Starting phenix.real_space_refine on Fri Sep 11 14:57:21 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8j1j_35926/09_2026/8j1j_35926.cif Found real_map, /net/cci-nas-00/data/ceres_data/8j1j_35926/09_2026/8j1j_35926.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.91 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8j1j_35926/09_2026/8j1j_35926.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8j1j_35926/09_2026/8j1j_35926.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8j1j_35926/09_2026/8j1j_35926.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8j1j_35926/09_2026/8j1j_35926.cif" model { file = "/net/cci-nas-00/data/ceres_data/8j1j_35926/09_2026/8j1j_35926.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8j1j_35926/09_2026/8j1j_35926.cif" } resolution = 2.91 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.010 sd= 0.077 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 151 5.49 5 Mg 2 5.21 5 S 34 5.16 5 C 5613 2.51 5 N 1771 2.21 5 O 2220 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9793 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 424, 3437 Classifications: {'peptide': 424} Link IDs: {'PTRANS': 10, 'TRANS': 413} 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: 2408 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 2408 Classifications: {'RNAv2': 112} Modifications used: {'rna2p_pur': 9, 'rna2p_pyr': 1, 'rna3p_pur': 58, 'rna3p_pyr': 44} Link IDs: {'rna2p': 10, 'rna3p': 101} Chain: "B" Number of atoms: 3150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 3150 Classifications: {'peptide': 387} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 377} Chain breaks: 4 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 3063 SG CYS A 372 89.022 57.120 33.002 1.00 89.59 S ATOM 3084 SG CYS A 375 91.419 56.554 33.615 1.00 77.07 S ATOM 3201 SG CYS A 391 90.464 58.956 36.815 1.00120.51 S ATOM 3223 SG CYS A 394 91.781 58.761 32.523 1.00109.28 S ATOM 9461 SG CYS B 372 62.724 88.689 63.390 1.00116.48 S ATOM 9482 SG CYS B 375 65.516 90.455 66.073 1.00132.46 S ATOM 9562 SG CYS B 391 65.774 89.756 62.345 1.00137.00 S ATOM 9584 SG CYS B 394 65.199 87.078 63.799 1.00140.29 S Time building chain proxies: 2.08, per 1000 atoms: 0.21 Number of scatterers: 9793 At special positions: 0 Unit cell: (103.584, 114.208, 112.88, 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 34 16.00 P 151 15.00 Mg 2 11.99 O 2220 8.00 N 1771 7.00 C 5613 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.85 Conformation dependent library (CDL) restraints added in 196.4 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 501 " pdb="ZN ZN A 501 " - pdb=" SG CYS A 375 " pdb="ZN ZN A 501 " - pdb=" SG CYS A 394 " pdb="ZN ZN A 501 " - pdb=" SG CYS A 372 " pdb="ZN ZN A 501 " - pdb=" SG CYS A 391 " pdb=" ZN B 501 " pdb="ZN ZN B 501 " - pdb=" SG CYS B 375 " pdb="ZN ZN B 501 " - pdb=" SG CYS B 394 " pdb="ZN ZN B 501 " - pdb=" SG CYS B 391 " pdb="ZN ZN B 501 " - pdb=" SG CYS B 372 " Number of angles added : 12 1598 Ramachandran restraints generated. 799 Oldfield, 0 Emsley, 799 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1518 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 10 sheets defined 47.3% alpha, 15.8% beta 55 base pairs and 101 stacking pairs defined. Time for finding SS restraints: 1.13 Creating SS restraints... Processing helix chain 'A' and resid 16 through 57 removed outlier: 3.650A pdb=" N THR A 22 " --> pdb=" O LYS A 18 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ARG A 32 " --> pdb=" O GLN A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 61 through 66 Processing helix chain 'A' and resid 70 through 80 removed outlier: 3.722A pdb=" N TYR A 74 " --> pdb=" O ASN A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 105 removed outlier: 3.516A pdb=" N ALA A 98 " --> pdb=" O THR A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 111 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 155 Processing helix chain 'A' and resid 171 through 181 removed outlier: 3.713A pdb=" N THR A 175 " --> pdb=" O GLY A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 268 removed outlier: 4.060A pdb=" N ARG A 260 " --> pdb=" O GLN A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 271 No H-bonds generated for 'chain 'A' and resid 269 through 271' Processing helix chain 'A' and resid 272 through 276 Processing helix chain 'A' and resid 278 through 284 removed outlier: 3.961A pdb=" N LYS A 282 " --> pdb=" O HIS A 278 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ARG A 283 " --> pdb=" O GLY A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 291 removed outlier: 3.951A pdb=" N GLN A 289 " --> pdb=" O PRO A 286 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ARG A 291 " --> pdb=" O GLU A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 316 Processing helix chain 'A' and resid 326 through 329 Processing helix chain 'A' and resid 341 through 355 removed outlier: 3.643A pdb=" N GLU A 355 " --> pdb=" O TYR A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 409 removed outlier: 4.009A pdb=" N ILE A 408 " --> pdb=" O ALA A 404 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ALA A 409 " --> pdb=" O ALA A 405 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 404 through 409' Processing helix chain 'A' and resid 412 through 419 removed outlier: 3.731A pdb=" N ALA A 418 " --> pdb=" O ASP A 414 " (cutoff:3.500A) Processing helix chain 'B' and resid 16 through 46 Processing helix chain 'B' and resid 50 through 55 removed outlier: 3.604A pdb=" N ASN B 55 " --> pdb=" O TYR B 52 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 through 81 removed outlier: 4.239A pdb=" N THR B 81 " --> pdb=" O HIS B 77 " (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 150 through 158 removed outlier: 3.533A pdb=" N GLU B 156 " --> pdb=" O PRO B 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 171 through 183 removed outlier: 3.577A pdb=" N THR B 175 " --> pdb=" O GLY B 171 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ARG B 179 " --> pdb=" O THR B 175 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N SER B 182 " --> pdb=" O ASP B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 264 Processing helix chain 'B' and resid 286 through 315 Processing helix chain 'B' and resid 341 through 354 removed outlier: 4.054A pdb=" N TYR B 351 " --> pdb=" O GLN B 347 " (cutoff:3.500A) Processing helix chain 'B' and resid 400 through 410 Processing helix chain 'B' and resid 412 through 421 removed outlier: 3.641A pdb=" N ILE B 416 " --> pdb=" O ASN B 412 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N SER B 420 " --> pdb=" O ILE B 416 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 5 Processing sheet with id=AA2, first strand: chain 'A' and resid 2 through 5 Processing sheet with id=AA3, first strand: chain 'A' and resid 9 through 12 removed outlier: 6.692A pdb=" N ILE A 166 " --> pdb=" O VAL A 10 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N SER A 164 " --> pdb=" O PRO A 12 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N TYR A 142 " --> pdb=" O ILE A 167 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 242 through 245 removed outlier: 3.630A pdb=" N ALA A 232 " --> pdb=" O LEU A 245 " (cutoff:3.500A) removed outlier: 4.303A 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 390 removed outlier: 3.653A pdb=" N ALA A 398 " --> pdb=" O PHE A 389 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 2 through 3 removed outlier: 6.748A pdb=" N ASN B 204 " --> pdb=" O SER B 190 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N SER B 190 " --> pdb=" O ASN B 204 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N SER B 206 " --> pdb=" O HIS B 188 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 9 through 12 removed outlier: 6.703A pdb=" N ILE B 166 " --> pdb=" O VAL B 10 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N SER B 164 " --> pdb=" O PRO B 12 " (cutoff:3.500A) removed outlier: 4.981A pdb=" N TYR B 142 " --> pdb=" O ILE B 167 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ASP B 141 " --> pdb=" O MET B 137 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 194 through 195 Processing sheet with id=AA9, first strand: chain 'B' and resid 242 through 245 removed outlier: 8.784A pdb=" N CYS B 318 " --> pdb=" O LEU B 218 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N LYS B 220 " --> pdb=" O CYS B 318 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N THR B 320 " --> pdb=" O LYS B 220 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 388 through 390 331 hydrogen bonds defined for protein. 939 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 138 hydrogen bonds 256 hydrogen bond angles 0 basepair planarities 55 basepair parallelities 101 stacking parallelities Total time for adding SS restraints: 2.23 Time building geometry restraints manager: 1.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2576 1.33 - 1.46: 2782 1.46 - 1.58: 4576 1.58 - 1.70: 299 1.70 - 1.82: 58 Bond restraints: 10291 Sorted by residual: bond pdb=" C3' DC D 10 " pdb=" C2' DC D 10 " ideal model delta sigma weight residual 1.516 1.538 -0.022 8.00e-03 1.56e+04 7.64e+00 bond pdb=" C3' DT D 14 " pdb=" C2' DT D 14 " ideal model delta sigma weight residual 1.516 1.536 -0.020 8.00e-03 1.56e+04 6.53e+00 bond pdb=" C3' DA E -5 " pdb=" C2' DA E -5 " ideal model delta sigma weight residual 1.516 1.536 -0.020 8.00e-03 1.56e+04 6.29e+00 bond pdb=" C ARG B 170 " pdb=" N GLY B 171 " ideal model delta sigma weight residual 1.335 1.316 0.018 7.50e-03 1.78e+04 5.95e+00 bond pdb=" O4' DT D 14 " pdb=" C1' DT D 14 " ideal model delta sigma weight residual 1.420 1.394 0.026 1.10e-02 8.26e+03 5.78e+00 ... (remaining 10286 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.04: 13226 1.04 - 2.08: 908 2.08 - 3.12: 368 3.12 - 4.16: 61 4.16 - 5.20: 23 Bond angle restraints: 14586 Sorted by residual: angle pdb=" N ILE A 284 " pdb=" CA ILE A 284 " pdb=" C ILE A 284 " ideal model delta sigma weight residual 112.29 107.22 5.07 9.40e-01 1.13e+00 2.91e+01 angle pdb=" O4' DC D 18 " pdb=" C4' DC D 18 " pdb=" C3' DC D 18 " ideal model delta sigma weight residual 106.00 103.06 2.94 6.00e-01 2.78e+00 2.40e+01 angle pdb=" N3 DT D 19 " pdb=" C4 DT D 19 " pdb=" O4 DT D 19 " ideal model delta sigma weight residual 119.90 122.54 -2.64 6.00e-01 2.78e+00 1.94e+01 angle pdb=" N3 DT D 11 " pdb=" C4 DT D 11 " pdb=" O4 DT D 11 " ideal model delta sigma weight residual 119.90 122.43 -2.53 6.00e-01 2.78e+00 1.77e+01 angle pdb=" O4 DT D 19 " pdb=" C4 DT D 19 " pdb=" C5 DT D 19 " ideal model delta sigma weight residual 124.90 121.98 2.92 7.00e-01 2.04e+00 1.74e+01 ... (remaining 14581 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.72: 4940 15.72 - 31.44: 534 31.44 - 47.15: 228 47.15 - 62.87: 148 62.87 - 78.59: 20 Dihedral angle restraints: 5870 sinusoidal: 3497 harmonic: 2373 Sorted by residual: dihedral pdb=" C4' G C -43 " pdb=" C3' G C -43 " pdb=" C2' G C -43 " pdb=" C1' G C -43 " ideal model delta sinusoidal sigma weight residual 36.35 -36.37 72.71 1 3.10e+00 1.04e-01 7.02e+02 dihedral pdb=" C4' G C 0 " pdb=" C3' G C 0 " pdb=" C2' G C 0 " pdb=" C1' G C 0 " ideal model delta sinusoidal sigma weight residual 36.34 -36.34 72.68 1 3.10e+00 1.04e-01 7.02e+02 dihedral pdb=" C4' A C -74 " pdb=" C3' A C -74 " pdb=" C2' A C -74 " pdb=" C1' A C -74 " ideal model delta sinusoidal sigma weight residual 36.34 -36.08 72.43 1 3.10e+00 1.04e-01 6.97e+02 ... (remaining 5867 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 1333 0.058 - 0.116: 201 0.116 - 0.174: 12 0.174 - 0.232: 95 0.232 - 0.290: 38 Chirality restraints: 1679 Sorted by residual: chirality pdb=" C2' G C -43 " pdb=" C3' G C -43 " pdb=" O2' G C -43 " pdb=" C1' G C -43 " both_signs ideal model delta sigma weight residual False -2.79 -2.50 -0.29 2.00e-01 2.50e+01 2.11e+00 chirality pdb=" C3' G C 0 " pdb=" C4' G C 0 " pdb=" O3' G C 0 " pdb=" C2' G C 0 " both_signs ideal model delta sigma weight residual False -2.50 -2.79 0.29 2.00e-01 2.50e+01 2.07e+00 chirality pdb=" C2' A C -57 " pdb=" C3' A C -57 " pdb=" O2' A C -57 " pdb=" C1' A C -57 " both_signs ideal model delta sigma weight residual False -2.79 -2.50 -0.29 2.00e-01 2.50e+01 2.05e+00 ... (remaining 1676 not shown) Planarity restraints: 1310 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G C -44 " -0.034 2.00e-02 2.50e+03 1.49e-02 6.64e+00 pdb=" N9 G C -44 " 0.037 2.00e-02 2.50e+03 pdb=" C8 G C -44 " 0.003 2.00e-02 2.50e+03 pdb=" N7 G C -44 " -0.002 2.00e-02 2.50e+03 pdb=" C5 G C -44 " -0.000 2.00e-02 2.50e+03 pdb=" C6 G C -44 " -0.002 2.00e-02 2.50e+03 pdb=" O6 G C -44 " -0.009 2.00e-02 2.50e+03 pdb=" N1 G C -44 " -0.003 2.00e-02 2.50e+03 pdb=" C2 G C -44 " 0.000 2.00e-02 2.50e+03 pdb=" N2 G C -44 " 0.001 2.00e-02 2.50e+03 pdb=" N3 G C -44 " 0.005 2.00e-02 2.50e+03 pdb=" C4 G C -44 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G C -68 " -0.028 2.00e-02 2.50e+03 1.18e-02 4.21e+00 pdb=" N9 G C -68 " 0.028 2.00e-02 2.50e+03 pdb=" C8 G C -68 " 0.004 2.00e-02 2.50e+03 pdb=" N7 G C -68 " 0.001 2.00e-02 2.50e+03 pdb=" C5 G C -68 " -0.001 2.00e-02 2.50e+03 pdb=" C6 G C -68 " -0.005 2.00e-02 2.50e+03 pdb=" O6 G C -68 " -0.007 2.00e-02 2.50e+03 pdb=" N1 G C -68 " -0.002 2.00e-02 2.50e+03 pdb=" C2 G C -68 " 0.000 2.00e-02 2.50e+03 pdb=" N2 G C -68 " 0.005 2.00e-02 2.50e+03 pdb=" N3 G C -68 " 0.001 2.00e-02 2.50e+03 pdb=" C4 G C -68 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE B 123 " 0.029 5.00e-02 4.00e+02 4.37e-02 3.06e+00 pdb=" N PRO B 124 " -0.076 5.00e-02 4.00e+02 pdb=" CA PRO B 124 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 124 " 0.024 5.00e-02 4.00e+02 ... (remaining 1307 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1588 2.76 - 3.30: 8613 3.30 - 3.83: 17692 3.83 - 4.37: 22088 4.37 - 4.90: 32757 Nonbonded interactions: 82738 Sorted by model distance: nonbonded pdb=" OP1 U C -41 " pdb=" NZ LYS B 103 " model vdw 2.228 3.120 nonbonded pdb=" O2' A C -54 " pdb=" OG SER B 92 " model vdw 2.248 3.040 nonbonded pdb=" NE2 GLN A 28 " pdb=" OD1 ASP A 122 " model vdw 2.266 3.120 nonbonded pdb=" NH1 ARG A 298 " pdb=" OP1 DA D 12 " model vdw 2.275 3.120 nonbonded pdb=" OG SER A 150 " pdb=" OP1 DT E -4 " model vdw 2.304 3.040 ... (remaining 82733 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 58 or resid 65 through 224 or (resid 225 and (na \ me N or name CA or name C or name O or name CB )) or resid 226 through 265 or re \ sid 285 through 326 or resid 331 through 379 or resid 385 through 421 or resid 5 \ 01)) 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: 0.090 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: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 12.710 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.010 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:9.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 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 : 0.005 0.100 10299 Z= 0.302 Angle : 1.053 44.446 14598 Z= 0.457 Chirality : 0.076 0.290 1679 Planarity : 0.003 0.044 1310 Dihedral : 17.127 78.587 4352 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.25 % Allowed : 2.88 % Favored : 96.87 % Rotamer: Outliers : 1.43 % Allowed : 6.71 % Favored : 91.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.23 (0.28), residues: 799 helix: -0.19 (0.26), residues: 362 sheet: -0.51 (0.42), residues: 151 loop : -1.66 (0.34), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 260 TYR 0.014 0.001 TYR A 52 PHE 0.009 0.002 PHE A 102 TRP 0.010 0.001 TRP B 43 HIS 0.006 0.001 HIS A 238 Details of bonding type rmsd/Z covalent geometry : bond 0.00443 / 0.30 (10291) covalent geometry : angle 0.70724 / 0.43 (14586) hydrogen bonds : bond 0.21352 / 13.52 ( 465) hydrogen bonds : angle 7.08989 / 4.97 ( 1195) metal coordination : bond 0.06495 / 3.84 ( 8) metal coordination : angle 27.21350 / 17.96 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1598 Ramachandran restraints generated. 799 Oldfield, 0 Emsley, 799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1598 Ramachandran restraints generated. 799 Oldfield, 0 Emsley, 799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 225 time to evaluate : 0.243 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 25 ARG cc_start: 0.8200 (mtp85) cc_final: 0.7892 (mpt90) REVERT: A 61 LYS cc_start: 0.8395 (mmtt) cc_final: 0.8128 (mptm) REVERT: A 87 ASN cc_start: 0.8819 (OUTLIER) cc_final: 0.8581 (t0) REVERT: A 108 GLU cc_start: 0.8340 (mp0) cc_final: 0.8056 (mp0) REVERT: A 129 LYS cc_start: 0.8605 (ttpt) cc_final: 0.8390 (ttpp) REVERT: A 174 LYS cc_start: 0.8731 (tttt) cc_final: 0.8398 (tttm) REVERT: A 178 ASP cc_start: 0.8808 (m-30) cc_final: 0.8531 (m-30) REVERT: A 222 MET cc_start: 0.9140 (ttp) cc_final: 0.8881 (ttp) REVERT: A 244 LYS cc_start: 0.8702 (pttt) cc_final: 0.8496 (pttt) REVERT: A 264 MET cc_start: 0.8490 (mtt) cc_final: 0.8186 (mtm) REVERT: A 312 MET cc_start: 0.8735 (mmp) cc_final: 0.7680 (mmt) REVERT: A 325 ASP cc_start: 0.8452 (t0) cc_final: 0.8161 (t70) REVERT: A 344 ASP cc_start: 0.8200 (t0) cc_final: 0.7899 (t70) REVERT: A 377 ASN cc_start: 0.8300 (t0) cc_final: 0.7044 (p0) REVERT: A 412 ASN cc_start: 0.8074 (m-40) cc_final: 0.7732 (p0) REVERT: B 18 LYS cc_start: 0.8399 (tttt) cc_final: 0.8199 (tttt) REVERT: B 26 GLN cc_start: 0.8543 (mt0) cc_final: 0.8170 (mt0) REVERT: B 29 GLN cc_start: 0.8380 (mm-40) cc_final: 0.8119 (mm-40) REVERT: B 71 VAL cc_start: 0.8937 (OUTLIER) cc_final: 0.8727 (p) REVERT: B 177 MET cc_start: 0.8347 (tpp) cc_final: 0.7888 (tpp) REVERT: B 199 ASN cc_start: 0.8373 (t0) cc_final: 0.8129 (t0) REVERT: B 208 ASP cc_start: 0.7571 (t0) cc_final: 0.7267 (t0) REVERT: B 222 MET cc_start: 0.8748 (ttp) cc_final: 0.8345 (ttt) REVERT: B 242 ARG cc_start: 0.8415 (ptp-170) cc_final: 0.8174 (ptp-170) REVERT: B 249 GLU cc_start: 0.8283 (pm20) cc_final: 0.8037 (pm20) REVERT: B 263 SER cc_start: 0.8550 (m) cc_final: 0.8330 (t) REVERT: B 306 SER cc_start: 0.8526 (m) cc_final: 0.8124 (p) REVERT: B 316 MET cc_start: 0.8328 (mmm) cc_final: 0.8006 (mmm) REVERT: B 339 ASN cc_start: 0.8424 (t0) cc_final: 0.8174 (t0) REVERT: B 351 TYR cc_start: 0.7885 (t80) cc_final: 0.7674 (t80) REVERT: B 364 ASP cc_start: 0.7420 (OUTLIER) cc_final: 0.7159 (m-30) outliers start: 10 outliers final: 2 residues processed: 235 average time/residue: 0.7140 time to fit residues: 177.3067 Evaluate side-chains 188 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 183 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 239 THR Chi-restraints excluded: chain B residue 364 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 49 optimal weight: 8.9990 chunk 53 optimal weight: 10.0000 chunk 5 optimal weight: 6.9990 chunk 33 optimal weight: 0.2980 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 6.9990 chunk 51 optimal weight: 10.0000 chunk 38 optimal weight: 9.9990 chunk 61 optimal weight: 7.9990 chunk 45 optimal weight: 6.9990 chunk 74 optimal weight: 10.0000 overall best weight: 5.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 87 ASN A 131 ASN A 186 GLN A 204 ASN A 322 GLN A 339 ASN A 346 GLN B 77 HIS B 252 ASN B 296 ASN B 377 ASN B 403 ASN B 412 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.118089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.096099 restraints weight = 14909.993| |-----------------------------------------------------------------------------| r_work (start): 0.3203 rms_B_bonded: 1.75 r_work: 0.3075 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2930 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 moved from start: 0.1600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.059 10299 Z= 0.337 Angle : 1.058 16.563 14598 Z= 0.474 Chirality : 0.086 1.173 1679 Planarity : 0.005 0.069 1310 Dihedral : 17.865 139.541 2704 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.25 % Allowed : 3.75 % Favored : 95.99 % Rotamer: Outliers : 3.57 % Allowed : 14.71 % Favored : 81.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.45 (0.29), residues: 799 helix: 0.83 (0.27), residues: 363 sheet: -0.38 (0.40), residues: 151 loop : -1.69 (0.33), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 406 TYR 0.020 0.002 TYR A 351 PHE 0.014 0.003 PHE B 20 TRP 0.014 0.002 TRP B 17 HIS 0.009 0.002 HIS A 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00736 / 0.34 (10291) covalent geometry : angle 1.02575 / 0.47 (14586) hydrogen bonds : bond 0.06596 / 4.35 ( 465) hydrogen bonds : angle 4.43760 / 3.14 ( 1195) metal coordination : bond 0.01904 / 1.14 ( 8) metal coordination : angle 9.15379 / 6.53 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1598 Ramachandran restraints generated. 799 Oldfield, 0 Emsley, 799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1598 Ramachandran restraints generated. 799 Oldfield, 0 Emsley, 799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 175 time to evaluate : 0.296 Fit side-chains REVERT: A 25 ARG cc_start: 0.8353 (mtp85) cc_final: 0.8119 (mpt90) REVERT: A 30 GLU cc_start: 0.8217 (mm-30) cc_final: 0.8009 (mt-10) REVERT: A 108 GLU cc_start: 0.8296 (mp0) cc_final: 0.8068 (mp0) REVERT: A 141 ASP cc_start: 0.8622 (OUTLIER) cc_final: 0.8398 (m-30) REVERT: A 222 MET cc_start: 0.9146 (ttp) cc_final: 0.8854 (ttp) REVERT: A 226 LEU cc_start: 0.8277 (OUTLIER) cc_final: 0.8051 (mt) REVERT: A 242 ARG cc_start: 0.8559 (ptp90) cc_final: 0.8108 (ptp90) REVERT: A 244 LYS cc_start: 0.8864 (pttt) cc_final: 0.8656 (pttt) REVERT: A 283 ARG cc_start: 0.8739 (tpp-160) cc_final: 0.8470 (tpt170) REVERT: A 344 ASP cc_start: 0.8108 (t0) cc_final: 0.7818 (t70) REVERT: A 377 ASN cc_start: 0.8516 (t0) cc_final: 0.7574 (p0) REVERT: A 419 GLU cc_start: 0.7700 (mm-30) cc_final: 0.7428 (mm-30) REVERT: B 18 LYS cc_start: 0.8432 (tttt) cc_final: 0.8161 (ttmm) REVERT: B 177 MET cc_start: 0.8381 (tpp) cc_final: 0.8110 (tpp) REVERT: B 199 ASN cc_start: 0.8475 (t0) cc_final: 0.8247 (t0) REVERT: B 208 ASP cc_start: 0.7641 (t0) cc_final: 0.7388 (t0) REVERT: B 222 MET cc_start: 0.8785 (ttp) cc_final: 0.8269 (ttt) REVERT: B 316 MET cc_start: 0.8519 (mmm) cc_final: 0.8266 (mmm) REVERT: B 339 ASN cc_start: 0.8473 (t0) cc_final: 0.8217 (t0) REVERT: B 407 ASN cc_start: 0.7693 (m-40) cc_final: 0.7334 (m110) outliers start: 25 outliers final: 6 residues processed: 194 average time/residue: 0.7928 time to fit residues: 161.7972 Evaluate side-chains 179 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 171 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 ASP Chi-restraints excluded: chain A residue 160 LYS Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain B residue 17 TRP Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 239 THR Chi-restraints excluded: chain B residue 325 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 62 optimal weight: 0.7980 chunk 15 optimal weight: 7.9990 chunk 25 optimal weight: 1.9990 chunk 84 optimal weight: 0.9990 chunk 6 optimal weight: 3.9990 chunk 47 optimal weight: 6.9990 chunk 49 optimal weight: 7.9990 chunk 33 optimal weight: 3.9990 chunk 44 optimal weight: 10.0000 chunk 67 optimal weight: 4.9990 chunk 76 optimal weight: 9.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 56 HIS A 70 ASN A 204 ASN ** A 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 237 GLN B 252 ASN B 412 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.120054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.098077 restraints weight = 14953.690| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 1.73 r_work: 0.3112 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2970 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 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 : 0.004 0.034 10299 Z= 0.192 Angle : 0.826 11.829 14598 Z= 0.383 Chirality : 0.069 0.911 1679 Planarity : 0.004 0.046 1310 Dihedral : 18.055 157.827 2698 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.25 % Allowed : 3.13 % Favored : 96.62 % Rotamer: Outliers : 3.43 % Allowed : 17.43 % Favored : 79.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.03 (0.29), residues: 799 helix: 1.31 (0.28), residues: 364 sheet: -0.24 (0.40), residues: 151 loop : -1.66 (0.33), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 406 TYR 0.016 0.001 TYR A 351 PHE 0.011 0.002 PHE A 389 TRP 0.010 0.001 TRP A 43 HIS 0.004 0.001 HIS A 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00404 / 0.19 (10291) covalent geometry : angle 0.80963 / 0.38 (14586) hydrogen bonds : bond 0.05638 / 3.69 ( 465) hydrogen bonds : angle 4.06061 / 2.87 ( 1195) metal coordination : bond 0.01090 / 0.65 ( 8) metal coordination : angle 5.77393 / 4.04 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1598 Ramachandran restraints generated. 799 Oldfield, 0 Emsley, 799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1598 Ramachandran restraints generated. 799 Oldfield, 0 Emsley, 799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 174 time to evaluate : 0.187 Fit side-chains revert: symmetry clash REVERT: A 25 ARG cc_start: 0.8326 (mtp85) cc_final: 0.8123 (mpt90) REVERT: A 30 GLU cc_start: 0.8165 (mm-30) cc_final: 0.7931 (mt-10) REVERT: A 141 ASP cc_start: 0.8637 (OUTLIER) cc_final: 0.8425 (m-30) REVERT: A 222 MET cc_start: 0.9078 (ttp) cc_final: 0.8855 (ttp) REVERT: A 242 ARG cc_start: 0.8452 (ptp90) cc_final: 0.8118 (ptp90) REVERT: A 244 LYS cc_start: 0.8850 (pttt) cc_final: 0.8623 (pttt) REVERT: A 283 ARG cc_start: 0.8699 (tpp-160) cc_final: 0.8386 (tpt170) REVERT: A 344 ASP cc_start: 0.8063 (t0) cc_final: 0.7808 (t70) REVERT: A 377 ASN cc_start: 0.8487 (t0) cc_final: 0.7476 (p0) REVERT: A 419 GLU cc_start: 0.7560 (mm-30) cc_final: 0.7198 (mm-30) REVERT: B 71 VAL cc_start: 0.8661 (OUTLIER) cc_final: 0.8450 (p) REVERT: B 222 MET cc_start: 0.8764 (ttp) cc_final: 0.8410 (ttt) REVERT: B 242 ARG cc_start: 0.8495 (ptp-170) cc_final: 0.7896 (ptp-170) REVERT: B 316 MET cc_start: 0.8506 (mmm) cc_final: 0.8263 (mmm) REVERT: B 339 ASN cc_start: 0.8434 (t0) cc_final: 0.8154 (t0) outliers start: 24 outliers final: 6 residues processed: 187 average time/residue: 0.7803 time to fit residues: 153.2714 Evaluate side-chains 179 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 171 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 ASP Chi-restraints excluded: chain A residue 160 LYS Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 370 GLN Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 114 MET Chi-restraints excluded: chain B residue 216 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 92 optimal weight: 4.9990 chunk 39 optimal weight: 0.8980 chunk 60 optimal weight: 3.9990 chunk 56 optimal weight: 9.9990 chunk 63 optimal weight: 5.9990 chunk 78 optimal weight: 3.9990 chunk 24 optimal weight: 5.9990 chunk 71 optimal weight: 3.9990 chunk 66 optimal weight: 0.1980 chunk 72 optimal weight: 5.9990 chunk 69 optimal weight: 2.9990 overall best weight: 2.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 70 ASN A 77 HIS A 204 ASN B 407 ASN B 412 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.120209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.098225 restraints weight = 15042.881| |-----------------------------------------------------------------------------| r_work (start): 0.3243 rms_B_bonded: 1.73 r_work: 0.3116 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2972 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.2170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 10299 Z= 0.192 Angle : 0.798 11.151 14598 Z= 0.370 Chirality : 0.064 0.710 1679 Planarity : 0.004 0.038 1310 Dihedral : 17.975 163.524 2697 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.25 % Allowed : 3.38 % Favored : 96.37 % Rotamer: Outliers : 3.86 % Allowed : 18.43 % Favored : 77.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.16 (0.29), residues: 799 helix: 1.59 (0.28), residues: 362 sheet: -0.27 (0.39), residues: 157 loop : -1.66 (0.33), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 406 TYR 0.016 0.001 TYR A 351 PHE 0.010 0.002 PHE A 389 TRP 0.011 0.001 TRP A 43 HIS 0.004 0.001 HIS A 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00409 / 0.19 (10291) covalent geometry : angle 0.78237 / 0.37 (14586) hydrogen bonds : bond 0.05249 / 3.47 ( 465) hydrogen bonds : angle 3.92346 / 2.78 ( 1195) metal coordination : bond 0.00947 / 0.54 ( 8) metal coordination : angle 5.59681 / 3.56 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1598 Ramachandran restraints generated. 799 Oldfield, 0 Emsley, 799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1598 Ramachandran restraints generated. 799 Oldfield, 0 Emsley, 799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 172 time to evaluate : 0.292 Fit side-chains REVERT: A 14 ASP cc_start: 0.8691 (OUTLIER) cc_final: 0.8445 (t70) REVERT: A 30 GLU cc_start: 0.8134 (mm-30) cc_final: 0.7888 (mt-10) REVERT: A 222 MET cc_start: 0.9132 (ttp) cc_final: 0.8897 (ttp) REVERT: A 242 ARG cc_start: 0.8498 (ptp90) cc_final: 0.8093 (ptp90) REVERT: A 244 LYS cc_start: 0.8849 (pttt) cc_final: 0.8627 (pttt) REVERT: A 266 ARG cc_start: 0.8195 (OUTLIER) cc_final: 0.7988 (mtt180) REVERT: A 344 ASP cc_start: 0.8055 (t0) cc_final: 0.7798 (t70) REVERT: A 377 ASN cc_start: 0.8486 (t0) cc_final: 0.7462 (p0) REVERT: B 16 ASP cc_start: 0.7738 (t0) cc_final: 0.7241 (p0) REVERT: B 177 MET cc_start: 0.8222 (tpt) cc_final: 0.7985 (tpp) REVERT: B 222 MET cc_start: 0.8761 (ttp) cc_final: 0.8536 (ttt) REVERT: B 242 ARG cc_start: 0.8592 (ptp-170) cc_final: 0.7863 (ptp-170) REVERT: B 254 ARG cc_start: 0.8102 (OUTLIER) cc_final: 0.7486 (mtt90) REVERT: B 316 MET cc_start: 0.8531 (mmm) cc_final: 0.8278 (mmm) REVERT: B 339 ASN cc_start: 0.8452 (t0) cc_final: 0.8173 (t0) REVERT: B 364 ASP cc_start: 0.7634 (OUTLIER) cc_final: 0.7339 (m-30) REVERT: B 407 ASN cc_start: 0.7302 (m-40) cc_final: 0.6866 (m-40) outliers start: 27 outliers final: 9 residues processed: 182 average time/residue: 0.8299 time to fit residues: 158.5033 Evaluate side-chains 181 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 168 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 ASP Chi-restraints excluded: chain A residue 61 LYS Chi-restraints excluded: chain A residue 174 LYS Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 266 ARG Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 370 GLN Chi-restraints excluded: chain B residue 208 ASP Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 239 THR Chi-restraints excluded: chain B residue 254 ARG Chi-restraints excluded: chain B residue 315 LYS Chi-restraints excluded: chain B residue 364 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 70 optimal weight: 4.9990 chunk 35 optimal weight: 0.7980 chunk 83 optimal weight: 8.9990 chunk 19 optimal weight: 9.9990 chunk 27 optimal weight: 8.9990 chunk 86 optimal weight: 0.4980 chunk 28 optimal weight: 10.0000 chunk 32 optimal weight: 8.9990 chunk 31 optimal weight: 3.9990 chunk 52 optimal weight: 10.0000 chunk 10 optimal weight: 5.9990 overall best weight: 3.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 70 ASN B 194 HIS B 412 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.119585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.097564 restraints weight = 15019.560| |-----------------------------------------------------------------------------| r_work (start): 0.3233 rms_B_bonded: 1.73 r_work: 0.3107 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2964 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 moved from start: 0.2314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 10299 Z= 0.226 Angle : 0.802 10.967 14598 Z= 0.374 Chirality : 0.063 0.710 1679 Planarity : 0.004 0.036 1310 Dihedral : 18.019 169.895 2696 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.25 % Allowed : 3.75 % Favored : 95.99 % Rotamer: Outliers : 3.43 % Allowed : 20.29 % Favored : 76.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.25 (0.29), residues: 799 helix: 1.67 (0.28), residues: 364 sheet: -0.30 (0.38), residues: 157 loop : -1.59 (0.34), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 170 TYR 0.032 0.001 TYR B 142 PHE 0.010 0.002 PHE A 102 TRP 0.011 0.001 TRP A 43 HIS 0.005 0.001 HIS A 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00487 / 0.23 (10291) covalent geometry : angle 0.79131 / 0.37 (14586) hydrogen bonds : bond 0.05313 / 3.49 ( 465) hydrogen bonds : angle 3.91159 / 2.77 ( 1195) metal coordination : bond 0.00970 / 0.57 ( 8) metal coordination : angle 4.69524 / 3.11 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1598 Ramachandran restraints generated. 799 Oldfield, 0 Emsley, 799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1598 Ramachandran restraints generated. 799 Oldfield, 0 Emsley, 799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 176 time to evaluate : 0.247 Fit side-chains revert: symmetry clash REVERT: A 14 ASP cc_start: 0.8679 (OUTLIER) cc_final: 0.8436 (t70) REVERT: A 177 MET cc_start: 0.9045 (tpp) cc_final: 0.8458 (tpt) REVERT: A 222 MET cc_start: 0.9103 (ttp) cc_final: 0.8895 (ttp) REVERT: A 234 MET cc_start: 0.8987 (mtp) cc_final: 0.8785 (mtp) REVERT: A 244 LYS cc_start: 0.8852 (pttt) cc_final: 0.8635 (pttt) REVERT: A 344 ASP cc_start: 0.8057 (t0) cc_final: 0.7795 (t70) REVERT: A 377 ASN cc_start: 0.8474 (t0) cc_final: 0.7483 (p0) REVERT: A 419 GLU cc_start: 0.7798 (tm-30) cc_final: 0.7595 (mp0) REVERT: B 16 ASP cc_start: 0.7808 (t0) cc_final: 0.7354 (p0) REVERT: B 222 MET cc_start: 0.8741 (ttp) cc_final: 0.8539 (ttt) REVERT: B 234 MET cc_start: 0.8377 (OUTLIER) cc_final: 0.7298 (mtp) REVERT: B 242 ARG cc_start: 0.8592 (ptp-170) cc_final: 0.7912 (ptp-170) REVERT: B 254 ARG cc_start: 0.8072 (OUTLIER) cc_final: 0.7468 (mtt90) REVERT: B 316 MET cc_start: 0.8550 (mmm) cc_final: 0.8299 (mmm) REVERT: B 339 ASN cc_start: 0.8459 (t0) cc_final: 0.8169 (t0) REVERT: B 407 ASN cc_start: 0.7221 (m-40) cc_final: 0.6938 (m110) outliers start: 24 outliers final: 10 residues processed: 184 average time/residue: 0.8399 time to fit residues: 162.0821 Evaluate side-chains 184 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 171 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 ASP Chi-restraints excluded: chain A residue 61 LYS Chi-restraints excluded: chain A residue 160 LYS Chi-restraints excluded: chain A residue 174 LYS Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 299 ASP Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 370 GLN Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 234 MET Chi-restraints excluded: chain B residue 254 ARG Chi-restraints excluded: chain B residue 262 ILE Chi-restraints excluded: chain B residue 325 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 53 optimal weight: 10.0000 chunk 3 optimal weight: 2.9990 chunk 58 optimal weight: 5.9990 chunk 61 optimal weight: 8.9990 chunk 70 optimal weight: 0.0870 chunk 45 optimal weight: 6.9990 chunk 66 optimal weight: 0.8980 chunk 48 optimal weight: 9.9990 chunk 23 optimal weight: 0.9980 chunk 4 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 overall best weight: 1.5962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 70 ASN B 412 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.121224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.099217 restraints weight = 15041.154| |-----------------------------------------------------------------------------| r_work (start): 0.3263 rms_B_bonded: 1.74 r_work: 0.3137 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2994 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.2461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10299 Z= 0.150 Angle : 0.748 10.618 14598 Z= 0.350 Chirality : 0.060 0.620 1679 Planarity : 0.004 0.034 1310 Dihedral : 18.022 175.230 2696 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.25 % Allowed : 3.38 % Favored : 96.37 % Rotamer: Outliers : 2.86 % Allowed : 21.86 % Favored : 75.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.47 (0.30), residues: 799 helix: 1.87 (0.28), residues: 365 sheet: -0.25 (0.38), residues: 157 loop : -1.49 (0.34), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 25 TYR 0.027 0.001 TYR B 142 PHE 0.011 0.002 PHE A 389 TRP 0.010 0.001 TRP A 43 HIS 0.003 0.001 HIS A 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.15 (10291) covalent geometry : angle 0.73988 / 0.35 (14586) hydrogen bonds : bond 0.04874 / 3.23 ( 465) hydrogen bonds : angle 3.77954 / 2.67 ( 1195) metal coordination : bond 0.00739 / 0.42 ( 8) metal coordination : angle 3.92029 / 2.65 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1598 Ramachandran restraints generated. 799 Oldfield, 0 Emsley, 799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1598 Ramachandran restraints generated. 799 Oldfield, 0 Emsley, 799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 174 time to evaluate : 0.305 Fit side-chains REVERT: A 14 ASP cc_start: 0.8663 (OUTLIER) cc_final: 0.8426 (t70) REVERT: A 44 GLU cc_start: 0.8768 (tt0) cc_final: 0.8545 (tt0) REVERT: A 242 ARG cc_start: 0.8488 (ptp90) cc_final: 0.8264 (ptp90) REVERT: A 244 LYS cc_start: 0.8880 (pttt) cc_final: 0.8631 (pttt) REVERT: A 344 ASP cc_start: 0.8037 (t0) cc_final: 0.7768 (t70) REVERT: A 377 ASN cc_start: 0.8412 (t0) cc_final: 0.7466 (p0) REVERT: B 187 VAL cc_start: 0.8336 (OUTLIER) cc_final: 0.8125 (m) REVERT: B 222 MET cc_start: 0.8673 (ttp) cc_final: 0.8472 (ttt) REVERT: B 234 MET cc_start: 0.8290 (OUTLIER) cc_final: 0.7286 (mtp) REVERT: B 242 ARG cc_start: 0.8583 (ptp-170) cc_final: 0.7946 (ptp-170) REVERT: B 254 ARG cc_start: 0.8024 (OUTLIER) cc_final: 0.7413 (mtt90) REVERT: B 339 ASN cc_start: 0.8461 (t0) cc_final: 0.8155 (t0) REVERT: B 407 ASN cc_start: 0.7370 (m-40) cc_final: 0.7111 (m110) outliers start: 20 outliers final: 7 residues processed: 185 average time/residue: 0.8339 time to fit residues: 162.2154 Evaluate side-chains 184 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 173 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 ASP Chi-restraints excluded: chain A residue 18 LYS Chi-restraints excluded: chain A residue 174 LYS Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 370 GLN Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 234 MET Chi-restraints excluded: chain B residue 239 THR Chi-restraints excluded: chain B residue 254 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 92 optimal weight: 0.6980 chunk 25 optimal weight: 1.9990 chunk 21 optimal weight: 0.2980 chunk 13 optimal weight: 7.9990 chunk 30 optimal weight: 5.9990 chunk 88 optimal weight: 6.9990 chunk 69 optimal weight: 0.0070 chunk 19 optimal weight: 6.9990 chunk 1 optimal weight: 1.9990 chunk 93 optimal weight: 0.9990 chunk 78 optimal weight: 8.9990 overall best weight: 0.8002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 70 ASN B 399 ASN B 412 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.123293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.101318 restraints weight = 14943.776| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 1.73 r_work: 0.3166 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3023 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.2671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10299 Z= 0.131 Angle : 0.741 10.741 14598 Z= 0.347 Chirality : 0.059 0.579 1679 Planarity : 0.004 0.058 1310 Dihedral : 18.043 178.359 2696 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.25 % Allowed : 3.38 % Favored : 96.37 % Rotamer: Outliers : 2.00 % Allowed : 23.57 % Favored : 74.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.66 (0.30), residues: 799 helix: 1.99 (0.28), residues: 366 sheet: -0.12 (0.39), residues: 155 loop : -1.37 (0.35), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.001 ARG A 280 TYR 0.024 0.001 TYR B 142 PHE 0.013 0.001 PHE A 389 TRP 0.009 0.001 TRP A 340 HIS 0.002 0.001 HIS B 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.13 (10291) covalent geometry : angle 0.73462 / 0.35 (14586) hydrogen bonds : bond 0.04663 / 3.08 ( 465) hydrogen bonds : angle 3.71524 / 2.63 ( 1195) metal coordination : bond 0.00583 / 0.33 ( 8) metal coordination : angle 3.57522 / 2.33 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1598 Ramachandran restraints generated. 799 Oldfield, 0 Emsley, 799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1598 Ramachandran restraints generated. 799 Oldfield, 0 Emsley, 799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 176 time to evaluate : 0.314 Fit side-chains REVERT: A 14 ASP cc_start: 0.8652 (OUTLIER) cc_final: 0.8418 (t70) REVERT: A 105 TYR cc_start: 0.9131 (m-80) cc_final: 0.8806 (m-80) REVERT: A 244 LYS cc_start: 0.8885 (pttt) cc_final: 0.8630 (pttt) REVERT: A 284 ILE cc_start: 0.7801 (OUTLIER) cc_final: 0.7427 (mt) REVERT: A 288 GLU cc_start: 0.7534 (mt-10) cc_final: 0.7099 (mt-10) REVERT: A 344 ASP cc_start: 0.7996 (t0) cc_final: 0.7698 (t70) REVERT: A 377 ASN cc_start: 0.8302 (t0) cc_final: 0.7459 (p0) REVERT: A 419 GLU cc_start: 0.7976 (tm-30) cc_final: 0.7391 (mm-30) REVERT: B 187 VAL cc_start: 0.8339 (OUTLIER) cc_final: 0.8120 (m) REVERT: B 242 ARG cc_start: 0.8541 (ptp-170) cc_final: 0.7673 (ptp-170) REVERT: B 338 GLN cc_start: 0.8408 (mm110) cc_final: 0.8161 (mm110) REVERT: B 339 ASN cc_start: 0.8470 (t0) cc_final: 0.8162 (t0) REVERT: B 407 ASN cc_start: 0.7414 (m-40) cc_final: 0.7155 (m110) outliers start: 14 outliers final: 7 residues processed: 184 average time/residue: 0.8061 time to fit residues: 156.1792 Evaluate side-chains 185 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 175 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 ASP Chi-restraints excluded: chain A residue 138 ASN Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 208 ASP Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 239 THR Chi-restraints excluded: chain B residue 262 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 1 optimal weight: 1.9990 chunk 8 optimal weight: 5.9990 chunk 71 optimal weight: 4.9990 chunk 0 optimal weight: 7.9990 chunk 62 optimal weight: 7.9990 chunk 87 optimal weight: 0.0970 chunk 51 optimal weight: 10.0000 chunk 10 optimal weight: 5.9990 chunk 9 optimal weight: 0.8980 chunk 2 optimal weight: 2.9990 chunk 58 optimal weight: 6.9990 overall best weight: 2.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 70 ASN B 399 ASN B 412 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.121878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.099814 restraints weight = 14978.446| |-----------------------------------------------------------------------------| r_work (start): 0.3268 rms_B_bonded: 1.74 r_work: 0.3141 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2997 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.2683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 10299 Z= 0.177 Angle : 0.758 11.372 14598 Z= 0.355 Chirality : 0.059 0.606 1679 Planarity : 0.005 0.107 1310 Dihedral : 18.060 178.234 2696 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.25 % Allowed : 3.50 % Favored : 96.25 % Rotamer: Outliers : 2.14 % Allowed : 24.14 % Favored : 73.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.71 (0.30), residues: 799 helix: 2.03 (0.28), residues: 365 sheet: -0.11 (0.38), residues: 155 loop : -1.33 (0.35), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG A 280 TYR 0.034 0.001 TYR B 142 PHE 0.012 0.002 PHE A 389 TRP 0.011 0.001 TRP A 340 HIS 0.004 0.001 HIS A 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.18 (10291) covalent geometry : angle 0.75215 / 0.35 (14586) hydrogen bonds : bond 0.04805 / 3.17 ( 465) hydrogen bonds : angle 3.74641 / 2.66 ( 1195) metal coordination : bond 0.00670 / 0.40 ( 8) metal coordination : angle 3.44827 / 2.23 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1598 Ramachandran restraints generated. 799 Oldfield, 0 Emsley, 799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1598 Ramachandran restraints generated. 799 Oldfield, 0 Emsley, 799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 176 time to evaluate : 0.304 Fit side-chains REVERT: A 14 ASP cc_start: 0.8669 (OUTLIER) cc_final: 0.8438 (t70) REVERT: A 105 TYR cc_start: 0.9164 (m-80) cc_final: 0.8873 (m-80) REVERT: A 242 ARG cc_start: 0.8527 (ptp90) cc_final: 0.8282 (ptp90) REVERT: A 244 LYS cc_start: 0.8875 (pttt) cc_final: 0.8649 (pttt) REVERT: A 288 GLU cc_start: 0.7519 (mt-10) cc_final: 0.7085 (mt-10) REVERT: A 344 ASP cc_start: 0.8037 (t0) cc_final: 0.7743 (t70) REVERT: A 377 ASN cc_start: 0.8310 (t0) cc_final: 0.7470 (p0) REVERT: B 170 ARG cc_start: 0.7974 (ptm-80) cc_final: 0.7590 (ptm-80) REVERT: B 242 ARG cc_start: 0.8588 (ptp-170) cc_final: 0.8097 (ptp-170) REVERT: B 254 ARG cc_start: 0.8027 (OUTLIER) cc_final: 0.7415 (mtt90) REVERT: B 339 ASN cc_start: 0.8486 (t0) cc_final: 0.8161 (t0) REVERT: B 407 ASN cc_start: 0.7466 (m-40) cc_final: 0.7208 (m110) outliers start: 15 outliers final: 9 residues processed: 184 average time/residue: 0.8351 time to fit residues: 161.5945 Evaluate side-chains 185 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 174 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 VAL Chi-restraints excluded: chain A residue 14 ASP Chi-restraints excluded: chain A residue 174 LYS Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 370 GLN Chi-restraints excluded: chain B residue 208 ASP Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 239 THR Chi-restraints excluded: chain B residue 254 ARG Chi-restraints excluded: chain B residue 262 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 70 optimal weight: 5.9990 chunk 84 optimal weight: 2.9990 chunk 92 optimal weight: 9.9990 chunk 20 optimal weight: 6.9990 chunk 44 optimal weight: 20.0000 chunk 76 optimal weight: 5.9990 chunk 65 optimal weight: 5.9990 chunk 90 optimal weight: 2.9990 chunk 43 optimal weight: 10.0000 chunk 37 optimal weight: 10.0000 chunk 8 optimal weight: 3.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 70 ASN B 399 ASN B 412 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.119291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.097313 restraints weight = 14918.511| |-----------------------------------------------------------------------------| r_work (start): 0.3225 rms_B_bonded: 1.72 r_work: 0.3098 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2954 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8518 moved from start: 0.2676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 10299 Z= 0.285 Angle : 0.836 11.602 14598 Z= 0.392 Chirality : 0.063 0.685 1679 Planarity : 0.005 0.093 1310 Dihedral : 18.113 175.696 2696 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.25 % Allowed : 4.01 % Favored : 95.74 % Rotamer: Outliers : 2.14 % Allowed : 24.86 % Favored : 73.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.47 (0.30), residues: 799 helix: 1.81 (0.28), residues: 364 sheet: -0.16 (0.38), residues: 155 loop : -1.43 (0.34), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.001 ARG A 280 TYR 0.028 0.002 TYR B 142 PHE 0.013 0.002 PHE A 102 TRP 0.019 0.002 TRP A 340 HIS 0.008 0.002 HIS A 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00627 / 0.28 (10291) covalent geometry : angle 0.82832 / 0.39 (14586) hydrogen bonds : bond 0.05449 / 3.59 ( 465) hydrogen bonds : angle 3.89988 / 2.77 ( 1195) metal coordination : bond 0.00971 / 0.59 ( 8) metal coordination : angle 3.99137 / 2.60 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1598 Ramachandran restraints generated. 799 Oldfield, 0 Emsley, 799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1598 Ramachandran restraints generated. 799 Oldfield, 0 Emsley, 799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 179 time to evaluate : 0.310 Fit side-chains REVERT: A 14 ASP cc_start: 0.8683 (OUTLIER) cc_final: 0.8454 (t70) REVERT: A 105 TYR cc_start: 0.9193 (m-80) cc_final: 0.8887 (m-80) REVERT: A 244 LYS cc_start: 0.8881 (pttt) cc_final: 0.8653 (pttt) REVERT: A 288 GLU cc_start: 0.7591 (mt-10) cc_final: 0.7169 (mt-10) REVERT: A 344 ASP cc_start: 0.8058 (t0) cc_final: 0.7788 (t70) REVERT: A 377 ASN cc_start: 0.8441 (t0) cc_final: 0.7519 (p0) REVERT: B 170 ARG cc_start: 0.7910 (ptm-80) cc_final: 0.7659 (ptm-80) REVERT: B 221 ILE cc_start: 0.8750 (mm) cc_final: 0.8521 (mm) REVERT: B 242 ARG cc_start: 0.8503 (ptp-170) cc_final: 0.7747 (ptp-170) REVERT: B 254 ARG cc_start: 0.8064 (OUTLIER) cc_final: 0.7459 (mtt90) REVERT: B 339 ASN cc_start: 0.8488 (t0) cc_final: 0.8140 (t0) outliers start: 15 outliers final: 9 residues processed: 186 average time/residue: 0.8413 time to fit residues: 164.4321 Evaluate side-chains 183 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 172 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 VAL Chi-restraints excluded: chain A residue 14 ASP Chi-restraints excluded: chain A residue 160 LYS Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 312 MET Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 370 GLN Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 239 THR Chi-restraints excluded: chain B residue 254 ARG Chi-restraints excluded: chain B residue 262 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 86 optimal weight: 8.9990 chunk 6 optimal weight: 5.9990 chunk 61 optimal weight: 4.9990 chunk 2 optimal weight: 1.9990 chunk 90 optimal weight: 9.9990 chunk 56 optimal weight: 3.9990 chunk 27 optimal weight: 8.9990 chunk 82 optimal weight: 10.0000 chunk 8 optimal weight: 0.6980 chunk 38 optimal weight: 6.9990 chunk 29 optimal weight: 10.0000 overall best weight: 3.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 70 ASN B 399 ASN B 412 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.119748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.097764 restraints weight = 14907.664| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 1.74 r_work: 0.3107 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2963 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.2711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 10299 Z= 0.241 Angle : 0.812 11.311 14598 Z= 0.382 Chirality : 0.062 0.659 1679 Planarity : 0.005 0.107 1310 Dihedral : 18.092 175.992 2696 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.25 % Allowed : 4.01 % Favored : 95.74 % Rotamer: Outliers : 1.86 % Allowed : 25.43 % Favored : 72.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.43 (0.30), residues: 799 helix: 1.79 (0.28), residues: 364 sheet: -0.24 (0.38), residues: 157 loop : -1.44 (0.34), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG A 280 TYR 0.029 0.002 TYR B 351 PHE 0.012 0.002 PHE A 102 TRP 0.027 0.002 TRP A 340 HIS 0.006 0.001 HIS A 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00528 / 0.24 (10291) covalent geometry : angle 0.80490 / 0.38 (14586) hydrogen bonds : bond 0.05196 / 3.42 ( 465) hydrogen bonds : angle 3.87127 / 2.75 ( 1195) metal coordination : bond 0.00856 / 0.51 ( 8) metal coordination : angle 3.75384 / 2.41 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1598 Ramachandran restraints generated. 799 Oldfield, 0 Emsley, 799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1598 Ramachandran restraints generated. 799 Oldfield, 0 Emsley, 799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 172 time to evaluate : 0.310 Fit side-chains REVERT: A 14 ASP cc_start: 0.8698 (m-30) cc_final: 0.8470 (t70) REVERT: A 105 TYR cc_start: 0.9198 (m-80) cc_final: 0.8896 (m-80) REVERT: A 242 ARG cc_start: 0.8577 (ptp90) cc_final: 0.8049 (ptp90) REVERT: A 244 LYS cc_start: 0.8852 (pttt) cc_final: 0.8627 (pttt) REVERT: A 288 GLU cc_start: 0.7557 (mt-10) cc_final: 0.7149 (mt-10) REVERT: A 344 ASP cc_start: 0.8104 (t0) cc_final: 0.7845 (t70) REVERT: A 377 ASN cc_start: 0.8441 (t0) cc_final: 0.7507 (p0) REVERT: B 136 ARG cc_start: 0.8270 (ttt-90) cc_final: 0.8069 (ttt-90) REVERT: B 242 ARG cc_start: 0.8493 (ptp-170) cc_final: 0.7748 (ptp-170) REVERT: B 254 ARG cc_start: 0.8058 (OUTLIER) cc_final: 0.7448 (mtt90) REVERT: B 338 GLN cc_start: 0.8377 (mm110) cc_final: 0.8124 (mm110) REVERT: B 339 ASN cc_start: 0.8493 (t0) cc_final: 0.8144 (t0) outliers start: 13 outliers final: 7 residues processed: 178 average time/residue: 0.8307 time to fit residues: 155.2031 Evaluate side-chains 183 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 175 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 LYS Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 312 MET Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 370 GLN Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 239 THR Chi-restraints excluded: chain B residue 254 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 84 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 31 optimal weight: 0.8980 chunk 53 optimal weight: 10.0000 chunk 60 optimal weight: 2.9990 chunk 45 optimal weight: 6.9990 chunk 65 optimal weight: 1.9990 chunk 28 optimal weight: 9.9990 chunk 52 optimal weight: 10.0000 chunk 59 optimal weight: 0.8980 chunk 55 optimal weight: 10.0000 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 70 ASN B 399 ASN B 412 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.122526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.100544 restraints weight = 15035.808| |-----------------------------------------------------------------------------| r_work (start): 0.3279 rms_B_bonded: 1.74 r_work: 0.3154 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3011 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.2864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10299 Z= 0.148 Angle : 0.774 12.007 14598 Z= 0.366 Chirality : 0.059 0.581 1679 Planarity : 0.004 0.078 1310 Dihedral : 18.050 178.604 2696 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.25 % Allowed : 3.50 % Favored : 96.25 % Rotamer: Outliers : 1.71 % Allowed : 26.00 % Favored : 72.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.62 (0.30), residues: 799 helix: 1.96 (0.27), residues: 363 sheet: -0.21 (0.39), residues: 155 loop : -1.31 (0.35), residues: 281 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG A 280 TYR 0.021 0.001 TYR B 142 PHE 0.012 0.001 PHE A 389 TRP 0.032 0.002 TRP A 340 HIS 0.003 0.001 HIS B 194 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.15 (10291) covalent geometry : angle 0.76932 / 0.37 (14586) hydrogen bonds : bond 0.04743 / 3.13 ( 465) hydrogen bonds : angle 3.79521 / 2.68 ( 1195) metal coordination : bond 0.00487 / 0.28 ( 8) metal coordination : angle 2.94868 / 1.92 ( 12) =============================================================================== Job complete usr+sys time: 4238.18 seconds wall clock time: 72 minutes 52.94 seconds (4372.94 seconds total)