Starting phenix.real_space_refine on Thu Jul 2 19:39:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8j1j_35926/07_2026/8j1j_35926.cif Found real_map, /net/cci-nas-00/data/ceres_data/8j1j_35926/07_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/8j1j_35926/07_2026/8j1j_35926.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8j1j_35926/07_2026/8j1j_35926.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8j1j_35926/07_2026/8j1j_35926.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8j1j_35926/07_2026/8j1j_35926.map" model { file = "/net/cci-nas-00/data/ceres_data/8j1j_35926/07_2026/8j1j_35926.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8j1j_35926/07_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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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: {'RNA': 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: 2.06, 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: 0.96 Conformation dependent library (CDL) restraints added in 197.4 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: 0.84 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: 1.57 Time building geometry restraints manager: 1.25 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: 13598 1.04 - 2.08: 797 2.08 - 3.12: 161 3.12 - 4.16: 25 4.16 - 5.20: 5 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: 5084 15.72 - 31.44: 522 31.44 - 47.15: 163 47.15 - 62.87: 90 62.87 - 78.59: 11 Dihedral angle restraints: 5870 sinusoidal: 3497 harmonic: 2373 Sorted by residual: dihedral pdb=" CA ARG A 392 " pdb=" C ARG A 392 " pdb=" N ALA A 393 " pdb=" CA ALA A 393 " ideal model delta harmonic sigma weight residual 180.00 155.41 24.59 0 5.00e+00 4.00e-02 2.42e+01 dihedral pdb=" CA ASN A 382 " pdb=" CB ASN A 382 " pdb=" CG ASN A 382 " pdb=" OD1 ASN A 382 " ideal model delta sinusoidal sigma weight residual 120.00 -172.29 -67.71 2 2.00e+01 2.50e-03 1.03e+01 dihedral pdb=" CA ASN A 87 " pdb=" CB ASN A 87 " pdb=" CG ASN A 87 " pdb=" OD1 ASN A 87 " ideal model delta sinusoidal sigma weight residual 120.00 -172.70 -67.30 2 2.00e+01 2.50e-03 1.02e+01 ... (remaining 5867 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 1167 0.035 - 0.071: 374 0.071 - 0.106: 108 0.106 - 0.141: 27 0.141 - 0.177: 3 Chirality restraints: 1679 Sorted by residual: chirality pdb=" C1' G C -68 " pdb=" O4' G C -68 " pdb=" C2' G C -68 " pdb=" N9 G C -68 " both_signs ideal model delta sigma weight residual False 2.46 2.28 0.18 2.00e-01 2.50e+01 7.79e-01 chirality pdb=" C1' G C -44 " pdb=" O4' G C -44 " pdb=" C2' G C -44 " pdb=" N9 G C -44 " both_signs ideal model delta sigma weight residual False 2.46 2.29 0.17 2.00e-01 2.50e+01 6.94e-01 chirality pdb=" C1' A C -18 " pdb=" O4' A C -18 " pdb=" C2' A C -18 " pdb=" N9 A C -18 " both_signs ideal model delta sigma weight residual False 2.46 2.31 0.15 2.00e-01 2.50e+01 5.74e-01 ... (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: 0.100 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: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.070 Find NCS groups from input model: 0.080 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:6.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.060 ------------------------------------------------------------------------------- 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= 0.297 Angle : 0.965 44.446 14598 Z= 0.434 Chirality : 0.039 0.177 1679 Planarity : 0.003 0.044 1310 Dihedral : 14.719 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 0.00428 / 0.29 (10291) covalent geometry : angle 0.56775 / 0.41 (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 : 0.175 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: 0.6204 time to fit residues: 154.1286 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 : 0.277 ------------------------------------------------------------------------------- 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: 10.0000 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: 8.9990 chunk 74 optimal weight: 10.0000 overall best weight: 5.2588 ------------------------------------------------------------------------------- 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 = 0.3529 r_free = 0.3529 target = 0.117627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.095540 restraints weight = 14892.032| |-----------------------------------------------------------------------------| r_work (start): 0.3196 rms_B_bonded: 1.77 r_work: 0.3068 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2923 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 moved from start: 0.1444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.060 10299 Z= 0.330 Angle : 0.706 16.372 14598 Z= 0.361 Chirality : 0.045 0.242 1679 Planarity : 0.005 0.039 1310 Dihedral : 15.232 75.247 2704 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.25 % Allowed : 3.88 % Favored : 95.87 % Rotamer: Outliers : 3.43 % Allowed : 15.14 % Favored : 81.43 % 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: -0.47 (0.29), residues: 799 helix: 0.79 (0.27), residues: 363 sheet: -0.38 (0.40), residues: 151 loop : -1.68 (0.33), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 25 TYR 0.023 0.002 TYR A 351 PHE 0.014 0.003 PHE A 389 TRP 0.013 0.003 TRP B 17 HIS 0.006 0.002 HIS A 238 Details of bonding type rmsd/Z covalent geometry : bond 0.00724 / 0.33 (10291) covalent geometry : angle 0.65604 / 0.36 (14586) hydrogen bonds : bond 0.06764 / 4.45 ( 465) hydrogen bonds : angle 4.44803 / 3.15 ( 1195) metal coordination : bond 0.01834 / 1.07 ( 8) metal coordination : angle 9.13325 / 6.51 ( 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 199 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 175 time to evaluate : 0.286 Fit side-chains REVERT: A 25 ARG cc_start: 0.8352 (mtp85) cc_final: 0.8115 (mpt90) REVERT: A 30 GLU cc_start: 0.8257 (mm-30) cc_final: 0.8008 (mt-10) REVERT: A 108 GLU cc_start: 0.8287 (mp0) cc_final: 0.8054 (mp0) REVERT: A 141 ASP cc_start: 0.8626 (OUTLIER) cc_final: 0.8397 (m-30) REVERT: A 222 MET cc_start: 0.9137 (ttp) cc_final: 0.8837 (ttp) REVERT: A 226 LEU cc_start: 0.8280 (OUTLIER) cc_final: 0.8036 (mt) REVERT: A 242 ARG cc_start: 0.8569 (ptp90) cc_final: 0.8118 (ptp90) REVERT: A 244 LYS cc_start: 0.8861 (pttt) cc_final: 0.8648 (pttt) REVERT: A 283 ARG cc_start: 0.8723 (tpp-160) cc_final: 0.8470 (tpt170) REVERT: A 344 ASP cc_start: 0.8100 (t0) cc_final: 0.7812 (t70) REVERT: A 377 ASN cc_start: 0.8522 (t0) cc_final: 0.7562 (p0) REVERT: B 18 LYS cc_start: 0.8434 (tttt) cc_final: 0.8149 (ttmm) REVERT: B 177 MET cc_start: 0.8368 (tpp) cc_final: 0.8123 (tpp) REVERT: B 199 ASN cc_start: 0.8472 (t0) cc_final: 0.8252 (t0) REVERT: B 208 ASP cc_start: 0.7637 (t0) cc_final: 0.7349 (t0) REVERT: B 222 MET cc_start: 0.8778 (ttp) cc_final: 0.8268 (ttt) REVERT: B 264 MET cc_start: 0.7471 (tpp) cc_final: 0.7259 (mpp) REVERT: B 316 MET cc_start: 0.8515 (mmm) cc_final: 0.8265 (mmm) REVERT: B 339 ASN cc_start: 0.8479 (t0) cc_final: 0.8226 (t0) REVERT: B 407 ASN cc_start: 0.7694 (m-40) cc_final: 0.7327 (m110) outliers start: 24 outliers final: 5 residues processed: 193 average time/residue: 0.7257 time to fit residues: 147.3144 Evaluate side-chains 179 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 172 time to evaluate : 0.290 ------------------------------------------------------------------------------- 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 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: 4.9990 chunk 15 optimal weight: 8.9990 chunk 25 optimal weight: 0.0670 chunk 84 optimal weight: 0.9990 chunk 6 optimal weight: 2.9990 chunk 47 optimal weight: 10.0000 chunk 49 optimal weight: 10.0000 chunk 33 optimal weight: 4.9990 chunk 44 optimal weight: 10.0000 chunk 67 optimal weight: 0.9980 chunk 76 optimal weight: 6.9990 overall best weight: 2.0124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 56 HIS A 204 ASN ** A 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 322 GLN B 412 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.120000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.097747 restraints weight = 14891.143| |-----------------------------------------------------------------------------| r_work (start): 0.3234 rms_B_bonded: 1.76 r_work: 0.3105 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2960 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.1744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10299 Z= 0.158 Angle : 0.572 11.380 14598 Z= 0.306 Chirality : 0.040 0.224 1679 Planarity : 0.004 0.035 1310 Dihedral : 15.102 73.859 2698 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.25 % Allowed : 3.00 % Favored : 96.75 % Rotamer: Outliers : 3.00 % Allowed : 17.86 % 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: -0.01 (0.29), residues: 799 helix: 1.34 (0.28), residues: 364 sheet: -0.24 (0.39), residues: 151 loop : -1.64 (0.33), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 25 TYR 0.015 0.001 TYR A 351 PHE 0.013 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 0.00325 / 0.16 (10291) covalent geometry : angle 0.54914 / 0.30 (14586) hydrogen bonds : bond 0.05307 / 3.53 ( 465) hydrogen bonds : angle 4.04542 / 2.86 ( 1195) metal coordination : bond 0.01056 / 0.64 ( 8) metal coordination : angle 5.66065 / 4.00 ( 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 193 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 172 time to evaluate : 0.298 Fit side-chains revert: symmetry clash REVERT: A 30 GLU cc_start: 0.8202 (mm-30) cc_final: 0.7955 (mt-10) REVERT: A 141 ASP cc_start: 0.8656 (OUTLIER) cc_final: 0.8441 (m-30) REVERT: A 242 ARG cc_start: 0.8457 (ptp90) cc_final: 0.8180 (ptp90) REVERT: A 244 LYS cc_start: 0.8873 (pttt) cc_final: 0.8661 (pttt) REVERT: A 283 ARG cc_start: 0.8684 (tpp-160) cc_final: 0.8466 (tpt170) REVERT: A 312 MET cc_start: 0.8674 (mmp) cc_final: 0.8439 (mmp) REVERT: A 344 ASP cc_start: 0.8067 (t0) cc_final: 0.7803 (t70) REVERT: A 377 ASN cc_start: 0.8504 (t0) cc_final: 0.7462 (p0) REVERT: B 71 VAL cc_start: 0.8664 (OUTLIER) cc_final: 0.8451 (p) REVERT: B 174 LYS cc_start: 0.8603 (tppp) cc_final: 0.8366 (tppp) REVERT: B 222 MET cc_start: 0.8745 (ttp) cc_final: 0.8368 (ttt) REVERT: B 242 ARG cc_start: 0.8578 (ptp-170) cc_final: 0.7786 (ptp-170) REVERT: B 316 MET cc_start: 0.8496 (mmm) cc_final: 0.8254 (mmm) REVERT: B 339 ASN cc_start: 0.8450 (t0) cc_final: 0.8181 (t0) outliers start: 21 outliers final: 5 residues processed: 183 average time/residue: 0.7758 time to fit residues: 149.1923 Evaluate side-chains 184 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 177 time to evaluate : 0.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 ASP 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 216 LEU Chi-restraints excluded: chain B residue 315 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 92 optimal weight: 9.9990 chunk 39 optimal weight: 4.9990 chunk 60 optimal weight: 3.9990 chunk 56 optimal weight: 10.0000 chunk 63 optimal weight: 4.9990 chunk 78 optimal weight: 0.5980 chunk 24 optimal weight: 9.9990 chunk 71 optimal weight: 4.9990 chunk 66 optimal weight: 8.9990 chunk 72 optimal weight: 0.8980 chunk 69 optimal weight: 1.9990 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 204 ASN B 237 GLN B 407 ASN B 412 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.119646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.097338 restraints weight = 15058.343| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 1.75 r_work: 0.3101 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2957 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 moved from start: 0.1906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 10299 Z= 0.182 Angle : 0.576 10.784 14598 Z= 0.308 Chirality : 0.040 0.221 1679 Planarity : 0.004 0.035 1310 Dihedral : 15.112 72.580 2697 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.25 % Allowed : 3.38 % Favored : 96.37 % Rotamer: Outliers : 3.43 % Allowed : 18.57 % Favored : 78.00 % 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: 0.18 (0.29), residues: 799 helix: 1.58 (0.28), residues: 363 sheet: -0.23 (0.39), residues: 151 loop : -1.62 (0.33), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 25 TYR 0.016 0.001 TYR A 351 PHE 0.008 0.002 PHE B 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 0.00386 / 0.18 (10291) covalent geometry : angle 0.55662 / 0.31 (14586) hydrogen bonds : bond 0.05050 / 3.36 ( 465) hydrogen bonds : angle 3.94934 / 2.79 ( 1195) metal coordination : bond 0.00965 / 0.55 ( 8) metal coordination : angle 5.22936 / 3.43 ( 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 196 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 172 time to evaluate : 0.316 Fit side-chains REVERT: A 16 ASP cc_start: 0.7964 (t0) cc_final: 0.7758 (t0) REVERT: A 30 GLU cc_start: 0.8127 (mm-30) cc_final: 0.7865 (mt-10) REVERT: A 242 ARG cc_start: 0.8491 (ptp90) cc_final: 0.7974 (ptp90) REVERT: A 244 LYS cc_start: 0.8852 (pttt) cc_final: 0.8637 (pttt) REVERT: A 264 MET cc_start: 0.8398 (mtt) cc_final: 0.7981 (mtp) REVERT: A 283 ARG cc_start: 0.8665 (tpp-160) cc_final: 0.8405 (tpt170) REVERT: A 344 ASP cc_start: 0.8041 (t0) cc_final: 0.7782 (t70) REVERT: A 377 ASN cc_start: 0.8494 (t0) cc_final: 0.7488 (p0) REVERT: A 419 GLU cc_start: 0.7876 (tm-30) cc_final: 0.7584 (mm-30) REVERT: B 16 ASP cc_start: 0.7734 (t0) cc_final: 0.7230 (p0) REVERT: B 222 MET cc_start: 0.8719 (ttp) cc_final: 0.8503 (ttt) REVERT: B 242 ARG cc_start: 0.8594 (ptp-170) cc_final: 0.7862 (ptp-170) REVERT: B 254 ARG cc_start: 0.8117 (OUTLIER) cc_final: 0.7524 (mtt90) REVERT: B 316 MET cc_start: 0.8529 (mmm) cc_final: 0.8269 (mmm) REVERT: B 339 ASN cc_start: 0.8466 (t0) cc_final: 0.8183 (t0) REVERT: B 364 ASP cc_start: 0.7626 (OUTLIER) cc_final: 0.7344 (m-30) REVERT: B 407 ASN cc_start: 0.7256 (m-40) cc_final: 0.6859 (m-40) outliers start: 24 outliers final: 9 residues processed: 181 average time/residue: 0.7504 time to fit residues: 142.4923 Evaluate side-chains 178 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 167 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LYS Chi-restraints excluded: chain A residue 160 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 71 VAL Chi-restraints excluded: chain B residue 208 ASP Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 254 ARG 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: 7.9990 chunk 19 optimal weight: 10.0000 chunk 27 optimal weight: 8.9990 chunk 86 optimal weight: 0.0050 chunk 28 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 52 optimal weight: 10.0000 chunk 10 optimal weight: 5.9990 overall best weight: 1.3600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 412 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.121024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.098760 restraints weight = 15025.008| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 1.77 r_work: 0.3127 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2984 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.2087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 10299 Z= 0.131 Angle : 0.530 10.244 14598 Z= 0.288 Chirality : 0.038 0.218 1679 Planarity : 0.004 0.035 1310 Dihedral : 15.058 72.232 2697 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.25 % Allowed : 3.13 % Favored : 96.62 % Rotamer: Outliers : 2.43 % Allowed : 20.57 % Favored : 77.00 % 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: 0.40 (0.30), residues: 799 helix: 1.79 (0.28), residues: 364 sheet: -0.18 (0.39), residues: 153 loop : -1.53 (0.34), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 25 TYR 0.023 0.001 TYR B 351 PHE 0.010 0.001 PHE B 389 TRP 0.009 0.001 TRP A 43 HIS 0.002 0.001 HIS A 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.13 (10291) covalent geometry : angle 0.51634 / 0.29 (14586) hydrogen bonds : bond 0.04591 / 3.07 ( 465) hydrogen bonds : angle 3.80475 / 2.69 ( 1195) metal coordination : bond 0.00775 / 0.44 ( 8) metal coordination : angle 4.19659 / 2.84 ( 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 187 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 170 time to evaluate : 0.285 Fit side-chains REVERT: A 16 ASP cc_start: 0.7940 (t0) cc_final: 0.7712 (t0) REVERT: A 44 GLU cc_start: 0.8778 (tt0) cc_final: 0.8544 (tt0) REVERT: A 242 ARG cc_start: 0.8514 (ptp90) cc_final: 0.8157 (ptp90) REVERT: A 244 LYS cc_start: 0.8872 (pttt) cc_final: 0.8627 (pttt) REVERT: A 264 MET cc_start: 0.8396 (mtt) cc_final: 0.7975 (mtp) REVERT: A 312 MET cc_start: 0.8688 (mmp) cc_final: 0.8312 (mmp) REVERT: A 344 ASP cc_start: 0.8027 (t0) cc_final: 0.7748 (t70) REVERT: A 377 ASN cc_start: 0.8441 (t0) cc_final: 0.7446 (p0) REVERT: B 16 ASP cc_start: 0.7750 (t0) cc_final: 0.7230 (p0) REVERT: B 222 MET cc_start: 0.8671 (ttp) cc_final: 0.8448 (ttt) REVERT: B 234 MET cc_start: 0.8284 (OUTLIER) cc_final: 0.7382 (mtp) REVERT: B 242 ARG cc_start: 0.8542 (ptp-170) cc_final: 0.7664 (ptp-170) REVERT: B 264 MET cc_start: 0.7592 (tpp) cc_final: 0.7277 (mpp) REVERT: B 339 ASN cc_start: 0.8478 (t0) cc_final: 0.8191 (t0) REVERT: B 407 ASN cc_start: 0.7249 (m-40) cc_final: 0.6907 (m110) outliers start: 17 outliers final: 8 residues processed: 176 average time/residue: 0.7053 time to fit residues: 130.5334 Evaluate side-chains 180 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 171 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LYS Chi-restraints excluded: chain A residue 138 ASN 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 216 LEU Chi-restraints excluded: chain B residue 234 MET Chi-restraints excluded: chain B residue 239 THR Chi-restraints excluded: chain B residue 315 LYS 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: 5.9990 chunk 58 optimal weight: 6.9990 chunk 61 optimal weight: 9.9990 chunk 70 optimal weight: 0.7980 chunk 45 optimal weight: 8.9990 chunk 66 optimal weight: 1.9990 chunk 48 optimal weight: 10.0000 chunk 23 optimal weight: 10.0000 chunk 4 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 77 HIS 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 = 0.3563 r_free = 0.3563 target = 0.119983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.097657 restraints weight = 15038.476| |-----------------------------------------------------------------------------| r_work (start): 0.3235 rms_B_bonded: 1.77 r_work: 0.3107 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2962 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.2149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 10299 Z= 0.178 Angle : 0.555 9.973 14598 Z= 0.299 Chirality : 0.039 0.214 1679 Planarity : 0.004 0.034 1310 Dihedral : 15.055 71.730 2696 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.25 % Allowed : 3.63 % Favored : 96.12 % Rotamer: Outliers : 3.00 % Allowed : 20.71 % 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: 0.50 (0.30), residues: 799 helix: 1.86 (0.28), residues: 365 sheet: -0.21 (0.38), residues: 155 loop : -1.44 (0.34), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 25 TYR 0.029 0.001 TYR B 142 PHE 0.009 0.002 PHE A 336 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 0.00376 / 0.18 (10291) covalent geometry : angle 0.54204 / 0.30 (14586) hydrogen bonds : bond 0.04721 / 3.13 ( 465) hydrogen bonds : angle 3.80230 / 2.70 ( 1195) metal coordination : bond 0.00800 / 0.47 ( 8) metal coordination : angle 4.21309 / 2.81 ( 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 192 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 171 time to evaluate : 0.234 Fit side-chains revert: symmetry clash REVERT: A 16 ASP cc_start: 0.8012 (t0) cc_final: 0.7768 (t0) REVERT: A 177 MET cc_start: 0.9013 (tpp) cc_final: 0.8593 (tpt) REVERT: A 244 LYS cc_start: 0.8886 (pttt) cc_final: 0.8651 (pttt) REVERT: A 264 MET cc_start: 0.8384 (mtt) cc_final: 0.7965 (mtp) REVERT: A 288 GLU cc_start: 0.7564 (mt-10) cc_final: 0.7128 (mt-10) REVERT: A 312 MET cc_start: 0.8694 (mmp) cc_final: 0.8153 (mmt) REVERT: A 344 ASP cc_start: 0.8026 (t0) cc_final: 0.7745 (t70) REVERT: A 377 ASN cc_start: 0.8453 (t0) cc_final: 0.7459 (p0) REVERT: B 142 TYR cc_start: 0.8071 (m-10) cc_final: 0.7739 (m-10) REVERT: B 177 MET cc_start: 0.8342 (tpp) cc_final: 0.8117 (tpp) REVERT: B 222 MET cc_start: 0.8666 (ttp) cc_final: 0.8455 (ttt) REVERT: B 234 MET cc_start: 0.8328 (OUTLIER) cc_final: 0.7349 (mtp) REVERT: B 242 ARG cc_start: 0.8573 (ptp-170) cc_final: 0.7628 (ptp-170) REVERT: B 254 ARG cc_start: 0.8061 (OUTLIER) cc_final: 0.7445 (mtt90) REVERT: B 339 ASN cc_start: 0.8486 (t0) cc_final: 0.8201 (t0) REVERT: B 407 ASN cc_start: 0.7294 (m-40) cc_final: 0.6985 (m110) outliers start: 21 outliers final: 7 residues processed: 179 average time/residue: 0.8265 time to fit residues: 155.4771 Evaluate side-chains 179 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 170 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LYS 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 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: 2.9990 chunk 25 optimal weight: 0.9990 chunk 21 optimal weight: 9.9990 chunk 13 optimal weight: 0.7980 chunk 30 optimal weight: 2.9990 chunk 88 optimal weight: 5.9990 chunk 69 optimal weight: 7.9990 chunk 19 optimal weight: 7.9990 chunk 1 optimal weight: 2.9990 chunk 93 optimal weight: 0.2980 chunk 78 optimal weight: 8.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 412 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.120966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.098712 restraints weight = 14982.474| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 1.75 r_work: 0.3123 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2979 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.2253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10299 Z= 0.140 Angle : 0.537 10.290 14598 Z= 0.292 Chirality : 0.038 0.212 1679 Planarity : 0.003 0.034 1310 Dihedral : 15.025 71.902 2696 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.25 % Allowed : 3.38 % Favored : 96.37 % Rotamer: Outliers : 2.14 % Allowed : 21.86 % Favored : 76.00 % 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: 0.57 (0.30), residues: 799 helix: 1.95 (0.28), residues: 365 sheet: -0.17 (0.38), residues: 155 loop : -1.44 (0.34), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 25 TYR 0.026 0.001 TYR B 351 PHE 0.009 0.001 PHE A 336 TRP 0.008 0.001 TRP A 43 HIS 0.003 0.001 HIS A 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.14 (10291) covalent geometry : angle 0.52704 / 0.29 (14586) hydrogen bonds : bond 0.04482 / 2.98 ( 465) hydrogen bonds : angle 3.72289 / 2.64 ( 1195) metal coordination : bond 0.00647 / 0.38 ( 8) metal coordination : angle 3.68959 / 2.43 ( 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: 15 poor density : 175 time to evaluate : 0.373 Fit side-chains REVERT: A 16 ASP cc_start: 0.7976 (t0) cc_final: 0.7725 (t0) REVERT: A 44 GLU cc_start: 0.8779 (tt0) cc_final: 0.8545 (tt0) REVERT: A 105 TYR cc_start: 0.9158 (m-80) cc_final: 0.8819 (m-80) REVERT: A 244 LYS cc_start: 0.8879 (pttt) cc_final: 0.8649 (pttt) REVERT: A 264 MET cc_start: 0.8362 (mtt) cc_final: 0.7958 (mtp) REVERT: A 288 GLU cc_start: 0.7559 (mt-10) cc_final: 0.7124 (mt-10) REVERT: A 312 MET cc_start: 0.8675 (mmp) cc_final: 0.8285 (mmp) REVERT: A 344 ASP cc_start: 0.8039 (t0) cc_final: 0.7763 (t70) REVERT: A 377 ASN cc_start: 0.8405 (t0) cc_final: 0.7480 (p0) REVERT: B 177 MET cc_start: 0.8321 (tpp) cc_final: 0.8099 (tpp) REVERT: B 187 VAL cc_start: 0.8356 (OUTLIER) cc_final: 0.8139 (m) REVERT: B 242 ARG cc_start: 0.8542 (ptp-170) cc_final: 0.7653 (ptp-170) REVERT: B 254 ARG cc_start: 0.8041 (OUTLIER) cc_final: 0.7421 (mtt90) REVERT: B 339 ASN cc_start: 0.8482 (t0) cc_final: 0.8194 (t0) REVERT: B 347 GLN cc_start: 0.8462 (OUTLIER) cc_final: 0.7827 (mp10) REVERT: B 407 ASN cc_start: 0.7397 (m-40) cc_final: 0.7154 (m110) outliers start: 15 outliers final: 7 residues processed: 182 average time/residue: 0.8243 time to fit residues: 157.8266 Evaluate side-chains 182 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 172 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LYS Chi-restraints excluded: chain A residue 239 THR 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 254 ARG Chi-restraints excluded: chain B residue 262 ILE Chi-restraints excluded: chain B residue 347 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 1 optimal weight: 3.9990 chunk 8 optimal weight: 3.9990 chunk 71 optimal weight: 0.9990 chunk 0 optimal weight: 8.9990 chunk 62 optimal weight: 5.9990 chunk 87 optimal weight: 3.9990 chunk 51 optimal weight: 10.0000 chunk 10 optimal weight: 5.9990 chunk 9 optimal weight: 5.9990 chunk 2 optimal weight: 0.9980 chunk 58 optimal weight: 6.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 399 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 = 0.3560 r_free = 0.3560 target = 0.119878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.097637 restraints weight = 15009.518| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 1.75 r_work: 0.3104 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2960 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.2290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 10299 Z= 0.194 Angle : 0.579 11.420 14598 Z= 0.309 Chirality : 0.040 0.212 1679 Planarity : 0.004 0.038 1310 Dihedral : 15.043 71.440 2696 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.25 % Allowed : 3.75 % Favored : 95.99 % Rotamer: Outliers : 2.71 % Allowed : 22.29 % Favored : 75.00 % 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: 0.54 (0.30), residues: 799 helix: 1.91 (0.28), residues: 365 sheet: -0.14 (0.38), residues: 155 loop : -1.47 (0.34), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 25 TYR 0.020 0.001 TYR B 142 PHE 0.010 0.002 PHE A 336 TRP 0.010 0.001 TRP A 340 HIS 0.004 0.001 HIS A 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00417 / 0.19 (10291) covalent geometry : angle 0.56945 / 0.31 (14586) hydrogen bonds : bond 0.04718 / 3.12 ( 465) hydrogen bonds : angle 3.77834 / 2.68 ( 1195) metal coordination : bond 0.00758 / 0.45 ( 8) metal coordination : angle 3.66269 / 2.40 ( 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 193 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 174 time to evaluate : 0.312 Fit side-chains revert: symmetry clash REVERT: A 16 ASP cc_start: 0.8014 (t0) cc_final: 0.7771 (t0) REVERT: A 105 TYR cc_start: 0.9175 (m-80) cc_final: 0.8880 (m-80) REVERT: A 242 ARG cc_start: 0.8544 (ptp90) cc_final: 0.8308 (ptp90) REVERT: A 244 LYS cc_start: 0.8880 (pttt) cc_final: 0.8632 (pttt) REVERT: A 288 GLU cc_start: 0.7578 (mt-10) cc_final: 0.7131 (mt-10) REVERT: A 312 MET cc_start: 0.8689 (mmp) cc_final: 0.8151 (mmt) REVERT: A 344 ASP cc_start: 0.8033 (t0) cc_final: 0.7739 (t70) REVERT: A 377 ASN cc_start: 0.8419 (t0) cc_final: 0.7492 (p0) REVERT: B 177 MET cc_start: 0.8367 (tpp) cc_final: 0.8156 (tpp) REVERT: B 187 VAL cc_start: 0.8394 (OUTLIER) cc_final: 0.8178 (m) REVERT: B 242 ARG cc_start: 0.8586 (ptp-170) cc_final: 0.7907 (ptp-170) REVERT: B 254 ARG cc_start: 0.8058 (OUTLIER) cc_final: 0.7439 (mtt90) REVERT: B 339 ASN cc_start: 0.8484 (t0) cc_final: 0.8203 (t0) REVERT: B 407 ASN cc_start: 0.7356 (m-40) cc_final: 0.7058 (m110) outliers start: 19 outliers final: 9 residues processed: 181 average time/residue: 0.7418 time to fit residues: 141.3996 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 : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LYS 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 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 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: 4.9990 chunk 84 optimal weight: 0.9990 chunk 92 optimal weight: 9.9990 chunk 20 optimal weight: 5.9990 chunk 44 optimal weight: 10.0000 chunk 76 optimal weight: 5.9990 chunk 65 optimal weight: 4.9990 chunk 90 optimal weight: 1.9990 chunk 43 optimal weight: 10.0000 chunk 37 optimal weight: 10.0000 chunk 8 optimal weight: 3.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 399 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 = 0.3550 r_free = 0.3550 target = 0.119179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.096938 restraints weight = 14928.096| |-----------------------------------------------------------------------------| r_work (start): 0.3222 rms_B_bonded: 1.77 r_work: 0.3093 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2948 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.2330 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= 0.221 Angle : 0.605 11.650 14598 Z= 0.322 Chirality : 0.041 0.217 1679 Planarity : 0.004 0.037 1310 Dihedral : 15.064 71.442 2696 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.25 % Allowed : 4.01 % Favored : 95.74 % Rotamer: Outliers : 2.14 % Allowed : 23.43 % 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: 0.49 (0.30), residues: 799 helix: 1.92 (0.28), residues: 365 sheet: -0.21 (0.38), residues: 155 loop : -1.54 (0.34), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 25 TYR 0.029 0.002 TYR B 351 PHE 0.011 0.002 PHE A 102 TRP 0.016 0.002 TRP A 340 HIS 0.006 0.001 HIS A 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00479 / 0.22 (10291) covalent geometry : angle 0.59594 / 0.32 (14586) hydrogen bonds : bond 0.04875 / 3.23 ( 465) hydrogen bonds : angle 3.79470 / 2.70 ( 1195) metal coordination : bond 0.00826 / 0.49 ( 8) metal coordination : angle 3.74568 / 2.42 ( 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 188 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 173 time to evaluate : 0.293 Fit side-chains revert: symmetry clash REVERT: A 16 ASP cc_start: 0.8022 (t0) cc_final: 0.7809 (t0) REVERT: A 244 LYS cc_start: 0.8851 (pttt) cc_final: 0.8626 (pttt) REVERT: A 288 GLU cc_start: 0.7583 (mt-10) cc_final: 0.7116 (mt-10) REVERT: A 312 MET cc_start: 0.8691 (mmp) cc_final: 0.8135 (mmt) REVERT: A 344 ASP cc_start: 0.8032 (t0) cc_final: 0.7746 (t70) REVERT: A 377 ASN cc_start: 0.8437 (t0) cc_final: 0.7496 (p0) REVERT: B 1 MET cc_start: 0.5576 (mmt) cc_final: 0.5325 (tpt) REVERT: B 187 VAL cc_start: 0.8422 (OUTLIER) cc_final: 0.8188 (m) REVERT: B 242 ARG cc_start: 0.8585 (ptp-170) cc_final: 0.7877 (ptp-170) REVERT: B 254 ARG cc_start: 0.8075 (OUTLIER) cc_final: 0.7460 (mtt90) REVERT: B 339 ASN cc_start: 0.8443 (t0) cc_final: 0.8141 (t0) outliers start: 15 outliers final: 9 residues processed: 179 average time/residue: 0.7546 time to fit residues: 142.0737 Evaluate side-chains 181 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 170 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LYS 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 13 LEU Chi-restraints excluded: chain B residue 187 VAL 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: 7.9990 chunk 6 optimal weight: 4.9990 chunk 61 optimal weight: 1.9990 chunk 2 optimal weight: 0.9990 chunk 90 optimal weight: 6.9990 chunk 56 optimal weight: 8.9990 chunk 27 optimal weight: 9.9990 chunk 82 optimal weight: 10.0000 chunk 8 optimal weight: 3.9990 chunk 38 optimal weight: 0.2980 chunk 29 optimal weight: 9.9990 overall best weight: 2.4588 ------------------------------------------------------------------------------- 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 = 0.3560 r_free = 0.3560 target = 0.119852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.097706 restraints weight = 14887.627| |-----------------------------------------------------------------------------| r_work (start): 0.3234 rms_B_bonded: 1.73 r_work: 0.3106 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2962 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.2387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 10299 Z= 0.177 Angle : 0.586 11.426 14598 Z= 0.313 Chirality : 0.040 0.216 1679 Planarity : 0.004 0.037 1310 Dihedral : 15.037 71.923 2696 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.25 % Allowed : 4.01 % Favored : 95.74 % Rotamer: Outliers : 2.14 % Allowed : 24.00 % Favored : 73.86 % 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: 0.53 (0.29), residues: 799 helix: 1.95 (0.28), residues: 365 sheet: -0.16 (0.38), residues: 155 loop : -1.54 (0.34), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 25 TYR 0.017 0.001 TYR B 142 PHE 0.011 0.002 PHE A 389 TRP 0.024 0.002 TRP A 340 HIS 0.004 0.001 HIS A 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.18 (10291) covalent geometry : angle 0.57804 / 0.31 (14586) hydrogen bonds : bond 0.04636 / 3.08 ( 465) hydrogen bonds : angle 3.76599 / 2.68 ( 1195) metal coordination : bond 0.00652 / 0.39 ( 8) metal coordination : angle 3.35673 / 2.21 ( 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 188 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 173 time to evaluate : 0.223 Fit side-chains REVERT: A 16 ASP cc_start: 0.8011 (t0) cc_final: 0.7758 (t70) REVERT: A 105 TYR cc_start: 0.9186 (m-80) cc_final: 0.8857 (m-80) REVERT: A 242 ARG cc_start: 0.8536 (ptp90) cc_final: 0.8311 (ptp90) REVERT: A 244 LYS cc_start: 0.8849 (pttt) cc_final: 0.8611 (pttt) REVERT: A 288 GLU cc_start: 0.7599 (mt-10) cc_final: 0.7136 (mt-10) REVERT: A 312 MET cc_start: 0.8678 (mmp) cc_final: 0.8350 (mmp) REVERT: A 344 ASP cc_start: 0.8040 (t0) cc_final: 0.7757 (t70) REVERT: A 377 ASN cc_start: 0.8428 (t0) cc_final: 0.7499 (p0) REVERT: B 1 MET cc_start: 0.5572 (mmt) cc_final: 0.5303 (tpt) REVERT: B 242 ARG cc_start: 0.8585 (ptp-170) cc_final: 0.7899 (ptp-170) REVERT: B 254 ARG cc_start: 0.8051 (OUTLIER) cc_final: 0.7430 (mtt90) REVERT: B 339 ASN cc_start: 0.8449 (t0) cc_final: 0.8150 (t0) REVERT: B 407 ASN cc_start: 0.7421 (m-40) cc_final: 0.7147 (m110) outliers start: 15 outliers final: 10 residues processed: 179 average time/residue: 0.7188 time to fit residues: 135.3092 Evaluate side-chains 182 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 171 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LYS Chi-restraints excluded: chain A residue 160 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 114 MET 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 84 optimal weight: 5.9990 chunk 25 optimal weight: 3.9990 chunk 31 optimal weight: 4.9990 chunk 53 optimal weight: 10.0000 chunk 60 optimal weight: 1.9990 chunk 45 optimal weight: 8.9990 chunk 65 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 52 optimal weight: 10.0000 chunk 59 optimal weight: 0.9980 chunk 55 optimal weight: 10.0000 overall best weight: 2.7988 ------------------------------------------------------------------------------- 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 = 0.119687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.097462 restraints weight = 15062.503| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 1.76 r_work: 0.3103 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2958 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.2423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 10299 Z= 0.194 Angle : 0.597 11.518 14598 Z= 0.319 Chirality : 0.040 0.215 1679 Planarity : 0.004 0.037 1310 Dihedral : 15.038 71.838 2696 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.25 % Allowed : 4.13 % Favored : 95.62 % Rotamer: Outliers : 1.86 % Allowed : 24.86 % Favored : 73.29 % 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: 0.51 (0.29), residues: 799 helix: 1.94 (0.28), residues: 365 sheet: -0.19 (0.38), residues: 155 loop : -1.55 (0.34), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 25 TYR 0.029 0.002 TYR B 351 PHE 0.010 0.002 PHE A 389 TRP 0.031 0.002 TRP A 340 HIS 0.005 0.001 HIS A 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00420 / 0.19 (10291) covalent geometry : angle 0.58981 / 0.32 (14586) hydrogen bonds : bond 0.04696 / 3.11 ( 465) hydrogen bonds : angle 3.77629 / 2.68 ( 1195) metal coordination : bond 0.00697 / 0.43 ( 8) metal coordination : angle 3.29933 / 2.19 ( 12) =============================================================================== Job complete usr+sys time: 3850.53 seconds wall clock time: 66 minutes 9.23 seconds (3969.23 seconds total)