Starting phenix.real_space_refine on Sat Aug 23 05:19:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8j1j_35926/08_2025/8j1j_35926.cif Found real_map, /net/cci-nas-00/data/ceres_data/8j1j_35926/08_2025/8j1j_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 { model { file = "/net/cci-nas-00/data/ceres_data/8j1j_35926/08_2025/8j1j_35926.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8j1j_35926/08_2025/8j1j_35926.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8j1j_35926/08_2025/8j1j_35926.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8j1j_35926/08_2025/8j1j_35926.map" } 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-2.0-5787/lib/python3.9/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: 2.88, per 1000 atoms: 0.29 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: 1.14 Conformation dependent library (CDL) restraints added in 278.7 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 1.48 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: 2.07 Time building geometry restraints manager: 1.36 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=" 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=" C LYS B 285 " pdb=" N PRO B 286 " ideal model delta sigma weight residual 1.335 1.358 -0.023 1.30e-02 5.92e+03 3.18e+00 bond pdb=" O4' DT D 14 " pdb=" C1' DT D 14 " ideal model delta sigma weight residual 1.414 1.394 0.020 2.00e-02 2.50e+03 1.05e+00 bond pdb=" N TYR A 270 " pdb=" CA TYR A 270 " ideal model delta sigma weight residual 1.464 1.452 0.012 1.36e-02 5.41e+03 7.72e-01 bond pdb=" CB VAL A 10 " pdb=" CG2 VAL A 10 " ideal model delta sigma weight residual 1.521 1.492 0.029 3.30e-02 9.18e+02 7.60e-01 ... (remaining 10286 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.04: 13761 1.04 - 2.08: 687 2.08 - 3.12: 110 3.12 - 4.16: 23 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=" N SER A 0 " pdb=" CA SER A 0 " pdb=" CB SER A 0 " ideal model delta sigma weight residual 114.17 110.22 3.95 1.14e+00 7.69e-01 1.20e+01 angle pdb=" N GLU A 156 " pdb=" CA GLU A 156 " pdb=" C GLU A 156 " ideal model delta sigma weight residual 113.43 109.32 4.11 1.26e+00 6.30e-01 1.06e+01 angle pdb=" N VAL A 71 " pdb=" CA VAL A 71 " pdb=" C VAL A 71 " ideal model delta sigma weight residual 112.50 108.20 4.30 1.39e+00 5.18e-01 9.55e+00 angle pdb=" N LYS B 198 " pdb=" CA LYS B 198 " pdb=" C LYS B 198 " ideal model delta sigma weight residual 114.39 110.30 4.09 1.45e+00 4.76e-01 7.94e+00 ... (remaining 14581 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.72: 5205 15.72 - 31.44: 567 31.44 - 47.15: 232 47.15 - 62.87: 163 62.87 - 78.59: 87 Dihedral angle restraints: 6254 sinusoidal: 3881 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 6251 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 1194 0.035 - 0.071: 379 0.071 - 0.106: 80 0.106 - 0.141: 23 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: 0.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 14.090 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 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 : 0.004 0.100 10299 Z= 0.198 Angle : 0.944 44.446 14598 Z= 0.354 Chirality : 0.038 0.177 1679 Planarity : 0.003 0.044 1310 Dihedral : 18.679 78.587 4736 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 aren 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 covalent geometry : bond 0.00386 (10291) covalent geometry : angle 0.53078 (14586) hydrogen bonds : bond 0.21352 ( 465) hydrogen bonds : angle 7.08989 ( 1195) metal coordination : bond 0.06495 ( 8) metal coordination : angle 27.21350 ( 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 : 0.319 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: 0.8400 (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: 0.8138 time to fit residues: 201.4293 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 : 0.326 ------------------------------------------------------------------------------- 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: 7.9990 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: 5.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 HIS A 87 ASN A 131 ASN A 186 GLN A 204 ASN A 322 GLN A 339 ASN 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 = 0.3519 r_free = 0.3519 target = 0.116906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.094782 restraints weight = 14976.340| |-----------------------------------------------------------------------------| r_work (start): 0.3186 rms_B_bonded: 1.78 r_work: 0.3058 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2913 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.1639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.061 10299 Z= 0.345 Angle : 0.680 15.738 14598 Z= 0.349 Chirality : 0.044 0.237 1679 Planarity : 0.005 0.036 1310 Dihedral : 20.550 73.877 3088 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.25 % Allowed : 4.01 % Favored : 95.74 % Rotamer: Outliers : 3.43 % Allowed : 15.57 % Favored : 81.00 % 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 aren not related in a simple way. whole: -0.46 (0.29), residues: 799 helix: 0.87 (0.28), residues: 363 sheet: -0.43 (0.40), residues: 151 loop : -1.75 (0.32), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 406 TYR 0.022 0.002 TYR A 351 PHE 0.018 0.003 PHE A 102 TRP 0.016 0.002 TRP B 43 HIS 0.008 0.002 HIS A 72 Details of bonding type rmsd covalent geometry : bond 0.00763 (10291) covalent geometry : angle 0.63252 (14586) hydrogen bonds : bond 0.06301 ( 465) hydrogen bonds : angle 4.34113 ( 1195) metal coordination : bond 0.01780 ( 8) metal coordination : angle 8.77356 ( 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 196 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 172 time to evaluate : 0.321 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 16 ASP cc_start: 0.8091 (t0) cc_final: 0.7879 (t70) REVERT: A 25 ARG cc_start: 0.8292 (mtp85) cc_final: 0.8063 (mpt90) REVERT: A 30 GLU cc_start: 0.8218 (mm-30) cc_final: 0.7951 (mt-10) REVERT: A 141 ASP cc_start: 0.8648 (OUTLIER) cc_final: 0.8439 (m-30) REVERT: A 177 MET cc_start: 0.9066 (tpp) cc_final: 0.8662 (tpt) REVERT: A 221 ILE cc_start: 0.8938 (mt) cc_final: 0.8716 (mp) REVERT: A 222 MET cc_start: 0.9112 (ttp) cc_final: 0.8853 (ttp) REVERT: A 242 ARG cc_start: 0.8528 (ptp90) cc_final: 0.8188 (ptp90) REVERT: A 244 LYS cc_start: 0.8862 (pttt) cc_final: 0.8647 (pttt) REVERT: A 264 MET cc_start: 0.8399 (mtt) cc_final: 0.8068 (mtp) REVERT: A 283 ARG cc_start: 0.8695 (tpp-160) cc_final: 0.8462 (tpt170) REVERT: A 344 ASP cc_start: 0.8101 (t0) cc_final: 0.7800 (t70) REVERT: A 377 ASN cc_start: 0.8567 (t0) cc_final: 0.7597 (p0) REVERT: B 199 ASN cc_start: 0.8495 (t0) cc_final: 0.8254 (t0) REVERT: B 208 ASP cc_start: 0.7606 (t0) cc_final: 0.7380 (t0) REVERT: B 222 MET cc_start: 0.8718 (ttp) cc_final: 0.8341 (ttt) REVERT: B 264 MET cc_start: 0.7524 (tpp) cc_final: 0.7264 (mpp) REVERT: B 316 MET cc_start: 0.8536 (mmm) cc_final: 0.8298 (mmm) REVERT: B 339 ASN cc_start: 0.8455 (t0) cc_final: 0.8203 (t0) REVERT: B 407 ASN cc_start: 0.7683 (m-40) cc_final: 0.7281 (m110) outliers start: 24 outliers final: 6 residues processed: 190 average time/residue: 0.8736 time to fit residues: 174.2088 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 : 0.325 ------------------------------------------------------------------------------- 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 B residue 71 VAL Chi-restraints excluded: chain B residue 239 THR Chi-restraints excluded: chain B residue 262 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 62 optimal weight: 0.9990 chunk 15 optimal weight: 0.9980 chunk 25 optimal weight: 0.8980 chunk 84 optimal weight: 0.9980 chunk 6 optimal weight: 1.9990 chunk 47 optimal weight: 10.0000 chunk 49 optimal weight: 10.0000 chunk 33 optimal weight: 4.9990 chunk 44 optimal weight: 4.9990 chunk 67 optimal weight: 0.9990 chunk 76 optimal weight: 5.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 131 ASN A 204 ASN B 139 HIS B 412 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.122035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.099982 restraints weight = 14960.176| |-----------------------------------------------------------------------------| r_work (start): 0.3273 rms_B_bonded: 1.76 r_work: 0.3149 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3006 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.2080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10299 Z= 0.123 Angle : 0.528 10.820 14598 Z= 0.284 Chirality : 0.037 0.223 1679 Planarity : 0.004 0.034 1310 Dihedral : 20.355 73.848 3082 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.25 % Allowed : 2.75 % Favored : 97.00 % Rotamer: Outliers : 3.00 % Allowed : 18.29 % Favored : 78.71 % 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 aren not related in a simple way. whole: 0.16 (0.30), residues: 799 helix: 1.57 (0.28), residues: 364 sheet: -0.27 (0.40), residues: 157 loop : -1.65 (0.34), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 406 TYR 0.018 0.001 TYR B 351 PHE 0.018 0.002 PHE A 389 TRP 0.011 0.001 TRP B 17 HIS 0.002 0.001 HIS B 72 Details of bonding type rmsd covalent geometry : bond 0.00258 (10291) covalent geometry : angle 0.51735 (14586) hydrogen bonds : bond 0.04440 ( 465) hydrogen bonds : angle 3.80445 ( 1195) metal coordination : bond 0.00717 ( 8) metal coordination : angle 3.65964 ( 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 195 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 174 time to evaluate : 0.325 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 16 ASP cc_start: 0.7973 (t0) cc_final: 0.7737 (t70) REVERT: A 221 ILE cc_start: 0.8930 (mt) cc_final: 0.8698 (mp) REVERT: A 244 LYS cc_start: 0.8857 (pttt) cc_final: 0.8615 (pttt) REVERT: A 324 GLU cc_start: 0.8318 (mt-10) cc_final: 0.7957 (mp0) REVERT: A 344 ASP cc_start: 0.8011 (t0) cc_final: 0.7717 (t70) REVERT: A 354 GLU cc_start: 0.8080 (OUTLIER) cc_final: 0.7851 (mp0) REVERT: A 377 ASN cc_start: 0.8301 (t0) cc_final: 0.7465 (p0) REVERT: B 199 ASN cc_start: 0.8584 (t0) cc_final: 0.8240 (t0) REVERT: B 242 ARG cc_start: 0.8557 (ptp-170) cc_final: 0.7642 (ptp-170) REVERT: B 339 ASN cc_start: 0.8496 (t0) cc_final: 0.8225 (t0) REVERT: B 347 GLN cc_start: 0.8387 (mm-40) cc_final: 0.8119 (mm-40) outliers start: 21 outliers final: 4 residues processed: 182 average time/residue: 0.8480 time to fit residues: 161.9231 Evaluate side-chains 176 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 171 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 354 GLU Chi-restraints excluded: chain A residue 370 GLN Chi-restraints excluded: chain B residue 160 LYS 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: 0.8980 chunk 39 optimal weight: 0.7980 chunk 60 optimal weight: 4.9990 chunk 56 optimal weight: 9.9990 chunk 63 optimal weight: 3.9990 chunk 78 optimal weight: 0.5980 chunk 24 optimal weight: 0.0870 chunk 71 optimal weight: 0.9980 chunk 66 optimal weight: 0.0040 chunk 72 optimal weight: 4.9990 chunk 69 optimal weight: 2.9990 overall best weight: 0.4770 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 ASN A 403 ASN B 237 GLN 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 = 0.3640 r_free = 0.3640 target = 0.125211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.103179 restraints weight = 15107.182| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 1.77 r_work: 0.3194 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3050 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.2598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 10299 Z= 0.106 Angle : 0.495 9.855 14598 Z= 0.266 Chirality : 0.035 0.194 1679 Planarity : 0.003 0.034 1310 Dihedral : 20.258 73.671 3080 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.25 % Allowed : 3.63 % Favored : 96.12 % Rotamer: Outliers : 2.57 % Allowed : 19.14 % Favored : 78.29 % 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 aren not related in a simple way. whole: 0.68 (0.30), residues: 799 helix: 2.03 (0.28), residues: 365 sheet: -0.15 (0.39), residues: 161 loop : -1.38 (0.35), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 25 TYR 0.010 0.001 TYR A 351 PHE 0.012 0.001 PHE B 389 TRP 0.007 0.001 TRP B 45 HIS 0.003 0.001 HIS B 139 Details of bonding type rmsd covalent geometry : bond 0.00220 (10291) covalent geometry : angle 0.48639 (14586) hydrogen bonds : bond 0.03888 ( 465) hydrogen bonds : angle 3.54995 ( 1195) metal coordination : bond 0.00572 ( 8) metal coordination : angle 3.23024 ( 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 194 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 176 time to evaluate : 0.234 Fit side-chains revert: symmetry clash REVERT: A 16 ASP cc_start: 0.7916 (t0) cc_final: 0.7640 (t70) REVERT: A 177 MET cc_start: 0.9044 (tpp) cc_final: 0.8512 (tpt) REVERT: A 221 ILE cc_start: 0.8888 (mt) cc_final: 0.8588 (mp) REVERT: A 242 ARG cc_start: 0.8464 (ptp90) cc_final: 0.7995 (ptp-110) REVERT: A 244 LYS cc_start: 0.8894 (pttt) cc_final: 0.8664 (pttt) REVERT: A 266 ARG cc_start: 0.8082 (mtp85) cc_final: 0.7832 (mtt180) REVERT: A 288 GLU cc_start: 0.7498 (mt-10) cc_final: 0.6994 (mt-10) REVERT: A 344 ASP cc_start: 0.7893 (t0) cc_final: 0.7611 (t0) REVERT: A 354 GLU cc_start: 0.8073 (OUTLIER) cc_final: 0.7325 (mp0) REVERT: A 377 ASN cc_start: 0.8199 (t0) cc_final: 0.7439 (p0) REVERT: B 199 ASN cc_start: 0.8555 (t0) cc_final: 0.8249 (t0) REVERT: B 221 ILE cc_start: 0.8440 (mm) cc_final: 0.8229 (mm) REVERT: B 242 ARG cc_start: 0.8515 (ptp-170) cc_final: 0.8285 (ptp-170) REVERT: B 261 ARG cc_start: 0.7320 (OUTLIER) cc_final: 0.7008 (ttm110) REVERT: B 339 ASN cc_start: 0.8491 (t0) cc_final: 0.8192 (t0) REVERT: B 406 ARG cc_start: 0.6794 (mtp85) cc_final: 0.6587 (ttt90) REVERT: B 407 ASN cc_start: 0.7298 (m-40) cc_final: 0.6861 (m-40) outliers start: 18 outliers final: 2 residues processed: 183 average time/residue: 0.8834 time to fit residues: 169.8168 Evaluate side-chains 180 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 176 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 354 GLU Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 261 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 70 optimal weight: 0.0070 chunk 35 optimal weight: 2.9990 chunk 83 optimal weight: 8.9990 chunk 19 optimal weight: 10.0000 chunk 27 optimal weight: 5.9990 chunk 86 optimal weight: 10.0000 chunk 28 optimal weight: 8.9990 chunk 32 optimal weight: 5.9990 chunk 31 optimal weight: 0.8980 chunk 52 optimal weight: 10.0000 chunk 10 optimal weight: 5.9990 overall best weight: 3.1804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 HIS ** A 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 403 ASN B 322 GLN B 399 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 = 0.3565 r_free = 0.3565 target = 0.120066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.097874 restraints weight = 15040.931| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 1.76 r_work: 0.3109 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2965 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 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 : 0.005 0.040 10299 Z= 0.217 Angle : 0.547 10.380 14598 Z= 0.296 Chirality : 0.039 0.198 1679 Planarity : 0.003 0.033 1310 Dihedral : 20.258 73.808 3080 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.25 % Allowed : 3.63 % Favored : 96.12 % Rotamer: Outliers : 2.71 % Allowed : 21.86 % Favored : 75.43 % 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 aren not related in a simple way. whole: 0.64 (0.30), residues: 799 helix: 2.04 (0.28), residues: 365 sheet: -0.23 (0.38), residues: 163 loop : -1.44 (0.35), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 406 TYR 0.017 0.002 TYR A 351 PHE 0.011 0.002 PHE A 102 TRP 0.010 0.001 TRP A 43 HIS 0.006 0.001 HIS A 72 Details of bonding type rmsd covalent geometry : bond 0.00479 (10291) covalent geometry : angle 0.54040 (14586) hydrogen bonds : bond 0.04695 ( 465) hydrogen bonds : angle 3.68067 ( 1195) metal coordination : bond 0.00816 ( 8) metal coordination : angle 3.02939 ( 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 198 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 179 time to evaluate : 0.338 Fit side-chains revert: symmetry clash REVERT: A 16 ASP cc_start: 0.8012 (t0) cc_final: 0.7768 (t70) REVERT: A 105 TYR cc_start: 0.9155 (m-80) cc_final: 0.8844 (m-80) REVERT: A 191 GLN cc_start: 0.8937 (mt0) cc_final: 0.8650 (mt0) REVERT: A 221 ILE cc_start: 0.8980 (mt) cc_final: 0.8743 (mp) REVERT: A 242 ARG cc_start: 0.8552 (ptp90) cc_final: 0.8304 (ptp90) REVERT: A 244 LYS cc_start: 0.8870 (pttt) cc_final: 0.8613 (pttt) REVERT: A 267 GLN cc_start: 0.8368 (tm-30) cc_final: 0.7909 (tm-30) REVERT: A 288 GLU cc_start: 0.7540 (mt-10) cc_final: 0.6998 (mt-10) REVERT: A 344 ASP cc_start: 0.7957 (t0) cc_final: 0.7640 (t70) REVERT: A 346 GLN cc_start: 0.8562 (mt0) cc_final: 0.8335 (mt0) REVERT: A 350 ILE cc_start: 0.8546 (mt) cc_final: 0.8271 (mt) REVERT: A 377 ASN cc_start: 0.8384 (t0) cc_final: 0.7557 (p0) REVERT: B 199 ASN cc_start: 0.8504 (t0) cc_final: 0.8160 (t0) REVERT: B 339 ASN cc_start: 0.8497 (t0) cc_final: 0.8133 (t0) REVERT: B 406 ARG cc_start: 0.7003 (mtp85) cc_final: 0.6802 (ttt90) REVERT: B 407 ASN cc_start: 0.7342 (m-40) cc_final: 0.7132 (m110) outliers start: 19 outliers final: 9 residues processed: 190 average time/residue: 0.9122 time to fit residues: 181.6645 Evaluate side-chains 193 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 184 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 50 SER Chi-restraints excluded: chain B residue 114 MET Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 320 THR 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: 1.9990 chunk 58 optimal weight: 2.9990 chunk 61 optimal weight: 9.9990 chunk 70 optimal weight: 2.9990 chunk 45 optimal weight: 8.9990 chunk 66 optimal weight: 1.9990 chunk 48 optimal weight: 10.0000 chunk 23 optimal weight: 2.9990 chunk 4 optimal weight: 4.9990 chunk 75 optimal weight: 0.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3574 r_free = 0.3574 target = 0.120731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.098528 restraints weight = 15047.365| |-----------------------------------------------------------------------------| r_work (start): 0.3251 rms_B_bonded: 1.76 r_work: 0.3123 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2980 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.2552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 10299 Z= 0.164 Angle : 0.530 9.994 14598 Z= 0.287 Chirality : 0.038 0.200 1679 Planarity : 0.003 0.033 1310 Dihedral : 20.203 73.713 3080 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.25 % Allowed : 3.25 % Favored : 96.50 % Rotamer: Outliers : 2.29 % Allowed : 22.43 % 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 aren not related in a simple way. whole: 0.69 (0.30), residues: 799 helix: 2.08 (0.28), residues: 365 sheet: -0.13 (0.38), residues: 155 loop : -1.43 (0.34), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 254 TYR 0.015 0.001 TYR A 351 PHE 0.009 0.001 PHE A 102 TRP 0.007 0.001 TRP A 43 HIS 0.003 0.001 HIS A 72 Details of bonding type rmsd covalent geometry : bond 0.00362 (10291) covalent geometry : angle 0.52449 (14586) hydrogen bonds : bond 0.04388 ( 465) hydrogen bonds : angle 3.63390 ( 1195) metal coordination : bond 0.00637 ( 8) metal coordination : angle 2.65967 ( 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 200 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 184 time to evaluate : 0.326 Fit side-chains revert: symmetry clash REVERT: A 16 ASP cc_start: 0.8007 (t0) cc_final: 0.7779 (t70) REVERT: A 44 GLU cc_start: 0.8827 (tt0) cc_final: 0.8520 (tt0) REVERT: A 105 TYR cc_start: 0.9144 (m-80) cc_final: 0.8848 (m-80) REVERT: A 121 ARG cc_start: 0.8629 (ptm160) cc_final: 0.8388 (ttp-110) REVERT: A 191 GLN cc_start: 0.8927 (mt0) cc_final: 0.8632 (mt0) REVERT: A 221 ILE cc_start: 0.8973 (mt) cc_final: 0.8730 (mp) REVERT: A 233 TYR cc_start: 0.8946 (OUTLIER) cc_final: 0.8529 (t80) REVERT: A 244 LYS cc_start: 0.8877 (pttt) cc_final: 0.8601 (pttt) REVERT: A 267 GLN cc_start: 0.8338 (tm-30) cc_final: 0.7867 (tm-30) REVERT: A 280 ARG cc_start: 0.7933 (ttm110) cc_final: 0.7727 (ttp-110) REVERT: A 288 GLU cc_start: 0.7560 (mt-10) cc_final: 0.6994 (mt-10) REVERT: A 344 ASP cc_start: 0.7871 (t0) cc_final: 0.7563 (t0) REVERT: A 346 GLN cc_start: 0.8556 (mt0) cc_final: 0.8327 (mt0) REVERT: A 350 ILE cc_start: 0.8505 (mt) cc_final: 0.7163 (mt) REVERT: A 354 GLU cc_start: 0.8083 (OUTLIER) cc_final: 0.7355 (mp0) REVERT: A 377 ASN cc_start: 0.8364 (t0) cc_final: 0.7543 (p0) REVERT: B 199 ASN cc_start: 0.8524 (t0) cc_final: 0.8198 (t0) REVERT: B 261 ARG cc_start: 0.7308 (OUTLIER) cc_final: 0.7068 (ttm110) REVERT: B 339 ASN cc_start: 0.8500 (t0) cc_final: 0.8152 (t0) REVERT: B 364 ASP cc_start: 0.7619 (OUTLIER) cc_final: 0.7307 (m-30) REVERT: B 406 ARG cc_start: 0.7031 (mtp85) cc_final: 0.6619 (ttt90) REVERT: B 407 ASN cc_start: 0.7352 (m-40) cc_final: 0.7130 (m110) outliers start: 16 outliers final: 6 residues processed: 192 average time/residue: 0.9200 time to fit residues: 185.4273 Evaluate side-chains 191 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 181 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 LYS Chi-restraints excluded: chain A residue 233 TYR Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 354 GLU Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 261 ARG Chi-restraints excluded: chain B residue 262 ILE Chi-restraints excluded: chain B residue 364 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 92 optimal weight: 10.0000 chunk 25 optimal weight: 10.0000 chunk 21 optimal weight: 9.9990 chunk 13 optimal weight: 8.9990 chunk 30 optimal weight: 7.9990 chunk 88 optimal weight: 2.9990 chunk 69 optimal weight: 10.0000 chunk 19 optimal weight: 3.9990 chunk 1 optimal weight: 2.9990 chunk 93 optimal weight: 9.9990 chunk 78 optimal weight: 2.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 ASN A 186 GLN B 194 HIS B 399 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 = 0.3534 r_free = 0.3534 target = 0.117927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.095642 restraints weight = 15043.080| |-----------------------------------------------------------------------------| r_work (start): 0.3206 rms_B_bonded: 1.79 r_work: 0.3075 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2931 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.2520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 10299 Z= 0.272 Angle : 0.597 10.859 14598 Z= 0.320 Chirality : 0.041 0.212 1679 Planarity : 0.004 0.033 1310 Dihedral : 20.291 73.901 3080 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.25 % Allowed : 4.38 % Favored : 95.37 % Rotamer: Outliers : 2.57 % Allowed : 22.43 % 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 aren not related in a simple way. whole: 0.51 (0.29), residues: 799 helix: 1.87 (0.28), residues: 367 sheet: -0.17 (0.37), residues: 157 loop : -1.49 (0.34), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 25 TYR 0.019 0.002 TYR A 351 PHE 0.015 0.002 PHE A 102 TRP 0.009 0.002 TRP A 43 HIS 0.006 0.001 HIS A 72 Details of bonding type rmsd covalent geometry : bond 0.00604 (10291) covalent geometry : angle 0.58867 (14586) hydrogen bonds : bond 0.05128 ( 465) hydrogen bonds : angle 3.78940 ( 1195) metal coordination : bond 0.00983 ( 8) metal coordination : angle 3.43139 ( 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 200 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 182 time to evaluate : 0.292 Fit side-chains revert: symmetry clash REVERT: A 16 ASP cc_start: 0.8067 (t0) cc_final: 0.7855 (t70) REVERT: A 18 LYS cc_start: 0.8334 (ttmt) cc_final: 0.7957 (mtpp) REVERT: A 105 TYR cc_start: 0.9181 (m-80) cc_final: 0.8867 (m-80) REVERT: A 191 GLN cc_start: 0.8969 (mt0) cc_final: 0.8637 (mt0) REVERT: A 221 ILE cc_start: 0.8990 (mt) cc_final: 0.8756 (mp) REVERT: A 242 ARG cc_start: 0.8561 (ptp90) cc_final: 0.8238 (ptp90) REVERT: A 244 LYS cc_start: 0.8892 (pttt) cc_final: 0.8609 (pttt) REVERT: A 288 GLU cc_start: 0.7549 (mt-10) cc_final: 0.7011 (mt-10) REVERT: A 344 ASP cc_start: 0.8088 (t0) cc_final: 0.7808 (t70) REVERT: A 346 GLN cc_start: 0.8603 (mt0) cc_final: 0.8333 (mt0) REVERT: A 377 ASN cc_start: 0.8450 (t0) cc_final: 0.7538 (p0) REVERT: B 17 TRP cc_start: 0.8682 (OUTLIER) cc_final: 0.8245 (m100) REVERT: B 199 ASN cc_start: 0.8471 (t0) cc_final: 0.8125 (t0) REVERT: B 339 ASN cc_start: 0.8488 (t0) cc_final: 0.8129 (t0) REVERT: B 406 ARG cc_start: 0.7156 (mtp85) cc_final: 0.6623 (ttt90) REVERT: B 407 ASN cc_start: 0.7318 (m-40) cc_final: 0.6910 (m-40) outliers start: 18 outliers final: 8 residues processed: 192 average time/residue: 0.9290 time to fit residues: 187.0952 Evaluate side-chains 185 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 176 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 17 TRP Chi-restraints excluded: chain B residue 114 MET Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 216 LEU 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: 0.9990 chunk 8 optimal weight: 4.9990 chunk 71 optimal weight: 8.9990 chunk 0 optimal weight: 6.9990 chunk 62 optimal weight: 2.9990 chunk 87 optimal weight: 0.7980 chunk 51 optimal weight: 10.0000 chunk 10 optimal weight: 3.9990 chunk 9 optimal weight: 0.8980 chunk 2 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 ASN A 186 GLN B 399 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 = 0.3583 r_free = 0.3583 target = 0.121465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.099343 restraints weight = 14977.769| |-----------------------------------------------------------------------------| r_work (start): 0.3263 rms_B_bonded: 1.76 r_work: 0.3133 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2991 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.2702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10299 Z= 0.139 Angle : 0.536 9.655 14598 Z= 0.288 Chirality : 0.037 0.203 1679 Planarity : 0.004 0.046 1310 Dihedral : 20.182 73.742 3080 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.25 % Allowed : 3.38 % Favored : 96.37 % Rotamer: Outliers : 1.71 % Allowed : 24.71 % Favored : 73.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.82 (0.30), residues: 799 helix: 2.11 (0.28), residues: 368 sheet: 0.05 (0.39), residues: 148 loop : -1.34 (0.34), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 121 TYR 0.016 0.001 TYR A 351 PHE 0.017 0.001 PHE A 389 TRP 0.008 0.001 TRP A 340 HIS 0.003 0.001 HIS B 72 Details of bonding type rmsd covalent geometry : bond 0.00305 (10291) covalent geometry : angle 0.53128 (14586) hydrogen bonds : bond 0.04216 ( 465) hydrogen bonds : angle 3.61512 ( 1195) metal coordination : bond 0.00500 ( 8) metal coordination : angle 2.51892 ( 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 181 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 169 time to evaluate : 0.327 Fit side-chains REVERT: A 16 ASP cc_start: 0.8000 (t0) cc_final: 0.7788 (t70) REVERT: A 25 ARG cc_start: 0.8335 (mpt90) cc_final: 0.8132 (mpt90) REVERT: A 105 TYR cc_start: 0.9156 (m-80) cc_final: 0.8874 (m-80) REVERT: A 177 MET cc_start: 0.9007 (tpp) cc_final: 0.8544 (tpt) REVERT: A 221 ILE cc_start: 0.8980 (mt) cc_final: 0.8737 (mp) REVERT: A 233 TYR cc_start: 0.8943 (OUTLIER) cc_final: 0.8513 (t80) REVERT: A 244 LYS cc_start: 0.8867 (pttt) cc_final: 0.8557 (pttt) REVERT: A 344 ASP cc_start: 0.7851 (t0) cc_final: 0.7555 (t0) REVERT: A 377 ASN cc_start: 0.8341 (t0) cc_final: 0.7403 (p0) REVERT: B 8 GLU cc_start: 0.8002 (tt0) cc_final: 0.6948 (tp30) REVERT: B 17 TRP cc_start: 0.8602 (OUTLIER) cc_final: 0.8259 (m100) REVERT: B 170 ARG cc_start: 0.7988 (ptm-80) cc_final: 0.7720 (ptm-80) REVERT: B 338 GLN cc_start: 0.8420 (mm110) cc_final: 0.8058 (mm110) REVERT: B 339 ASN cc_start: 0.8493 (t0) cc_final: 0.8146 (t0) REVERT: B 406 ARG cc_start: 0.7029 (mtp85) cc_final: 0.6640 (ttt90) REVERT: B 407 ASN cc_start: 0.7351 (m-40) cc_final: 0.7076 (m110) outliers start: 12 outliers final: 5 residues processed: 175 average time/residue: 0.9308 time to fit residues: 171.0366 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 : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 233 TYR Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain B residue 17 TRP Chi-restraints excluded: chain B residue 114 MET Chi-restraints excluded: chain B residue 216 LEU 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: 0.6980 chunk 84 optimal weight: 2.9990 chunk 92 optimal weight: 10.0000 chunk 20 optimal weight: 6.9990 chunk 44 optimal weight: 6.9990 chunk 76 optimal weight: 0.5980 chunk 65 optimal weight: 6.9990 chunk 90 optimal weight: 2.9990 chunk 43 optimal weight: 6.9990 chunk 37 optimal weight: 9.9990 chunk 8 optimal weight: 3.9990 overall best weight: 2.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 ASN A 377 ASN B 399 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 = 0.3575 r_free = 0.3575 target = 0.120831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.098679 restraints weight = 14898.308| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 1.75 r_work: 0.3121 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2977 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.2760 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= 0.172 Angle : 0.566 11.373 14598 Z= 0.304 Chirality : 0.038 0.199 1679 Planarity : 0.004 0.036 1310 Dihedral : 20.203 73.755 3080 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.25 % Allowed : 4.01 % Favored : 95.74 % Rotamer: Outliers : 1.14 % Allowed : 25.71 % Favored : 73.14 % 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 aren not related in a simple way. whole: 0.76 (0.30), residues: 799 helix: 2.09 (0.27), residues: 368 sheet: -0.22 (0.37), residues: 161 loop : -1.28 (0.35), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 25 TYR 0.017 0.001 TYR A 351 PHE 0.016 0.002 PHE A 389 TRP 0.017 0.001 TRP A 340 HIS 0.004 0.001 HIS A 72 Details of bonding type rmsd covalent geometry : bond 0.00382 (10291) covalent geometry : angle 0.56158 (14586) hydrogen bonds : bond 0.04395 ( 465) hydrogen bonds : angle 3.65620 ( 1195) metal coordination : bond 0.00603 ( 8) metal coordination : angle 2.65064 ( 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 173 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 165 time to evaluate : 0.451 Fit side-chains revert: symmetry clash REVERT: A 16 ASP cc_start: 0.8029 (t0) cc_final: 0.7816 (t70) REVERT: A 105 TYR cc_start: 0.9173 (m-80) cc_final: 0.8870 (m-80) REVERT: A 221 ILE cc_start: 0.8988 (mt) cc_final: 0.8760 (mp) REVERT: A 244 LYS cc_start: 0.8885 (pttt) cc_final: 0.8553 (pttt) REVERT: A 344 ASP cc_start: 0.7893 (t0) cc_final: 0.7596 (t70) REVERT: B 17 TRP cc_start: 0.8643 (OUTLIER) cc_final: 0.8298 (m100) REVERT: B 339 ASN cc_start: 0.8484 (t0) cc_final: 0.8137 (t0) REVERT: B 406 ARG cc_start: 0.7035 (mtp85) cc_final: 0.6620 (ttt90) REVERT: B 407 ASN cc_start: 0.7358 (m-40) cc_final: 0.7133 (m110) outliers start: 8 outliers final: 4 residues processed: 169 average time/residue: 0.9177 time to fit residues: 162.6477 Evaluate side-chains 171 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 166 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain B residue 17 TRP Chi-restraints excluded: chain B residue 114 MET Chi-restraints excluded: chain B residue 216 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 86 optimal weight: 5.9990 chunk 6 optimal weight: 4.9990 chunk 61 optimal weight: 4.9990 chunk 2 optimal weight: 1.9990 chunk 90 optimal weight: 10.0000 chunk 56 optimal weight: 9.9990 chunk 27 optimal weight: 9.9990 chunk 82 optimal weight: 8.9990 chunk 8 optimal weight: 4.9990 chunk 38 optimal weight: 0.0980 chunk 29 optimal weight: 4.9990 overall best weight: 3.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 ASN ** A 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3553 r_free = 0.3553 target = 0.119401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.097247 restraints weight = 14829.027| |-----------------------------------------------------------------------------| r_work (start): 0.3227 rms_B_bonded: 1.75 r_work: 0.3098 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2954 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.2728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 10299 Z= 0.232 Angle : 0.617 12.128 14598 Z= 0.329 Chirality : 0.040 0.209 1679 Planarity : 0.004 0.067 1310 Dihedral : 20.245 73.794 3080 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.25 % Allowed : 4.26 % Favored : 95.49 % Rotamer: Outliers : 1.14 % Allowed : 25.86 % 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 aren not related in a simple way. whole: 0.57 (0.29), residues: 799 helix: 1.94 (0.27), residues: 367 sheet: -0.27 (0.38), residues: 157 loop : -1.39 (0.35), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG A 121 TYR 0.029 0.002 TYR B 351 PHE 0.016 0.002 PHE A 389 TRP 0.026 0.002 TRP A 340 HIS 0.005 0.001 HIS B 194 Details of bonding type rmsd covalent geometry : bond 0.00518 (10291) covalent geometry : angle 0.61170 (14586) hydrogen bonds : bond 0.04777 ( 465) hydrogen bonds : angle 3.73692 ( 1195) metal coordination : bond 0.00809 ( 8) metal coordination : angle 3.00799 ( 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 170 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 162 time to evaluate : 0.328 Fit side-chains revert: symmetry clash REVERT: A 16 ASP cc_start: 0.8032 (t0) cc_final: 0.7788 (t70) REVERT: A 121 ARG cc_start: 0.8533 (ttp-110) cc_final: 0.8316 (ptm160) REVERT: A 221 ILE cc_start: 0.9001 (mt) cc_final: 0.8770 (mp) REVERT: A 242 ARG cc_start: 0.8533 (ptp90) cc_final: 0.7989 (ptp90) REVERT: A 244 LYS cc_start: 0.8862 (pttt) cc_final: 0.8583 (pttt) REVERT: A 312 MET cc_start: 0.8709 (tpp) cc_final: 0.8259 (tpp) REVERT: A 344 ASP cc_start: 0.7950 (t0) cc_final: 0.7660 (t70) REVERT: B 8 GLU cc_start: 0.7754 (tp30) cc_final: 0.7369 (tp30) REVERT: B 17 TRP cc_start: 0.8696 (OUTLIER) cc_final: 0.8269 (m100) REVERT: B 338 GLN cc_start: 0.8419 (mm110) cc_final: 0.8116 (mm110) REVERT: B 339 ASN cc_start: 0.8486 (t0) cc_final: 0.8147 (t0) REVERT: B 406 ARG cc_start: 0.7070 (mtp85) cc_final: 0.6597 (ttt90) REVERT: B 407 ASN cc_start: 0.7375 (m-40) cc_final: 0.6909 (m-40) outliers start: 8 outliers final: 4 residues processed: 166 average time/residue: 0.8992 time to fit residues: 156.7551 Evaluate side-chains 170 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 165 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain B residue 17 TRP Chi-restraints excluded: chain B residue 114 MET Chi-restraints excluded: chain B residue 216 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 84 optimal weight: 0.9990 chunk 25 optimal weight: 10.0000 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: 4.9990 chunk 28 optimal weight: 7.9990 chunk 52 optimal weight: 10.0000 chunk 59 optimal weight: 0.9990 chunk 55 optimal weight: 10.0000 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 ASN ** A 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3563 r_free = 0.3563 target = 0.120105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.097850 restraints weight = 15006.168| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 1.78 r_work: 0.3108 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2963 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.2788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 10299 Z= 0.199 Angle : 0.593 11.797 14598 Z= 0.317 Chirality : 0.039 0.209 1679 Planarity : 0.004 0.065 1310 Dihedral : 20.225 73.743 3080 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.25 % Allowed : 4.01 % Favored : 95.74 % Rotamer: Outliers : 1.29 % Allowed : 25.71 % 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 aren not related in a simple way. whole: 0.64 (0.30), residues: 799 helix: 1.97 (0.27), residues: 367 sheet: -0.12 (0.39), residues: 146 loop : -1.36 (0.34), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 121 TYR 0.017 0.001 TYR A 84 PHE 0.016 0.002 PHE A 389 TRP 0.029 0.002 TRP A 340 HIS 0.004 0.001 HIS A 72 Details of bonding type rmsd covalent geometry : bond 0.00442 (10291) covalent geometry : angle 0.58764 (14586) hydrogen bonds : bond 0.04550 ( 465) hydrogen bonds : angle 3.67644 ( 1195) metal coordination : bond 0.00693 ( 8) metal coordination : angle 2.86168 ( 12) =============================================================================== Job complete usr+sys time: 4698.75 seconds wall clock time: 80 minutes 42.14 seconds (4842.14 seconds total)