restraints weight = 17512.462| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 1.74 r_work: 0.3116 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2976 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.2392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 11302 Z= 0.404 Angle : 0.606 8.816 16162 Z= 0.323 Chirality : 0.042 0.172 1894 Planarity : 0.004 0.036 1352 Dihedral : 21.429 94.562 3743 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 3.42 % Allowed : 23.93 % Favored : 72.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.02 (0.30), residues: 797 helix: 2.48 (0.25), residues: 366 sheet: -0.19 (0.38), residues: 166 loop : -1.37 (0.37), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 43 HIS 0.003 0.001 HIS B 238 PHE 0.021 0.002 PHE B 389 TYR 0.021 0.002 TYR A 351 ARG 0.004 0.001 ARG B 254 =============================================================================== Job complete usr+sys time: 2554.16 seconds wall clock time: 47 minutes 27.96 seconds (2847.96 seconds total)