Starting phenix.real_space_refine on Sun Apr 7 06:07:32 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j1j_35926/04_2024/8j1j_35926.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j1j_35926/04_2024/8j1j_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j1j_35926/04_2024/8j1j_35926.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j1j_35926/04_2024/8j1j_35926.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j1j_35926/04_2024/8j1j_35926.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j1j_35926/04_2024/8j1j_35926.pdb" } 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 Residue "A TYR 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 270": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 324": "OE1" <-> "OE2" Residue "B TYR 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 343": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/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: 6.23, 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.21 Conformation dependent library (CDL) restraints added in 1.2 seconds 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: 4.08 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: 4.28 Time building geometry restraints manager: 5.34 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: 99.25 - 106.20: 973 106.20 - 113.16: 5630 113.16 - 120.11: 3751 120.11 - 127.06: 3823 127.06 - 134.01: 409 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 2.520 nonbonded pdb=" O2' A C -54 " pdb=" OG SER B 92 " model vdw 2.248 2.440 nonbonded pdb=" NE2 GLN A 28 " pdb=" OD1 ASP A 122 " model vdw 2.266 2.520 nonbonded pdb=" NH1 ARG A 298 " pdb=" OP1 DA D 12 " model vdw 2.275 2.520 nonbonded pdb=" OG SER A 150 " pdb=" OP1 DT E -4 " model vdw 2.304 2.440 ... (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 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: 0.860 Check model and map are aligned: 0.140 Set scattering table: 0.080 Process input model: 36.200 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.050 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:13.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.510 ------------------------------------------------------------------------------- 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 0.032 10291 Z= 0.235 Angle : 0.531 5.196 14586 Z= 0.324 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 *********************** 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 fitting. rotamer outliers: 10 poor density : 225 time to evaluate : 0.891 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: 1.5898 time to fit residues: 393.4433 Evaluate side-chains 188 residues out of total 701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 183 time to evaluate : 0.893 ------------------------------------------------------------------------------- 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: 0.0020 chunk 71 optimal weight: 9.9990 chunk 39 optimal weight: 2.9990 chunk 24 optimal weight: 0.0010 chunk 48 optimal weight: 10.0000 chunk 38 optimal weight: 7.9990 chunk 73 optimal weight: 2.9990 chunk 28 optimal weight: 0.3980 chunk 44 optimal weight: 6.9990 chunk 54 optimal weight: 8.9990 chunk 85 optimal weight: 9.9990 overall best weight: 1.2798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 186 GLN A 204 ASN A 339 ASN A 346 GLN B 252 ASN B 296 ASN B 377 ASN B 403 ASN B 412 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.1569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 10291 Z= 0.166 Angle : 0.505 10.975 14586 Z= 0.280 Chirality : 0.037 0.206 1679 Planarity : 0.004 0.035 1310 Dihedral : 20.426 73.708 3088 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.25 % Allowed : 3.50 % Favored : 96.25 % Rotamer: Outliers : 2.86 % Allowed : 15.43 % Favored : 81.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.05 (0.29), residues: 799 helix: 1.32 (0.28), residues: 361 sheet: -0.32 (0.41), residues: 151 loop : -1.62 (0.33), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 43 HIS 0.003 0.001 HIS B 303 PHE 0.015 0.002 PHE A 389 TYR 0.015 0.001 TYR A 351 ARG 0.005 0.000 ARG B 25 *********************** 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 194 residues out of total 701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 174 time to evaluate : 0.919 Fit side-chains revert: symmetry clash REVERT: A 14 ASP cc_start: 0.8346 (OUTLIER) cc_final: 0.8091 (t70) REVERT: A 25 ARG cc_start: 0.7992 (mtp85) cc_final: 0.7790 (mpt90) REVERT: A 108 GLU cc_start: 0.8363 (mp0) cc_final: 0.8117 (mp0) REVERT: A 141 ASP cc_start: 0.8576 (OUTLIER) cc_final: 0.8337 (m-30) REVERT: A 221 ILE cc_start: 0.8957 (mt) cc_final: 0.8716 (mp) REVERT: A 242 ARG cc_start: 0.8278 (ptp90) cc_final: 0.8043 (ptp90) REVERT: A 244 LYS cc_start: 0.8634 (pttt) cc_final: 0.8415 (pttt) REVERT: A 283 ARG cc_start: 0.8725 (tpp-160) cc_final: 0.8496 (tpt170) REVERT: A 344 ASP cc_start: 0.8174 (t0) cc_final: 0.7915 (t70) REVERT: A 377 ASN cc_start: 0.8280 (t0) cc_final: 0.7293 (p0) REVERT: A 415 LYS cc_start: 0.7453 (mttt) cc_final: 0.6946 (mttt) REVERT: A 419 GLU cc_start: 0.7310 (mm-30) cc_final: 0.6851 (mp0) REVERT: B 177 MET cc_start: 0.8231 (tpp) cc_final: 0.7991 (tpp) REVERT: B 222 MET cc_start: 0.8640 (ttp) cc_final: 0.8331 (ttt) REVERT: B 316 MET cc_start: 0.8490 (mmm) cc_final: 0.8203 (mmm) REVERT: B 324 GLU cc_start: 0.7399 (mp0) cc_final: 0.7092 (mp0) REVERT: B 339 ASN cc_start: 0.8388 (t0) cc_final: 0.8127 (t0) REVERT: B 407 ASN cc_start: 0.7569 (m-40) cc_final: 0.7203 (m-40) outliers start: 20 outliers final: 5 residues processed: 187 average time/residue: 1.8550 time to fit residues: 363.9115 Evaluate side-chains 177 residues out of total 701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 170 time to evaluate : 0.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 ASP Chi-restraints excluded: chain A residue 141 ASP Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain B residue 51 ASP Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 219 ASN 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 47 optimal weight: 10.0000 chunk 26 optimal weight: 9.9990 chunk 71 optimal weight: 6.9990 chunk 58 optimal weight: 6.9990 chunk 23 optimal weight: 0.4980 chunk 85 optimal weight: 7.9990 chunk 92 optimal weight: 9.9990 chunk 76 optimal weight: 9.9990 chunk 84 optimal weight: 0.6980 chunk 29 optimal weight: 7.9990 chunk 68 optimal weight: 7.9990 overall best weight: 4.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 HIS A 77 HIS ** A 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 204 ASN ** A 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 77 HIS B 199 ASN B 412 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.1882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 10291 Z= 0.396 Angle : 0.583 10.786 14586 Z= 0.317 Chirality : 0.042 0.220 1679 Planarity : 0.004 0.034 1310 Dihedral : 20.403 73.841 3082 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.25 % Allowed : 3.63 % Favored : 96.12 % Rotamer: Outliers : 3.43 % Allowed : 17.71 % Favored : 78.86 % 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: 0.04 (0.29), residues: 799 helix: 1.41 (0.28), residues: 362 sheet: -0.23 (0.39), residues: 151 loop : -1.63 (0.32), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 43 HIS 0.007 0.002 HIS A 72 PHE 0.016 0.002 PHE A 102 TYR 0.021 0.002 TYR A 351 ARG 0.006 0.001 ARG B 25 *********************** 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 202 residues out of total 701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 178 time to evaluate : 0.911 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 ASP cc_start: 0.8396 (OUTLIER) cc_final: 0.8153 (t70) REVERT: A 16 ASP cc_start: 0.7970 (t0) cc_final: 0.7662 (t0) REVERT: A 108 GLU cc_start: 0.8346 (mp0) cc_final: 0.8116 (mp0) REVERT: A 221 ILE cc_start: 0.9025 (mt) cc_final: 0.8783 (mp) REVERT: A 242 ARG cc_start: 0.8356 (ptp90) cc_final: 0.7966 (ptp90) REVERT: A 244 LYS cc_start: 0.8692 (pttt) cc_final: 0.8461 (pttt) REVERT: A 264 MET cc_start: 0.8433 (mtt) cc_final: 0.8137 (mtp) REVERT: A 283 ARG cc_start: 0.8735 (tpp-160) cc_final: 0.8443 (tpt170) REVERT: A 312 MET cc_start: 0.8621 (mmp) cc_final: 0.8068 (mmt) REVERT: A 344 ASP cc_start: 0.8193 (t0) cc_final: 0.7912 (t70) REVERT: A 377 ASN cc_start: 0.8296 (t0) cc_final: 0.7276 (p0) REVERT: A 402 TYR cc_start: 0.8583 (t80) cc_final: 0.7920 (t80) REVERT: B 147 SER cc_start: 0.9054 (m) cc_final: 0.8589 (p) REVERT: B 222 MET cc_start: 0.8659 (ttp) cc_final: 0.8264 (ttt) REVERT: B 264 MET cc_start: 0.7349 (OUTLIER) cc_final: 0.7019 (mpp) REVERT: B 316 MET cc_start: 0.8507 (mmm) cc_final: 0.8266 (mmm) REVERT: B 339 ASN cc_start: 0.8423 (t0) cc_final: 0.8145 (t0) outliers start: 24 outliers final: 8 residues processed: 189 average time/residue: 1.8296 time to fit residues: 362.4369 Evaluate side-chains 182 residues out of total 701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 172 time to evaluate : 0.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 ASP Chi-restraints excluded: chain A residue 160 LYS Chi-restraints excluded: chain A residue 196 ASP Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 370 GLN Chi-restraints excluded: chain B residue 51 ASP Chi-restraints excluded: chain B residue 262 ILE Chi-restraints excluded: chain B residue 264 MET Chi-restraints excluded: chain B residue 325 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 84 optimal weight: 5.9990 chunk 64 optimal weight: 4.9990 chunk 44 optimal weight: 5.9990 chunk 9 optimal weight: 2.9990 chunk 40 optimal weight: 5.9990 chunk 57 optimal weight: 6.9990 chunk 85 optimal weight: 9.9990 chunk 90 optimal weight: 10.0000 chunk 81 optimal weight: 0.9990 chunk 24 optimal weight: 0.2980 chunk 75 optimal weight: 5.9990 overall best weight: 3.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 199 ASN B 412 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.2052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 10291 Z= 0.274 Angle : 0.532 10.201 14586 Z= 0.295 Chirality : 0.039 0.222 1679 Planarity : 0.004 0.032 1310 Dihedral : 20.315 73.771 3080 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.25 % Allowed : 3.25 % Favored : 96.50 % Rotamer: Outliers : 3.00 % Allowed : 19.86 % Favored : 77.14 % 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: 0.24 (0.29), residues: 799 helix: 1.61 (0.28), residues: 364 sheet: -0.19 (0.39), residues: 157 loop : -1.62 (0.33), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 43 HIS 0.005 0.001 HIS A 72 PHE 0.014 0.002 PHE A 389 TYR 0.016 0.001 TYR A 351 ARG 0.006 0.000 ARG B 25 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1598 Ramachandran restraints generated. 799 Oldfield, 0 Emsley, 799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1598 Ramachandran restraints generated. 799 Oldfield, 0 Emsley, 799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 175 time to evaluate : 0.841 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 ASP cc_start: 0.8365 (m-30) cc_final: 0.8109 (t70) REVERT: A 16 ASP cc_start: 0.7922 (t0) cc_final: 0.7598 (t70) REVERT: A 108 GLU cc_start: 0.8347 (mp0) cc_final: 0.8116 (mp0) REVERT: A 177 MET cc_start: 0.9075 (tpp) cc_final: 0.8674 (tpt) REVERT: A 221 ILE cc_start: 0.8958 (mt) cc_final: 0.8649 (mp) REVERT: A 242 ARG cc_start: 0.8353 (ptp90) cc_final: 0.7769 (ptp90) REVERT: A 244 LYS cc_start: 0.8667 (pttt) cc_final: 0.8435 (pttt) REVERT: A 283 ARG cc_start: 0.8722 (tpp-160) cc_final: 0.8484 (tpt170) REVERT: A 312 MET cc_start: 0.8637 (mmp) cc_final: 0.8162 (mmt) REVERT: A 344 ASP cc_start: 0.8127 (t0) cc_final: 0.7877 (t70) REVERT: A 377 ASN cc_start: 0.8219 (t0) cc_final: 0.7169 (p0) REVERT: B 142 TYR cc_start: 0.8368 (m-80) cc_final: 0.8127 (m-10) REVERT: B 264 MET cc_start: 0.7311 (OUTLIER) cc_final: 0.7089 (mpp) REVERT: B 316 MET cc_start: 0.8510 (mmm) cc_final: 0.8248 (mmm) REVERT: B 338 GLN cc_start: 0.8301 (mm110) cc_final: 0.8041 (mm110) REVERT: B 339 ASN cc_start: 0.8391 (t0) cc_final: 0.8104 (t0) outliers start: 21 outliers final: 10 residues processed: 187 average time/residue: 1.8276 time to fit residues: 358.3129 Evaluate side-chains 182 residues out of total 701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 171 time to evaluate : 0.978 ------------------------------------------------------------------------------- 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 351 TYR Chi-restraints excluded: chain A residue 370 GLN Chi-restraints excluded: chain B residue 51 ASP Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 239 THR Chi-restraints excluded: chain B residue 264 MET Chi-restraints excluded: chain B residue 325 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 51 optimal weight: 10.0000 chunk 1 optimal weight: 0.9980 chunk 67 optimal weight: 0.5980 chunk 37 optimal weight: 8.9990 chunk 77 optimal weight: 7.9990 chunk 62 optimal weight: 5.9990 chunk 0 optimal weight: 7.9990 chunk 46 optimal weight: 8.9990 chunk 81 optimal weight: 6.9990 chunk 22 optimal weight: 9.9990 chunk 30 optimal weight: 7.9990 overall best weight: 4.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 199 ASN B 412 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.2219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 10291 Z= 0.387 Angle : 0.583 10.043 14586 Z= 0.317 Chirality : 0.042 0.230 1679 Planarity : 0.004 0.036 1310 Dihedral : 20.378 73.846 3080 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.25 % Allowed : 4.51 % Favored : 95.24 % Rotamer: Outliers : 4.43 % Allowed : 19.57 % Favored : 76.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.19 (0.29), residues: 799 helix: 1.62 (0.28), residues: 365 sheet: -0.28 (0.38), residues: 157 loop : -1.69 (0.33), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 43 HIS 0.007 0.002 HIS A 72 PHE 0.015 0.002 PHE A 102 TYR 0.020 0.002 TYR A 351 ARG 0.007 0.001 ARG B 406 *********************** 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 203 residues out of total 701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 172 time to evaluate : 0.937 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 14 ASP cc_start: 0.8385 (OUTLIER) cc_final: 0.8139 (t70) REVERT: A 16 ASP cc_start: 0.7940 (t0) cc_final: 0.7696 (t70) REVERT: A 108 GLU cc_start: 0.8342 (mp0) cc_final: 0.8126 (mp0) REVERT: A 138 ASN cc_start: 0.7371 (p0) cc_final: 0.7152 (p0) REVERT: A 177 MET cc_start: 0.9112 (tpp) cc_final: 0.8653 (tpt) REVERT: A 221 ILE cc_start: 0.9034 (mt) cc_final: 0.8789 (mp) REVERT: A 242 ARG cc_start: 0.8418 (ptp90) cc_final: 0.8150 (ptp90) REVERT: A 244 LYS cc_start: 0.8686 (pttt) cc_final: 0.8448 (pttt) REVERT: A 283 ARG cc_start: 0.8711 (tpp-160) cc_final: 0.8391 (tpt170) REVERT: A 312 MET cc_start: 0.8660 (mmp) cc_final: 0.7991 (mmt) REVERT: A 344 ASP cc_start: 0.8139 (t0) cc_final: 0.7907 (t70) REVERT: A 355 GLU cc_start: 0.8524 (OUTLIER) cc_final: 0.8319 (mt-10) REVERT: A 377 ASN cc_start: 0.8175 (t0) cc_final: 0.7202 (p0) REVERT: B 210 GLU cc_start: 0.8049 (tp30) cc_final: 0.7826 (tp30) REVERT: B 264 MET cc_start: 0.7391 (OUTLIER) cc_final: 0.7143 (mpp) REVERT: B 316 MET cc_start: 0.8512 (mmm) cc_final: 0.8261 (mmm) REVERT: B 338 GLN cc_start: 0.8230 (mm110) cc_final: 0.7929 (mm110) REVERT: B 339 ASN cc_start: 0.8410 (t0) cc_final: 0.8137 (t0) REVERT: B 407 ASN cc_start: 0.7517 (m-40) cc_final: 0.7250 (m110) outliers start: 31 outliers final: 13 residues processed: 186 average time/residue: 1.7739 time to fit residues: 345.9944 Evaluate side-chains 192 residues out of total 701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 176 time to evaluate : 0.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 ASP Chi-restraints excluded: chain A residue 160 LYS Chi-restraints excluded: chain A residue 174 LYS Chi-restraints excluded: chain A residue 196 ASP Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 355 GLU Chi-restraints excluded: chain A residue 370 GLN Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 51 ASP 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 Chi-restraints excluded: chain B residue 264 MET Chi-restraints excluded: chain B residue 325 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 81 optimal weight: 2.9990 chunk 17 optimal weight: 0.8980 chunk 53 optimal weight: 10.0000 chunk 22 optimal weight: 4.9990 chunk 90 optimal weight: 7.9990 chunk 75 optimal weight: 0.8980 chunk 42 optimal weight: 10.0000 chunk 7 optimal weight: 2.9990 chunk 30 optimal weight: 8.9990 chunk 47 optimal weight: 10.0000 chunk 87 optimal weight: 0.9980 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 199 ASN B 412 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.2362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10291 Z= 0.189 Angle : 0.510 9.864 14586 Z= 0.281 Chirality : 0.037 0.218 1679 Planarity : 0.003 0.034 1310 Dihedral : 20.249 73.745 3080 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.25 % Allowed : 3.25 % Favored : 96.50 % Rotamer: Outliers : 2.86 % Allowed : 22.29 % Favored : 74.86 % 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: 0.47 (0.29), residues: 799 helix: 1.85 (0.28), residues: 367 sheet: -0.09 (0.38), residues: 157 loop : -1.61 (0.34), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 17 HIS 0.003 0.001 HIS B 72 PHE 0.013 0.001 PHE A 389 TYR 0.013 0.001 TYR A 351 ARG 0.007 0.000 ARG B 25 *********************** 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 205 residues out of total 701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 185 time to evaluate : 0.921 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 14 ASP cc_start: 0.8325 (m-30) cc_final: 0.8085 (t70) REVERT: A 16 ASP cc_start: 0.7907 (t0) cc_final: 0.7700 (t70) REVERT: A 105 TYR cc_start: 0.9173 (m-80) cc_final: 0.8874 (m-80) REVERT: A 191 GLN cc_start: 0.8942 (mt0) cc_final: 0.8646 (mt0) REVERT: A 221 ILE cc_start: 0.9017 (mt) cc_final: 0.8774 (mp) REVERT: A 244 LYS cc_start: 0.8651 (pttt) cc_final: 0.8392 (pttt) REVERT: A 266 ARG cc_start: 0.8132 (mtp85) cc_final: 0.7753 (mtt180) REVERT: A 267 GLN cc_start: 0.8416 (tm-30) cc_final: 0.8041 (tm-30) REVERT: A 283 ARG cc_start: 0.8688 (tpp-160) cc_final: 0.8482 (tpt170) REVERT: A 288 GLU cc_start: 0.7480 (mt-10) cc_final: 0.6911 (mt-10) REVERT: A 312 MET cc_start: 0.8606 (mmp) cc_final: 0.8210 (mmp) REVERT: A 344 ASP cc_start: 0.8111 (t0) cc_final: 0.7851 (t70) REVERT: A 377 ASN cc_start: 0.8074 (t0) cc_final: 0.6966 (p0) REVERT: A 419 GLU cc_start: 0.7737 (tm-30) cc_final: 0.7243 (mp0) REVERT: B 129 LYS cc_start: 0.8773 (ptmt) cc_final: 0.8517 (ttmt) REVERT: B 142 TYR cc_start: 0.8390 (m-80) cc_final: 0.8166 (m-10) REVERT: B 174 LYS cc_start: 0.8475 (tppp) cc_final: 0.7846 (tppp) REVERT: B 187 VAL cc_start: 0.8388 (OUTLIER) cc_final: 0.8183 (m) REVERT: B 210 GLU cc_start: 0.8038 (tp30) cc_final: 0.7792 (tp30) REVERT: B 262 ILE cc_start: 0.8285 (OUTLIER) cc_final: 0.8048 (mp) REVERT: B 316 MET cc_start: 0.8521 (mmm) cc_final: 0.8255 (mmm) REVERT: B 338 GLN cc_start: 0.8217 (mm110) cc_final: 0.7959 (mm110) REVERT: B 339 ASN cc_start: 0.8402 (t0) cc_final: 0.8105 (t0) outliers start: 20 outliers final: 8 residues processed: 195 average time/residue: 1.8031 time to fit residues: 368.9952 Evaluate side-chains 192 residues out of total 701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 182 time to evaluate : 0.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LYS Chi-restraints excluded: chain A residue 196 ASP Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain B residue 51 ASP Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 262 ILE Chi-restraints excluded: chain B residue 325 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 10 optimal weight: 5.9990 chunk 51 optimal weight: 10.0000 chunk 66 optimal weight: 7.9990 chunk 76 optimal weight: 10.0000 chunk 50 optimal weight: 10.0000 chunk 90 optimal weight: 10.0000 chunk 56 optimal weight: 4.9990 chunk 55 optimal weight: 10.0000 chunk 41 optimal weight: 8.9990 chunk 36 optimal weight: 4.9990 chunk 54 optimal weight: 8.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 ASN ** A 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 199 ASN B 399 ASN B 412 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.2464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.073 10291 Z= 0.549 Angle : 0.671 10.095 14586 Z= 0.359 Chirality : 0.046 0.240 1679 Planarity : 0.005 0.053 1310 Dihedral : 20.427 73.917 3080 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.25 % Allowed : 4.63 % Favored : 95.12 % Rotamer: Outliers : 4.00 % Allowed : 21.86 % Favored : 74.14 % 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: 0.06 (0.29), residues: 799 helix: 1.46 (0.27), residues: 366 sheet: -0.28 (0.38), residues: 157 loop : -1.72 (0.33), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 17 HIS 0.008 0.002 HIS A 238 PHE 0.018 0.003 PHE A 102 TYR 0.022 0.002 TYR A 351 ARG 0.014 0.001 ARG A 121 *********************** 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 208 residues out of total 701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 180 time to evaluate : 0.989 Fit side-chains revert: symmetry clash REVERT: A 14 ASP cc_start: 0.8423 (m-30) cc_final: 0.8158 (t70) REVERT: A 16 ASP cc_start: 0.7951 (t0) cc_final: 0.7708 (t70) REVERT: A 121 ARG cc_start: 0.8413 (ttp-110) cc_final: 0.8197 (ptm160) REVERT: A 177 MET cc_start: 0.9139 (tpp) cc_final: 0.8714 (tpt) REVERT: A 244 LYS cc_start: 0.8708 (pttt) cc_final: 0.8461 (pttt) REVERT: A 252 ASN cc_start: 0.8196 (OUTLIER) cc_final: 0.7149 (p0) REVERT: A 288 GLU cc_start: 0.7512 (mt-10) cc_final: 0.7135 (mt-10) REVERT: A 344 ASP cc_start: 0.8125 (t0) cc_final: 0.7863 (t70) REVERT: A 355 GLU cc_start: 0.8532 (OUTLIER) cc_final: 0.8312 (mt-10) REVERT: B 187 VAL cc_start: 0.8451 (OUTLIER) cc_final: 0.8229 (m) REVERT: B 210 GLU cc_start: 0.8056 (tp30) cc_final: 0.7796 (tp30) REVERT: B 316 MET cc_start: 0.8522 (mmm) cc_final: 0.8300 (mmm) REVERT: B 338 GLN cc_start: 0.8264 (mm110) cc_final: 0.7969 (mm110) REVERT: B 339 ASN cc_start: 0.8412 (t0) cc_final: 0.8140 (t0) outliers start: 28 outliers final: 14 residues processed: 194 average time/residue: 1.8417 time to fit residues: 374.2953 Evaluate side-chains 197 residues out of total 701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 180 time to evaluate : 1.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain A residue 160 LYS Chi-restraints excluded: chain A residue 174 LYS Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 252 ASN Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 355 GLU Chi-restraints excluded: chain A residue 370 GLN Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 51 ASP 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 219 ASN Chi-restraints excluded: chain B residue 239 THR Chi-restraints excluded: chain B residue 325 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 27 optimal weight: 5.9990 chunk 17 optimal weight: 0.9990 chunk 57 optimal weight: 4.9990 chunk 61 optimal weight: 4.9990 chunk 44 optimal weight: 4.9990 chunk 8 optimal weight: 0.9990 chunk 71 optimal weight: 1.9990 chunk 82 optimal weight: 3.9990 chunk 86 optimal weight: 8.9990 chunk 79 optimal weight: 1.9990 chunk 84 optimal weight: 0.8980 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 186 GLN A 338 GLN B 199 ASN B 399 ASN B 407 ASN B 412 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.2541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10291 Z= 0.181 Angle : 0.534 9.908 14586 Z= 0.292 Chirality : 0.038 0.221 1679 Planarity : 0.004 0.042 1310 Dihedral : 20.236 73.827 3080 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.25 % Allowed : 2.75 % Favored : 97.00 % Rotamer: Outliers : 2.43 % Allowed : 24.86 % Favored : 72.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.50 (0.30), residues: 799 helix: 1.85 (0.27), residues: 367 sheet: -0.05 (0.39), residues: 157 loop : -1.57 (0.34), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 43 HIS 0.003 0.001 HIS B 72 PHE 0.015 0.001 PHE A 389 TYR 0.013 0.001 TYR A 351 ARG 0.010 0.000 ARG A 121 *********************** 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 189 residues out of total 701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 172 time to evaluate : 1.084 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 14 ASP cc_start: 0.8321 (m-30) cc_final: 0.8091 (t70) REVERT: A 16 ASP cc_start: 0.7913 (t0) cc_final: 0.7651 (t70) REVERT: A 29 GLN cc_start: 0.7906 (tm-30) cc_final: 0.7594 (tm130) REVERT: A 105 TYR cc_start: 0.9195 (m-80) cc_final: 0.8869 (m-80) REVERT: A 121 ARG cc_start: 0.8452 (ttp-110) cc_final: 0.8226 (ptm160) REVERT: A 177 MET cc_start: 0.9073 (tpp) cc_final: 0.8562 (tpt) REVERT: A 221 ILE cc_start: 0.8997 (mt) cc_final: 0.8777 (mp) REVERT: A 242 ARG cc_start: 0.8368 (ptp90) cc_final: 0.8105 (ptp90) REVERT: A 244 LYS cc_start: 0.8670 (pttt) cc_final: 0.8391 (pttt) REVERT: A 266 ARG cc_start: 0.8092 (mtp85) cc_final: 0.7747 (mtt180) REVERT: A 312 MET cc_start: 0.8600 (mmp) cc_final: 0.8309 (mmp) REVERT: A 344 ASP cc_start: 0.8062 (t0) cc_final: 0.7804 (t70) REVERT: B 187 VAL cc_start: 0.8430 (OUTLIER) cc_final: 0.8176 (m) REVERT: B 338 GLN cc_start: 0.8180 (mm110) cc_final: 0.7896 (mm110) REVERT: B 339 ASN cc_start: 0.8393 (t0) cc_final: 0.8098 (t0) outliers start: 17 outliers final: 9 residues processed: 183 average time/residue: 1.8157 time to fit residues: 348.9599 Evaluate side-chains 180 residues out of total 701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 170 time to evaluate : 0.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 ASP Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain B residue 51 ASP 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 325 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 86 optimal weight: 6.9990 chunk 50 optimal weight: 10.0000 chunk 36 optimal weight: 4.9990 chunk 66 optimal weight: 0.0000 chunk 25 optimal weight: 10.0000 chunk 76 optimal weight: 2.9990 chunk 79 optimal weight: 7.9990 chunk 84 optimal weight: 0.7980 chunk 55 optimal weight: 10.0000 chunk 89 optimal weight: 0.4980 chunk 54 optimal weight: 8.9990 overall best weight: 1.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 ASN ** A 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 194 HIS B 199 ASN B 237 GLN B 399 ASN B 412 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.2584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10291 Z= 0.202 Angle : 0.533 11.164 14586 Z= 0.290 Chirality : 0.037 0.210 1679 Planarity : 0.004 0.041 1310 Dihedral : 20.214 73.736 3080 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.25 % Allowed : 3.38 % Favored : 96.37 % Rotamer: Outliers : 2.29 % Allowed : 25.57 % Favored : 72.14 % 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: 0.68 (0.30), residues: 799 helix: 1.98 (0.28), residues: 367 sheet: 0.05 (0.39), residues: 157 loop : -1.47 (0.35), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 340 HIS 0.003 0.001 HIS A 72 PHE 0.013 0.002 PHE A 389 TYR 0.014 0.001 TYR A 351 ARG 0.009 0.000 ARG A 121 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1598 Ramachandran restraints generated. 799 Oldfield, 0 Emsley, 799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1598 Ramachandran restraints generated. 799 Oldfield, 0 Emsley, 799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 178 time to evaluate : 0.883 Fit side-chains revert: symmetry clash REVERT: A 14 ASP cc_start: 0.8321 (m-30) cc_final: 0.8084 (t70) REVERT: A 16 ASP cc_start: 0.7911 (t0) cc_final: 0.7650 (t70) REVERT: A 105 TYR cc_start: 0.9205 (m-80) cc_final: 0.8928 (m-80) REVERT: A 177 MET cc_start: 0.9054 (tpp) cc_final: 0.8807 (tpt) REVERT: A 191 GLN cc_start: 0.8927 (mt0) cc_final: 0.8573 (mt0) REVERT: A 221 ILE cc_start: 0.9000 (mt) cc_final: 0.8780 (mp) REVERT: A 234 MET cc_start: 0.8978 (mtm) cc_final: 0.8713 (mtp) REVERT: A 242 ARG cc_start: 0.8340 (ptp90) cc_final: 0.8077 (ptp90) REVERT: A 244 LYS cc_start: 0.8665 (pttt) cc_final: 0.8398 (pttt) REVERT: A 264 MET cc_start: 0.8486 (mtt) cc_final: 0.8039 (mtp) REVERT: A 267 GLN cc_start: 0.8419 (tm-30) cc_final: 0.8054 (tm-30) REVERT: A 312 MET cc_start: 0.8585 (mmp) cc_final: 0.8345 (mmp) REVERT: A 344 ASP cc_start: 0.7935 (t0) cc_final: 0.7663 (t70) REVERT: B 129 LYS cc_start: 0.8766 (ptmt) cc_final: 0.8537 (ttmt) REVERT: B 187 VAL cc_start: 0.8370 (OUTLIER) cc_final: 0.8149 (m) REVERT: B 306 SER cc_start: 0.8533 (m) cc_final: 0.8097 (p) REVERT: B 338 GLN cc_start: 0.8176 (mm110) cc_final: 0.7892 (mm110) REVERT: B 339 ASN cc_start: 0.8399 (t0) cc_final: 0.8098 (t0) outliers start: 16 outliers final: 12 residues processed: 188 average time/residue: 1.7868 time to fit residues: 352.2310 Evaluate side-chains 192 residues out of total 701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 179 time to evaluate : 0.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 ASN Chi-restraints excluded: chain A residue 174 LYS Chi-restraints excluded: chain A residue 196 ASP Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 370 GLN Chi-restraints excluded: chain B residue 51 ASP 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 325 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 42 optimal weight: 10.0000 chunk 62 optimal weight: 5.9990 chunk 93 optimal weight: 4.9990 chunk 86 optimal weight: 6.9990 chunk 74 optimal weight: 6.9990 chunk 7 optimal weight: 6.9990 chunk 57 optimal weight: 2.9990 chunk 45 optimal weight: 10.0000 chunk 59 optimal weight: 2.9990 chunk 79 optimal weight: 0.9990 chunk 22 optimal weight: 6.9990 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 A 186 GLN ** A 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 399 ASN ** B 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 412 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.2580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 10291 Z= 0.321 Angle : 0.585 12.511 14586 Z= 0.316 Chirality : 0.041 0.215 1679 Planarity : 0.004 0.037 1310 Dihedral : 20.233 73.788 3080 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.25 % Allowed : 3.75 % Favored : 95.99 % Rotamer: Outliers : 2.29 % Allowed : 26.00 % Favored : 71.71 % 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: 0.54 (0.30), residues: 799 helix: 1.82 (0.28), residues: 367 sheet: -0.05 (0.39), residues: 157 loop : -1.43 (0.35), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 340 HIS 0.006 0.001 HIS A 72 PHE 0.011 0.002 PHE A 102 TYR 0.025 0.002 TYR B 351 ARG 0.008 0.001 ARG B 25 ********************** 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 190 residues out of total 701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 174 time to evaluate : 0.905 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 ASP cc_start: 0.8349 (m-30) cc_final: 0.8100 (t70) REVERT: A 16 ASP cc_start: 0.7936 (t0) cc_final: 0.7678 (t70) REVERT: A 221 ILE cc_start: 0.9007 (mt) cc_final: 0.8786 (mp) REVERT: A 234 MET cc_start: 0.8976 (mtm) cc_final: 0.8684 (mtp) REVERT: A 244 LYS cc_start: 0.8671 (pttt) cc_final: 0.8423 (pttt) REVERT: A 344 ASP cc_start: 0.8118 (t0) cc_final: 0.7868 (t70) REVERT: B 177 MET cc_start: 0.8309 (tpp) cc_final: 0.8059 (tpp) REVERT: B 187 VAL cc_start: 0.8415 (OUTLIER) cc_final: 0.8182 (m) REVERT: B 338 GLN cc_start: 0.8240 (mm110) cc_final: 0.7973 (mm110) REVERT: B 339 ASN cc_start: 0.8407 (t0) cc_final: 0.8105 (t0) outliers start: 16 outliers final: 12 residues processed: 182 average time/residue: 1.8952 time to fit residues: 361.3669 Evaluate side-chains 182 residues out of total 701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 169 time to evaluate : 0.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 LYS Chi-restraints excluded: chain A residue 196 ASP Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 370 GLN Chi-restraints excluded: chain B residue 29 GLN Chi-restraints excluded: chain B residue 51 ASP 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 325 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 68 optimal weight: 0.0770 chunk 11 optimal weight: 0.9980 chunk 20 optimal weight: 6.9990 chunk 74 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 76 optimal weight: 8.9990 chunk 9 optimal weight: 4.9990 chunk 13 optimal weight: 0.6980 chunk 65 optimal weight: 4.9990 chunk 4 optimal weight: 1.9990 chunk 53 optimal weight: 10.0000 overall best weight: 1.3542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 ASN ** A 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 399 ASN B 407 ASN B 412 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.121985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.100112 restraints weight = 14793.568| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 1.72 r_work: 0.3145 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3003 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.2743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10291 Z= 0.179 Angle : 0.537 12.169 14586 Z= 0.290 Chirality : 0.037 0.204 1679 Planarity : 0.003 0.036 1310 Dihedral : 20.171 73.792 3080 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.25 % Allowed : 3.25 % Favored : 96.50 % Rotamer: Outliers : 1.71 % Allowed : 26.57 % Favored : 71.71 % 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: 0.81 (0.30), residues: 799 helix: 2.07 (0.27), residues: 366 sheet: 0.02 (0.39), residues: 157 loop : -1.27 (0.36), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 340 HIS 0.003 0.001 HIS A 72 PHE 0.014 0.001 PHE A 389 TYR 0.017 0.001 TYR A 84 ARG 0.007 0.000 ARG B 25 =============================================================================== Job complete usr+sys time: 5201.70 seconds wall clock time: 93 minutes 12.02 seconds (5592.02 seconds total)