Starting phenix.real_space_refine on Wed Apr 30 22:26:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8j1j_35926/04_2025/8j1j_35926.cif Found real_map, /net/cci-nas-00/data/ceres_data/8j1j_35926/04_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8j1j_35926/04_2025/8j1j_35926.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8j1j_35926/04_2025/8j1j_35926.map" model { file = "/net/cci-nas-00/data/ceres_data/8j1j_35926/04_2025/8j1j_35926.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8j1j_35926/04_2025/8j1j_35926.cif" } resolution = 2.91 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.010 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/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: 6.31, per 1000 atoms: 0.64 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: 2.40 Conformation dependent library (CDL) restraints added in 967.9 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: 4.44 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: 4.04 Time building geometry restraints manager: 2.84 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: 0.060 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: 0.320 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 31.010 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.530 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.23 (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 TRP 0.010 0.001 TRP B 43 HIS 0.006 0.001 HIS A 238 PHE 0.009 0.002 PHE A 102 TYR 0.014 0.001 TYR A 52 ARG 0.002 0.000 ARG A 260 Details of bonding type rmsd hydrogen bonds : bond 0.21352 ( 465) hydrogen bonds : angle 7.08989 ( 1195) metal coordination : bond 0.06495 ( 8) metal coordination : angle 27.21350 ( 12) covalent geometry : bond 0.00386 (10291) covalent geometry : angle 0.53078 (14586) *********************** 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 : 0.768 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: 1.6037 time to fit residues: 397.2401 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 : 0.930 ------------------------------------------------------------------------------- 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 79 optimal weight: 0.4980 chunk 71 optimal weight: 9.9990 chunk 39 optimal weight: 1.9990 chunk 24 optimal weight: 4.9990 chunk 48 optimal weight: 10.0000 chunk 38 optimal weight: 20.0000 chunk 73 optimal weight: 3.9990 chunk 28 optimal weight: 5.9990 chunk 44 optimal weight: 6.9990 chunk 54 optimal weight: 8.9990 chunk 85 optimal weight: 10.0000 overall best weight: 3.4988 ------------------------------------------------------------------------------- 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 = 0.3545 r_free = 0.3545 target = 0.118777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.096675 restraints weight = 14734.704| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 1.76 r_work: 0.3089 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2945 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.1570 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= 0.237 Angle : 0.611 14.496 14598 Z= 0.317 Chirality : 0.041 0.226 1679 Planarity : 0.004 0.035 1310 Dihedral : 20.485 74.689 3088 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.25 % Allowed : 3.88 % Favored : 95.87 % Rotamer: Outliers : 3.00 % Allowed : 15.57 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.29), residues: 799 helix: 1.06 (0.28), residues: 363 sheet: -0.36 (0.40), residues: 151 loop : -1.66 (0.33), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 17 HIS 0.006 0.001 HIS A 72 PHE 0.015 0.002 PHE A 389 TYR 0.020 0.002 TYR A 351 ARG 0.006 0.001 ARG B 406 Details of bonding type rmsd hydrogen bonds : bond 0.05541 ( 465) hydrogen bonds : angle 4.17524 ( 1195) metal coordination : bond 0.01519 ( 8) metal coordination : angle 7.61645 ( 12) covalent geometry : bond 0.00522 (10291) covalent geometry : angle 0.57083 (14586) *********************** 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 190 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 169 time to evaluate : 0.777 Fit side-chains revert: symmetry clash REVERT: A 16 ASP cc_start: 0.8055 (t0) cc_final: 0.7819 (t70) REVERT: A 25 ARG cc_start: 0.8295 (mtp85) cc_final: 0.8063 (mpt90) REVERT: A 30 GLU cc_start: 0.8182 (mm-30) cc_final: 0.7963 (mt-10) REVERT: A 141 ASP cc_start: 0.8657 (OUTLIER) cc_final: 0.8444 (m-30) REVERT: A 221 ILE cc_start: 0.8933 (mt) cc_final: 0.8711 (mp) REVERT: A 222 MET cc_start: 0.9110 (ttp) cc_final: 0.8891 (ttp) REVERT: A 242 ARG cc_start: 0.8506 (ptp90) cc_final: 0.8186 (ptp90) REVERT: A 244 LYS cc_start: 0.8846 (pttt) cc_final: 0.8631 (pttt) REVERT: A 264 MET cc_start: 0.8412 (mtt) cc_final: 0.8097 (mtp) REVERT: A 283 ARG cc_start: 0.8701 (tpp-160) cc_final: 0.8433 (tpt170) REVERT: A 344 ASP cc_start: 0.8096 (t0) cc_final: 0.7808 (t70) REVERT: A 377 ASN cc_start: 0.8553 (t0) cc_final: 0.7575 (p0) REVERT: B 71 VAL cc_start: 0.8629 (OUTLIER) cc_final: 0.8408 (p) REVERT: B 199 ASN cc_start: 0.8462 (t0) cc_final: 0.8068 (t0) REVERT: B 208 ASP cc_start: 0.7525 (t0) cc_final: 0.7320 (t0) REVERT: B 222 MET cc_start: 0.8682 (ttp) cc_final: 0.8309 (ttt) REVERT: B 242 ARG cc_start: 0.8491 (ptp-170) cc_final: 0.7657 (ptp-170) REVERT: B 264 MET cc_start: 0.7478 (tpp) cc_final: 0.7265 (mpp) REVERT: B 316 MET cc_start: 0.8520 (mmm) cc_final: 0.8278 (mmm) REVERT: B 339 ASN cc_start: 0.8489 (t0) cc_final: 0.8220 (t0) outliers start: 21 outliers final: 5 residues processed: 184 average time/residue: 1.7319 time to fit residues: 334.6423 Evaluate side-chains 176 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 169 time to evaluate : 0.785 ------------------------------------------------------------------------------- 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 216 LEU 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 60 optimal weight: 2.9990 chunk 61 optimal weight: 8.9990 chunk 82 optimal weight: 1.9990 chunk 6 optimal weight: 4.9990 chunk 88 optimal weight: 4.9990 chunk 7 optimal weight: 0.7980 chunk 17 optimal weight: 0.7980 chunk 13 optimal weight: 0.7980 chunk 22 optimal weight: 9.9990 chunk 63 optimal weight: 3.9990 chunk 30 optimal weight: 8.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- 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 204 ASN B 322 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 = 0.3586 r_free = 0.3586 target = 0.121625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.099475 restraints weight = 14986.113| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 1.76 r_work: 0.3136 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2993 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.2035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10299 Z= 0.137 Angle : 0.533 10.525 14598 Z= 0.283 Chirality : 0.037 0.215 1679 Planarity : 0.003 0.033 1310 Dihedral : 20.353 73.703 3083 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.25 % Allowed : 2.88 % Favored : 96.87 % Rotamer: Outliers : 3.14 % Allowed : 17.14 % Favored : 79.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.30), residues: 799 helix: 1.61 (0.28), residues: 364 sheet: -0.22 (0.40), residues: 157 loop : -1.65 (0.34), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 43 HIS 0.002 0.001 HIS B 303 PHE 0.012 0.002 PHE B 389 TYR 0.013 0.001 TYR A 351 ARG 0.006 0.000 ARG B 406 Details of bonding type rmsd hydrogen bonds : bond 0.04503 ( 465) hydrogen bonds : angle 3.80391 ( 1195) metal coordination : bond 0.00832 ( 8) metal coordination : angle 5.00364 ( 12) covalent geometry : bond 0.00291 (10291) covalent geometry : angle 0.51383 (14586) *********************** 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: 22 poor density : 173 time to evaluate : 0.805 Fit side-chains revert: symmetry clash REVERT: A 16 ASP cc_start: 0.7979 (t0) cc_final: 0.7741 (t70) REVERT: A 30 GLU cc_start: 0.8136 (mm-30) cc_final: 0.7920 (mt-10) REVERT: A 141 ASP cc_start: 0.8605 (OUTLIER) cc_final: 0.8404 (m-30) REVERT: A 177 MET cc_start: 0.9018 (tpp) cc_final: 0.8526 (tpt) REVERT: A 221 ILE cc_start: 0.8939 (mt) cc_final: 0.8702 (mp) REVERT: A 222 MET cc_start: 0.9127 (ttp) cc_final: 0.8910 (ttp) REVERT: A 244 LYS cc_start: 0.8833 (pttt) cc_final: 0.8608 (pttt) REVERT: A 324 GLU cc_start: 0.8349 (mt-10) cc_final: 0.7968 (mp0) REVERT: A 344 ASP cc_start: 0.8045 (t0) cc_final: 0.7749 (t70) REVERT: A 354 GLU cc_start: 0.8086 (OUTLIER) cc_final: 0.7858 (mp0) REVERT: A 377 ASN cc_start: 0.8407 (t0) cc_final: 0.7467 (p0) REVERT: B 199 ASN cc_start: 0.8544 (t0) cc_final: 0.8191 (t0) REVERT: B 222 MET cc_start: 0.8686 (ttp) cc_final: 0.8483 (ttt) REVERT: B 242 ARG cc_start: 0.8576 (ptp-170) cc_final: 0.7633 (ptp-170) REVERT: B 339 ASN cc_start: 0.8536 (t0) cc_final: 0.8270 (t0) REVERT: B 407 ASN cc_start: 0.7424 (m-40) cc_final: 0.7003 (m-40) outliers start: 22 outliers final: 5 residues processed: 182 average time/residue: 1.8285 time to fit residues: 349.4365 Evaluate side-chains 177 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 170 time to evaluate : 0.825 ------------------------------------------------------------------------------- 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 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 Chi-restraints excluded: chain B residue 239 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 87 optimal weight: 0.2980 chunk 61 optimal weight: 9.9990 chunk 79 optimal weight: 0.9990 chunk 44 optimal weight: 6.9990 chunk 28 optimal weight: 7.9990 chunk 41 optimal weight: 9.9990 chunk 6 optimal weight: 7.9990 chunk 16 optimal weight: 7.9990 chunk 40 optimal weight: 0.0370 chunk 4 optimal weight: 0.9980 chunk 26 optimal weight: 7.9990 overall best weight: 1.8662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 237 GLN B 412 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.121069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.098847 restraints weight = 14935.087| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 1.75 r_work: 0.3125 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2981 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.2216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10299 Z= 0.149 Angle : 0.513 10.285 14598 Z= 0.277 Chirality : 0.037 0.204 1679 Planarity : 0.003 0.034 1310 Dihedral : 20.306 73.710 3082 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.25 % Allowed : 3.50 % Favored : 96.25 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.30), residues: 799 helix: 1.84 (0.28), residues: 364 sheet: -0.11 (0.40), residues: 155 loop : -1.52 (0.34), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 43 HIS 0.004 0.001 HIS A 72 PHE 0.009 0.002 PHE B 389 TYR 0.014 0.001 TYR A 351 ARG 0.008 0.000 ARG B 406 Details of bonding type rmsd hydrogen bonds : bond 0.04378 ( 465) hydrogen bonds : angle 3.69609 ( 1195) metal coordination : bond 0.00780 ( 8) metal coordination : angle 3.94178 ( 12) covalent geometry : bond 0.00322 (10291) covalent geometry : angle 0.50085 (14586) *********************** 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 192 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 174 time to evaluate : 0.899 Fit side-chains revert: symmetry clash REVERT: A 16 ASP cc_start: 0.7949 (t0) cc_final: 0.7693 (t70) REVERT: A 30 GLU cc_start: 0.8108 (mm-30) cc_final: 0.7901 (mt-10) REVERT: A 105 TYR cc_start: 0.9141 (m-80) cc_final: 0.8848 (m-80) REVERT: A 221 ILE cc_start: 0.8965 (mt) cc_final: 0.8733 (mp) REVERT: A 244 LYS cc_start: 0.8875 (pttt) cc_final: 0.8644 (pttt) REVERT: A 266 ARG cc_start: 0.8186 (mtp85) cc_final: 0.7872 (mtt180) REVERT: A 344 ASP cc_start: 0.8057 (t0) cc_final: 0.7768 (t70) REVERT: A 354 GLU cc_start: 0.8127 (OUTLIER) cc_final: 0.7411 (mp0) REVERT: A 377 ASN cc_start: 0.8268 (t0) cc_final: 0.7424 (p0) REVERT: B 11 LYS cc_start: 0.9027 (OUTLIER) cc_final: 0.8806 (pttt) REVERT: B 142 TYR cc_start: 0.8205 (m-80) cc_final: 0.7971 (m-10) REVERT: B 177 MET cc_start: 0.8409 (tpp) cc_final: 0.8055 (tpp) REVERT: B 199 ASN cc_start: 0.8538 (t0) cc_final: 0.8203 (t0) REVERT: B 254 ARG cc_start: 0.8022 (mtt90) cc_final: 0.7672 (mtp85) REVERT: B 264 MET cc_start: 0.7560 (tpp) cc_final: 0.7308 (mpp) REVERT: B 339 ASN cc_start: 0.8473 (t0) cc_final: 0.8084 (t0) REVERT: B 406 ARG cc_start: 0.6946 (mtp85) cc_final: 0.6674 (ttt90) REVERT: B 407 ASN cc_start: 0.7359 (m-40) cc_final: 0.7107 (m110) outliers start: 18 outliers final: 7 residues processed: 181 average time/residue: 1.9966 time to fit residues: 378.6229 Evaluate side-chains 177 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 168 time to evaluate : 0.841 ------------------------------------------------------------------------------- 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 354 GLU Chi-restraints excluded: chain B residue 11 LYS Chi-restraints excluded: chain B residue 160 LYS Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 239 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 62 optimal weight: 4.9990 chunk 46 optimal weight: 10.0000 chunk 78 optimal weight: 0.8980 chunk 61 optimal weight: 9.9990 chunk 71 optimal weight: 0.9980 chunk 12 optimal weight: 0.9980 chunk 29 optimal weight: 10.0000 chunk 80 optimal weight: 5.9990 chunk 55 optimal weight: 10.0000 chunk 22 optimal weight: 9.9990 chunk 89 optimal weight: 8.9990 overall best weight: 2.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 412 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.119865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.097700 restraints weight = 14882.418| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 1.74 r_work: 0.3107 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2963 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.2259 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= 0.194 Angle : 0.540 10.177 14598 Z= 0.289 Chirality : 0.038 0.206 1679 Planarity : 0.003 0.033 1310 Dihedral : 20.289 73.769 3082 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.25 % Allowed : 3.38 % Favored : 96.37 % Rotamer: Outliers : 2.57 % Allowed : 21.00 % Favored : 76.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.30), residues: 799 helix: 1.90 (0.28), residues: 365 sheet: -0.10 (0.39), residues: 155 loop : -1.51 (0.34), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 43 HIS 0.005 0.001 HIS A 72 PHE 0.013 0.002 PHE A 389 TYR 0.016 0.001 TYR A 351 ARG 0.006 0.000 ARG B 25 Details of bonding type rmsd hydrogen bonds : bond 0.04627 ( 465) hydrogen bonds : angle 3.72109 ( 1195) metal coordination : bond 0.00836 ( 8) metal coordination : angle 3.66221 ( 12) covalent geometry : bond 0.00426 (10291) covalent geometry : angle 0.53006 (14586) *********************** 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 191 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 173 time to evaluate : 0.852 Fit side-chains revert: symmetry clash REVERT: A 16 ASP cc_start: 0.8026 (t0) cc_final: 0.7790 (t70) REVERT: A 105 TYR cc_start: 0.9160 (m-80) cc_final: 0.8868 (m-80) REVERT: A 221 ILE cc_start: 0.8940 (mt) cc_final: 0.8685 (mp) REVERT: A 244 LYS cc_start: 0.8862 (pttt) cc_final: 0.8614 (pttt) REVERT: A 344 ASP cc_start: 0.8087 (t0) cc_final: 0.7782 (t70) REVERT: A 350 ILE cc_start: 0.8536 (mt) cc_final: 0.7356 (mt) REVERT: A 354 GLU cc_start: 0.8138 (OUTLIER) cc_final: 0.7429 (mp0) REVERT: A 377 ASN cc_start: 0.8348 (t0) cc_final: 0.7465 (p0) REVERT: B 142 TYR cc_start: 0.8423 (m-80) cc_final: 0.7998 (m-10) REVERT: B 177 MET cc_start: 0.8441 (tpp) cc_final: 0.8063 (tpp) REVERT: B 199 ASN cc_start: 0.8557 (t0) cc_final: 0.8218 (t0) REVERT: B 254 ARG cc_start: 0.8018 (mtt90) cc_final: 0.7678 (mtp85) REVERT: B 338 GLN cc_start: 0.8377 (mm110) cc_final: 0.8113 (mm110) REVERT: B 339 ASN cc_start: 0.8484 (t0) cc_final: 0.8091 (t0) REVERT: B 406 ARG cc_start: 0.7031 (mtp85) cc_final: 0.6635 (ttt90) REVERT: B 407 ASN cc_start: 0.7455 (m-40) cc_final: 0.7192 (m110) outliers start: 18 outliers final: 7 residues processed: 181 average time/residue: 1.7797 time to fit residues: 337.7317 Evaluate side-chains 184 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 176 time to evaluate : 0.925 ------------------------------------------------------------------------------- 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 354 GLU Chi-restraints excluded: chain A residue 370 GLN Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 239 THR Chi-restraints excluded: chain B residue 262 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 63 optimal weight: 5.9990 chunk 33 optimal weight: 2.9990 chunk 70 optimal weight: 0.1980 chunk 46 optimal weight: 10.0000 chunk 28 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 48 optimal weight: 10.0000 chunk 69 optimal weight: 8.9990 chunk 50 optimal weight: 8.9990 chunk 31 optimal weight: 0.9980 chunk 72 optimal weight: 9.9990 overall best weight: 2.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 412 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.120517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.098233 restraints weight = 14851.384| |-----------------------------------------------------------------------------| r_work (start): 0.3243 rms_B_bonded: 1.76 r_work: 0.3115 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2972 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.2407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 10299 Z= 0.166 Angle : 0.524 10.179 14598 Z= 0.283 Chirality : 0.037 0.204 1679 Planarity : 0.003 0.033 1310 Dihedral : 20.240 73.733 3082 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 : 1.86 % Allowed : 22.86 % Favored : 75.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.30), residues: 799 helix: 1.99 (0.28), residues: 365 sheet: -0.04 (0.38), residues: 155 loop : -1.48 (0.34), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 43 HIS 0.003 0.001 HIS A 72 PHE 0.015 0.002 PHE A 389 TYR 0.015 0.001 TYR A 351 ARG 0.006 0.000 ARG B 25 Details of bonding type rmsd hydrogen bonds : bond 0.04407 ( 465) hydrogen bonds : angle 3.67172 ( 1195) metal coordination : bond 0.00704 ( 8) metal coordination : angle 3.19341 ( 12) covalent geometry : bond 0.00364 (10291) covalent geometry : angle 0.51655 (14586) *********************** 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 193 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 180 time to evaluate : 0.725 Fit side-chains revert: symmetry clash REVERT: A 16 ASP cc_start: 0.7998 (t0) cc_final: 0.7776 (t70) REVERT: A 44 GLU cc_start: 0.8766 (tt0) cc_final: 0.8554 (tt0) REVERT: A 105 TYR cc_start: 0.9155 (m-80) cc_final: 0.8831 (m-80) REVERT: A 221 ILE cc_start: 0.8965 (mt) cc_final: 0.8732 (mp) REVERT: A 244 LYS cc_start: 0.8860 (pttt) cc_final: 0.8598 (pttt) REVERT: A 266 ARG cc_start: 0.8179 (mtp85) cc_final: 0.7822 (mtt180) REVERT: A 288 GLU cc_start: 0.7593 (mt-10) cc_final: 0.7021 (mt-10) REVERT: A 344 ASP cc_start: 0.7892 (t0) cc_final: 0.7588 (t70) REVERT: A 350 ILE cc_start: 0.8509 (mt) cc_final: 0.7356 (mt) REVERT: A 354 GLU cc_start: 0.8173 (OUTLIER) cc_final: 0.7450 (mp0) REVERT: A 377 ASN cc_start: 0.8348 (t0) cc_final: 0.7489 (p0) REVERT: B 11 LYS cc_start: 0.9013 (OUTLIER) cc_final: 0.8791 (pttt) REVERT: B 142 TYR cc_start: 0.8408 (m-80) cc_final: 0.7843 (m-10) REVERT: B 174 LYS cc_start: 0.8622 (tppp) cc_final: 0.7961 (tppp) REVERT: B 177 MET cc_start: 0.8435 (tpp) cc_final: 0.8083 (tpp) REVERT: B 199 ASN cc_start: 0.8532 (t0) cc_final: 0.8185 (t0) REVERT: B 262 ILE cc_start: 0.8252 (OUTLIER) cc_final: 0.8018 (mp) REVERT: B 264 MET cc_start: 0.7504 (ttm) cc_final: 0.7147 (ttm) REVERT: B 312 MET cc_start: 0.8215 (mmp) cc_final: 0.8000 (mmm) REVERT: B 338 GLN cc_start: 0.8397 (mm110) cc_final: 0.8156 (mm110) REVERT: B 339 ASN cc_start: 0.8497 (t0) cc_final: 0.8159 (t0) REVERT: B 406 ARG cc_start: 0.6990 (mtp85) cc_final: 0.6613 (ttt90) REVERT: B 407 ASN cc_start: 0.7479 (m-40) cc_final: 0.7212 (m110) outliers start: 13 outliers final: 7 residues processed: 185 average time/residue: 1.9546 time to fit residues: 378.5342 Evaluate side-chains 189 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 179 time to evaluate : 0.895 ------------------------------------------------------------------------------- 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 354 GLU Chi-restraints excluded: chain A residue 370 GLN Chi-restraints excluded: chain B residue 11 LYS 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 262 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 43 optimal weight: 6.9990 chunk 12 optimal weight: 4.9990 chunk 48 optimal weight: 10.0000 chunk 18 optimal weight: 0.6980 chunk 23 optimal weight: 1.9990 chunk 93 optimal weight: 7.9990 chunk 33 optimal weight: 6.9990 chunk 52 optimal weight: 10.0000 chunk 0 optimal weight: 8.9990 chunk 3 optimal weight: 0.9990 chunk 30 optimal weight: 7.9990 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3551 r_free = 0.3551 target = 0.119271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.096959 restraints weight = 15034.711| |-----------------------------------------------------------------------------| r_work (start): 0.3220 rms_B_bonded: 1.77 r_work: 0.3090 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2946 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.2438 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= 0.213 Angle : 0.554 10.280 14598 Z= 0.298 Chirality : 0.039 0.206 1679 Planarity : 0.004 0.033 1310 Dihedral : 20.261 73.795 3082 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.25 % Allowed : 4.01 % Favored : 95.74 % Rotamer: Outliers : 2.43 % Allowed : 23.29 % Favored : 74.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.30), residues: 799 helix: 1.97 (0.28), residues: 365 sheet: -0.05 (0.38), residues: 155 loop : -1.49 (0.34), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 43 HIS 0.006 0.001 HIS A 72 PHE 0.013 0.002 PHE A 389 TYR 0.017 0.001 TYR A 351 ARG 0.006 0.001 ARG B 25 Details of bonding type rmsd hydrogen bonds : bond 0.04727 ( 465) hydrogen bonds : angle 3.72710 ( 1195) metal coordination : bond 0.00808 ( 8) metal coordination : angle 3.20323 ( 12) covalent geometry : bond 0.00471 (10291) covalent geometry : angle 0.54647 (14586) *********************** 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 194 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 177 time to evaluate : 0.824 Fit side-chains revert: symmetry clash REVERT: A 16 ASP cc_start: 0.8021 (t0) cc_final: 0.7820 (t70) REVERT: A 105 TYR cc_start: 0.9165 (m-80) cc_final: 0.8882 (m-80) REVERT: A 221 ILE cc_start: 0.8996 (mt) cc_final: 0.8771 (mp) REVERT: A 244 LYS cc_start: 0.8878 (pttt) cc_final: 0.8618 (pttt) REVERT: A 312 MET cc_start: 0.8725 (tpp) cc_final: 0.8297 (mpp) REVERT: A 344 ASP cc_start: 0.8050 (t0) cc_final: 0.7777 (t70) REVERT: A 350 ILE cc_start: 0.8504 (mt) cc_final: 0.7395 (mt) REVERT: A 354 GLU cc_start: 0.8214 (OUTLIER) cc_final: 0.7389 (mp0) REVERT: A 355 GLU cc_start: 0.8553 (OUTLIER) cc_final: 0.8344 (mt-10) REVERT: A 377 ASN cc_start: 0.8442 (t0) cc_final: 0.7523 (p0) REVERT: B 11 LYS cc_start: 0.9040 (OUTLIER) cc_final: 0.8831 (pttt) REVERT: B 177 MET cc_start: 0.8435 (tpp) cc_final: 0.8084 (tpp) REVERT: B 199 ASN cc_start: 0.8562 (t0) cc_final: 0.8192 (t0) REVERT: B 254 ARG cc_start: 0.8031 (mtt90) cc_final: 0.7685 (mtp85) REVERT: B 264 MET cc_start: 0.7593 (ttm) cc_final: 0.7194 (ttm) REVERT: B 312 MET cc_start: 0.8290 (mmp) cc_final: 0.8044 (mmm) REVERT: B 338 GLN cc_start: 0.8411 (mm110) cc_final: 0.8116 (mm110) REVERT: B 339 ASN cc_start: 0.8495 (t0) cc_final: 0.8120 (t0) REVERT: B 406 ARG cc_start: 0.7004 (mtp85) cc_final: 0.6585 (ttt90) outliers start: 17 outliers final: 8 residues processed: 184 average time/residue: 2.2123 time to fit residues: 426.4923 Evaluate side-chains 186 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 175 time to evaluate : 0.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 GLN 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 354 GLU Chi-restraints excluded: chain A residue 355 GLU Chi-restraints excluded: chain A residue 370 GLN Chi-restraints excluded: chain B residue 11 LYS Chi-restraints excluded: chain B residue 114 MET Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 239 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 42 optimal weight: 10.0000 chunk 66 optimal weight: 0.9990 chunk 48 optimal weight: 10.0000 chunk 50 optimal weight: 8.9990 chunk 88 optimal weight: 7.9990 chunk 51 optimal weight: 10.0000 chunk 83 optimal weight: 7.9990 chunk 43 optimal weight: 5.9990 chunk 44 optimal weight: 5.9990 chunk 25 optimal weight: 9.9990 chunk 28 optimal weight: 3.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 377 ASN B 194 HIS 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 = 0.3525 r_free = 0.3525 target = 0.117468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.095121 restraints weight = 15105.337| |-----------------------------------------------------------------------------| r_work (start): 0.3192 rms_B_bonded: 1.80 r_work: 0.3061 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2916 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.2525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.058 10299 Z= 0.315 Angle : 0.636 10.976 14598 Z= 0.339 Chirality : 0.043 0.220 1679 Planarity : 0.004 0.039 1310 Dihedral : 20.354 73.798 3082 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.25 % Allowed : 4.51 % Favored : 95.24 % Rotamer: Outliers : 2.29 % Allowed : 23.86 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.29), residues: 799 helix: 1.73 (0.28), residues: 364 sheet: -0.12 (0.38), residues: 157 loop : -1.56 (0.33), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 340 HIS 0.007 0.002 HIS A 72 PHE 0.017 0.002 PHE A 102 TYR 0.020 0.002 TYR A 351 ARG 0.008 0.001 ARG B 25 Details of bonding type rmsd hydrogen bonds : bond 0.05410 ( 465) hydrogen bonds : angle 3.89283 ( 1195) metal coordination : bond 0.01120 ( 8) metal coordination : angle 3.83582 ( 12) covalent geometry : bond 0.00701 (10291) covalent geometry : angle 0.62669 (14586) *********************** 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 190 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 174 time to evaluate : 0.774 Fit side-chains revert: symmetry clash REVERT: A 16 ASP cc_start: 0.8049 (t0) cc_final: 0.7815 (t70) REVERT: A 138 ASN cc_start: 0.7319 (p0) cc_final: 0.7105 (p0) REVERT: A 177 MET cc_start: 0.9061 (tpp) cc_final: 0.8647 (tpt) REVERT: A 221 ILE cc_start: 0.8999 (mt) cc_final: 0.8766 (mp) REVERT: A 244 LYS cc_start: 0.8898 (pttt) cc_final: 0.8644 (pttt) REVERT: A 264 MET cc_start: 0.8445 (mtt) cc_final: 0.7996 (mtp) REVERT: A 344 ASP cc_start: 0.8122 (t0) cc_final: 0.7867 (t70) REVERT: B 174 LYS cc_start: 0.8558 (tppp) cc_final: 0.8284 (tppp) REVERT: B 177 MET cc_start: 0.8423 (tpp) cc_final: 0.8053 (tpp) REVERT: B 187 VAL cc_start: 0.8393 (OUTLIER) cc_final: 0.8177 (m) REVERT: B 199 ASN cc_start: 0.8546 (t0) cc_final: 0.8143 (t0) REVERT: B 264 MET cc_start: 0.7607 (ttm) cc_final: 0.7247 (ttm) REVERT: B 312 MET cc_start: 0.8366 (mmp) cc_final: 0.8113 (mmm) REVERT: B 338 GLN cc_start: 0.8433 (mm110) cc_final: 0.8160 (mm110) REVERT: B 339 ASN cc_start: 0.8484 (t0) cc_final: 0.8152 (t0) REVERT: B 406 ARG cc_start: 0.7107 (mtp85) cc_final: 0.6627 (ttt90) outliers start: 16 outliers final: 10 residues processed: 184 average time/residue: 1.7689 time to fit residues: 341.4073 Evaluate side-chains 183 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 172 time to evaluate : 0.866 ------------------------------------------------------------------------------- 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 114 MET Chi-restraints excluded: chain B residue 134 VAL 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 262 ILE Chi-restraints excluded: chain B residue 325 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 78 optimal weight: 3.9990 chunk 13 optimal weight: 5.9990 chunk 45 optimal weight: 7.9990 chunk 90 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 34 optimal weight: 6.9990 chunk 61 optimal weight: 6.9990 chunk 0 optimal weight: 6.9990 chunk 71 optimal weight: 6.9990 chunk 73 optimal weight: 5.9990 chunk 40 optimal weight: 3.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- 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 ** A 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3538 r_free = 0.3538 target = 0.118380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.096116 restraints weight = 15025.497| |-----------------------------------------------------------------------------| r_work (start): 0.3208 rms_B_bonded: 1.77 r_work: 0.3080 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2937 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.2545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 10299 Z= 0.249 Angle : 0.599 10.521 14598 Z= 0.323 Chirality : 0.041 0.231 1679 Planarity : 0.004 0.036 1310 Dihedral : 20.302 73.724 3082 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.25 % Allowed : 4.01 % Favored : 95.74 % Rotamer: Outliers : 1.86 % Allowed : 24.57 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.29), residues: 799 helix: 1.80 (0.28), residues: 365 sheet: -0.10 (0.38), residues: 157 loop : -1.57 (0.34), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 17 HIS 0.006 0.001 HIS A 72 PHE 0.015 0.002 PHE A 389 TYR 0.034 0.002 TYR B 351 ARG 0.008 0.001 ARG B 25 Details of bonding type rmsd hydrogen bonds : bond 0.04945 ( 465) hydrogen bonds : angle 3.83894 ( 1195) metal coordination : bond 0.00957 ( 8) metal coordination : angle 3.27390 ( 12) covalent geometry : bond 0.00552 (10291) covalent geometry : angle 0.59234 (14586) *********************** 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 186 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 173 time to evaluate : 0.880 Fit side-chains REVERT: A 16 ASP cc_start: 0.8012 (t0) cc_final: 0.7784 (t70) REVERT: A 44 GLU cc_start: 0.8780 (tt0) cc_final: 0.8544 (tt0) REVERT: A 138 ASN cc_start: 0.7309 (p0) cc_final: 0.7109 (p0) REVERT: A 244 LYS cc_start: 0.8888 (pttt) cc_final: 0.8631 (pttt) REVERT: A 264 MET cc_start: 0.8425 (mtt) cc_final: 0.7993 (mtp) REVERT: A 344 ASP cc_start: 0.8119 (t0) cc_final: 0.7868 (t70) REVERT: B 8 GLU cc_start: 0.8027 (tt0) cc_final: 0.7137 (tp30) REVERT: B 177 MET cc_start: 0.8434 (tpp) cc_final: 0.8098 (tpp) REVERT: B 199 ASN cc_start: 0.8541 (t0) cc_final: 0.8147 (t0) REVERT: B 264 MET cc_start: 0.7619 (ttm) cc_final: 0.7299 (ttm) REVERT: B 312 MET cc_start: 0.8360 (mmp) cc_final: 0.8103 (mmm) REVERT: B 338 GLN cc_start: 0.8406 (mm110) cc_final: 0.8139 (mm110) REVERT: B 339 ASN cc_start: 0.8487 (t0) cc_final: 0.8174 (t0) REVERT: B 406 ARG cc_start: 0.7066 (mtp85) cc_final: 0.6636 (ttt90) outliers start: 13 outliers final: 8 residues processed: 180 average time/residue: 2.2648 time to fit residues: 427.8601 Evaluate side-chains 181 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 173 time to evaluate : 0.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 LYS Chi-restraints excluded: chain A residue 174 LYS Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 370 GLN Chi-restraints excluded: chain B residue 114 MET Chi-restraints excluded: chain B residue 239 THR 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 75 optimal weight: 1.9990 chunk 45 optimal weight: 8.9990 chunk 51 optimal weight: 10.0000 chunk 69 optimal weight: 7.9990 chunk 71 optimal weight: 7.9990 chunk 22 optimal weight: 0.8980 chunk 32 optimal weight: 2.9990 chunk 19 optimal weight: 8.9990 chunk 65 optimal weight: 3.9990 chunk 89 optimal weight: 1.9990 chunk 25 optimal weight: 9.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 ASN ** A 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 = 0.3561 r_free = 0.3561 target = 0.119987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.097823 restraints weight = 14960.222| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 1.75 r_work: 0.3110 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2967 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.2618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 10299 Z= 0.180 Angle : 0.572 10.107 14598 Z= 0.309 Chirality : 0.039 0.223 1679 Planarity : 0.004 0.035 1310 Dihedral : 20.259 73.762 3080 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.25 % Allowed : 3.88 % Favored : 95.87 % Rotamer: Outliers : 1.71 % Allowed : 25.14 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.30), residues: 799 helix: 1.91 (0.28), residues: 365 sheet: -0.01 (0.39), residues: 153 loop : -1.44 (0.34), residues: 281 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 340 HIS 0.004 0.001 HIS A 72 PHE 0.015 0.002 PHE A 389 TYR 0.017 0.001 TYR A 84 ARG 0.008 0.001 ARG B 25 Details of bonding type rmsd hydrogen bonds : bond 0.04507 ( 465) hydrogen bonds : angle 3.73347 ( 1195) metal coordination : bond 0.00688 ( 8) metal coordination : angle 2.60393 ( 12) covalent geometry : bond 0.00398 (10291) covalent geometry : angle 0.56736 (14586) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1598 Ramachandran restraints generated. 799 Oldfield, 0 Emsley, 799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1598 Ramachandran restraints generated. 799 Oldfield, 0 Emsley, 799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 173 time to evaluate : 0.887 Fit side-chains REVERT: A 16 ASP cc_start: 0.7987 (t0) cc_final: 0.7749 (t70) REVERT: A 221 ILE cc_start: 0.8949 (mt) cc_final: 0.8736 (mp) REVERT: A 242 ARG cc_start: 0.8534 (ptp90) cc_final: 0.8028 (ptp90) REVERT: A 244 LYS cc_start: 0.8849 (pttt) cc_final: 0.8587 (pttt) REVERT: A 264 MET cc_start: 0.8436 (mtt) cc_final: 0.8019 (mtp) REVERT: A 344 ASP cc_start: 0.7920 (t0) cc_final: 0.7642 (t70) REVERT: B 177 MET cc_start: 0.8408 (tpp) cc_final: 0.8069 (tpp) REVERT: B 187 VAL cc_start: 0.8360 (OUTLIER) cc_final: 0.8118 (m) REVERT: B 199 ASN cc_start: 0.8458 (t0) cc_final: 0.8242 (t0) REVERT: B 264 MET cc_start: 0.7604 (ttm) cc_final: 0.7262 (ttm) REVERT: B 312 MET cc_start: 0.8287 (mmp) cc_final: 0.8027 (mmm) REVERT: B 338 GLN cc_start: 0.8366 (mm110) cc_final: 0.8119 (mm110) REVERT: B 339 ASN cc_start: 0.8471 (t0) cc_final: 0.8164 (t0) REVERT: B 406 ARG cc_start: 0.6915 (mtp85) cc_final: 0.6551 (ttt90) outliers start: 12 outliers final: 8 residues processed: 179 average time/residue: 1.7435 time to fit residues: 327.1695 Evaluate side-chains 182 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 173 time to evaluate : 0.838 ------------------------------------------------------------------------------- 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 114 MET 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 262 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 93 optimal weight: 5.9990 chunk 32 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 58 optimal weight: 3.9990 chunk 46 optimal weight: 10.0000 chunk 34 optimal weight: 4.9990 chunk 83 optimal weight: 7.9990 chunk 33 optimal weight: 8.9990 chunk 13 optimal weight: 8.9990 chunk 52 optimal weight: 10.0000 chunk 54 optimal weight: 8.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- 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 = 0.3543 r_free = 0.3543 target = 0.118677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.096407 restraints weight = 15023.114| |-----------------------------------------------------------------------------| r_work (start): 0.3213 rms_B_bonded: 1.79 r_work: 0.3083 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2937 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.2613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 10299 Z= 0.241 Angle : 0.598 9.992 14598 Z= 0.322 Chirality : 0.040 0.226 1679 Planarity : 0.004 0.038 1310 Dihedral : 20.284 73.767 3080 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.25 % Allowed : 4.38 % Favored : 95.37 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.29), residues: 799 helix: 1.83 (0.27), residues: 365 sheet: -0.03 (0.39), residues: 157 loop : -1.54 (0.34), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A 340 HIS 0.006 0.001 HIS A 72 PHE 0.014 0.002 PHE A 389 TYR 0.032 0.002 TYR B 351 ARG 0.008 0.001 ARG B 25 Details of bonding type rmsd hydrogen bonds : bond 0.04840 ( 465) hydrogen bonds : angle 3.79317 ( 1195) metal coordination : bond 0.00869 ( 8) metal coordination : angle 2.66592 ( 12) covalent geometry : bond 0.00537 (10291) covalent geometry : angle 0.59337 (14586) =============================================================================== Job complete usr+sys time: 9244.93 seconds wall clock time: 161 minutes 29.21 seconds (9689.21 seconds total)