Starting phenix.real_space_refine on Sat Nov 16 00:17:43 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j1j_35926/11_2024/8j1j_35926.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j1j_35926/11_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_35926/11_2024/8j1j_35926.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j1j_35926/11_2024/8j1j_35926.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j1j_35926/11_2024/8j1j_35926.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j1j_35926/11_2024/8j1j_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-5513/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: 6.36, per 1000 atoms: 0.65 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: 3.22 Conformation dependent library (CDL) restraints added in 800.3 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: 3.91 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: 4.18 Time building geometry restraints manager: 3.04 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: 0.070 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: 0.370 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 30.410 Find NCS groups from input model: 0.240 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: 0.010 Load rotamer database and sin/cos tables:14.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.760 ------------------------------------------------------------------------------- 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 to be fit. rotamer outliers: 10 poor density : 225 time to evaluate : 0.841 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: 1.6283 time to fit residues: 403.7365 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 : 0.825 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.1534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 10291 Z= 0.317 Angle : 0.570 11.333 14586 Z= 0.314 Chirality : 0.041 0.223 1679 Planarity : 0.004 0.035 1310 Dihedral : 20.486 74.591 3088 Min Nonbonded Distance : 2.523 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: -0.25 (0.29), residues: 799 helix: 1.06 (0.28), residues: 363 sheet: -0.34 (0.40), residues: 151 loop : -1.65 (0.33), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 43 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 A 298 *********************** 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 189 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 168 time to evaluate : 0.851 Fit side-chains REVERT: A 25 ARG cc_start: 0.8009 (mtp85) cc_final: 0.7781 (mpt90) REVERT: A 30 GLU cc_start: 0.8017 (mm-30) cc_final: 0.7776 (mt-10) REVERT: A 108 GLU cc_start: 0.8333 (mp0) cc_final: 0.8110 (mp0) REVERT: A 141 ASP cc_start: 0.8596 (OUTLIER) cc_final: 0.8363 (m-30) REVERT: A 221 ILE cc_start: 0.8976 (mt) cc_final: 0.8741 (mp) REVERT: A 222 MET cc_start: 0.9197 (ttp) cc_final: 0.8976 (ttp) REVERT: A 242 ARG cc_start: 0.8312 (ptp90) cc_final: 0.8003 (ptp90) REVERT: A 244 LYS cc_start: 0.8669 (pttt) cc_final: 0.8445 (pttt) REVERT: A 264 MET cc_start: 0.8422 (mtt) cc_final: 0.8093 (mtp) REVERT: A 344 ASP cc_start: 0.8230 (t0) cc_final: 0.7946 (t70) REVERT: A 377 ASN cc_start: 0.8345 (t0) cc_final: 0.7378 (p0) REVERT: B 71 VAL cc_start: 0.8756 (OUTLIER) cc_final: 0.8521 (p) REVERT: B 199 ASN cc_start: 0.8340 (t0) cc_final: 0.8130 (t0) REVERT: B 222 MET cc_start: 0.8650 (ttp) cc_final: 0.8197 (ttt) REVERT: B 242 ARG cc_start: 0.8372 (ptp-170) cc_final: 0.7518 (ptp-170) REVERT: B 316 MET cc_start: 0.8497 (mmm) cc_final: 0.8236 (mmm) REVERT: B 339 ASN cc_start: 0.8431 (t0) cc_final: 0.8179 (t0) REVERT: B 407 ASN cc_start: 0.7514 (m-40) cc_final: 0.7305 (m110) outliers start: 21 outliers final: 5 residues processed: 183 average time/residue: 1.7731 time to fit residues: 340.6537 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 : 1.023 ------------------------------------------------------------------------------- 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 47 optimal weight: 10.0000 chunk 26 optimal weight: 8.9990 chunk 71 optimal weight: 0.5980 chunk 58 optimal weight: 5.9990 chunk 23 optimal weight: 10.0000 chunk 85 optimal weight: 9.9990 chunk 92 optimal weight: 1.9990 chunk 76 optimal weight: 0.5980 chunk 84 optimal weight: 0.9980 chunk 29 optimal weight: 0.9990 chunk 68 optimal weight: 0.6980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 204 ASN B 322 GLN B 412 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.2156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 10291 Z= 0.147 Angle : 0.508 10.456 14586 Z= 0.278 Chirality : 0.037 0.212 1679 Planarity : 0.004 0.035 1310 Dihedral : 20.330 73.838 3083 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.25 % Allowed : 2.88 % Favored : 96.87 % Rotamer: Outliers : 3.14 % Allowed : 17.00 % Favored : 79.86 % 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: 0.29 (0.30), residues: 799 helix: 1.67 (0.28), residues: 364 sheet: -0.20 (0.40), residues: 157 loop : -1.59 (0.34), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 43 HIS 0.003 0.001 HIS A 303 PHE 0.014 0.001 PHE B 389 TYR 0.012 0.001 TYR A 351 ARG 0.006 0.000 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 201 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 179 time to evaluate : 1.099 Fit side-chains REVERT: A 16 ASP cc_start: 0.7846 (t0) cc_final: 0.7578 (t70) REVERT: A 108 GLU cc_start: 0.8342 (mp0) cc_final: 0.8131 (mp0) REVERT: A 177 MET cc_start: 0.9065 (tpp) cc_final: 0.8629 (tpt) REVERT: A 221 ILE cc_start: 0.8967 (mt) cc_final: 0.8712 (mp) REVERT: A 242 ARG cc_start: 0.8285 (ptp90) cc_final: 0.8083 (ptp90) REVERT: A 244 LYS cc_start: 0.8635 (pttt) cc_final: 0.8402 (pttt) REVERT: A 264 MET cc_start: 0.8389 (mtt) cc_final: 0.8113 (mtp) REVERT: A 344 ASP cc_start: 0.8170 (t0) cc_final: 0.7886 (t70) REVERT: A 354 GLU cc_start: 0.7854 (OUTLIER) cc_final: 0.7148 (mp0) REVERT: A 377 ASN cc_start: 0.7967 (t0) cc_final: 0.7198 (p0) REVERT: A 415 LYS cc_start: 0.7680 (mttt) cc_final: 0.7129 (mtmm) REVERT: B 242 ARG cc_start: 0.8423 (ptp-170) cc_final: 0.7697 (ptp-170) REVERT: B 254 ARG cc_start: 0.7843 (mtt90) cc_final: 0.7553 (mtp85) REVERT: B 264 MET cc_start: 0.7286 (OUTLIER) cc_final: 0.7082 (mpp) REVERT: B 339 ASN cc_start: 0.8464 (t0) cc_final: 0.8159 (t0) REVERT: B 403 ASN cc_start: 0.7652 (t0) cc_final: 0.6341 (t0) outliers start: 22 outliers final: 4 residues processed: 187 average time/residue: 1.7360 time to fit residues: 341.0991 Evaluate side-chains 172 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 166 time to evaluate : 0.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 354 GLU Chi-restraints excluded: chain B residue 160 LYS Chi-restraints excluded: chain B residue 198 LYS Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 264 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 84 optimal weight: 3.9990 chunk 64 optimal weight: 0.9990 chunk 44 optimal weight: 6.9990 chunk 9 optimal weight: 4.9990 chunk 40 optimal weight: 3.9990 chunk 57 optimal weight: 7.9990 chunk 85 optimal weight: 10.0000 chunk 90 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 chunk 24 optimal weight: 0.0870 chunk 75 optimal weight: 2.9990 overall best weight: 1.8166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 HIS B 135 ASN B 237 GLN B 252 ASN B 399 ASN ** B 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 412 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.2276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10291 Z= 0.193 Angle : 0.512 10.191 14586 Z= 0.279 Chirality : 0.037 0.194 1679 Planarity : 0.003 0.034 1310 Dihedral : 20.300 73.741 3082 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.25 % Allowed : 3.38 % Favored : 96.37 % Rotamer: Outliers : 2.43 % Allowed : 19.29 % 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: 0.56 (0.30), residues: 799 helix: 1.95 (0.28), residues: 365 sheet: -0.17 (0.40), residues: 155 loop : -1.47 (0.34), residues: 279 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 0.007 0.001 PHE A 389 TYR 0.015 0.001 TYR A 351 ARG 0.008 0.000 ARG B 406 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1598 Ramachandran restraints generated. 799 Oldfield, 0 Emsley, 799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1598 Ramachandran restraints generated. 799 Oldfield, 0 Emsley, 799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 177 time to evaluate : 0.811 Fit side-chains revert: symmetry clash REVERT: A 16 ASP cc_start: 0.7793 (t0) cc_final: 0.7520 (t70) REVERT: A 44 GLU cc_start: 0.8776 (tt0) cc_final: 0.8570 (tt0) REVERT: A 108 GLU cc_start: 0.8356 (mp0) cc_final: 0.8145 (mp0) REVERT: A 177 MET cc_start: 0.9117 (tpp) cc_final: 0.8632 (tpt) REVERT: A 221 ILE cc_start: 0.8976 (mt) cc_final: 0.8706 (mp) REVERT: A 242 ARG cc_start: 0.8310 (ptp90) cc_final: 0.8091 (ptp90) REVERT: A 244 LYS cc_start: 0.8665 (pttt) cc_final: 0.8408 (pttt) REVERT: A 264 MET cc_start: 0.8421 (mtt) cc_final: 0.8128 (mtp) REVERT: A 266 ARG cc_start: 0.8131 (mtp85) cc_final: 0.7798 (mtt180) REVERT: A 288 GLU cc_start: 0.7423 (mt-10) cc_final: 0.7018 (mt-10) REVERT: A 299 ASP cc_start: 0.7697 (OUTLIER) cc_final: 0.7197 (m-30) REVERT: A 344 ASP cc_start: 0.8045 (t0) cc_final: 0.7769 (t70) REVERT: A 354 GLU cc_start: 0.7866 (OUTLIER) cc_final: 0.7199 (mp0) REVERT: A 377 ASN cc_start: 0.8051 (t0) cc_final: 0.7269 (p0) REVERT: B 11 LYS cc_start: 0.8951 (OUTLIER) cc_final: 0.8707 (pttt) REVERT: B 147 SER cc_start: 0.9051 (m) cc_final: 0.8534 (p) REVERT: B 174 LYS cc_start: 0.8545 (tppp) cc_final: 0.8286 (tppp) REVERT: B 242 ARG cc_start: 0.8368 (ptp-170) cc_final: 0.7341 (ptp-170) REVERT: B 339 ASN cc_start: 0.8454 (t0) cc_final: 0.8140 (t0) REVERT: B 406 ARG cc_start: 0.6552 (mtp85) cc_final: 0.6307 (ttt90) REVERT: B 407 ASN cc_start: 0.7159 (m-40) cc_final: 0.6876 (m-40) outliers start: 17 outliers final: 7 residues processed: 183 average time/residue: 1.7657 time to fit residues: 339.1949 Evaluate side-chains 185 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 175 time to evaluate : 0.848 ------------------------------------------------------------------------------- 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 299 ASP 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 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 51 optimal weight: 10.0000 chunk 1 optimal weight: 5.9990 chunk 67 optimal weight: 0.4980 chunk 37 optimal weight: 9.9990 chunk 77 optimal weight: 5.9990 chunk 62 optimal weight: 6.9990 chunk 0 optimal weight: 7.9990 chunk 46 optimal weight: 10.0000 chunk 81 optimal weight: 5.9990 chunk 22 optimal weight: 10.0000 chunk 30 optimal weight: 6.9990 overall best weight: 5.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 199 ASN B 399 ASN B 412 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.2267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.061 10291 Z= 0.437 Angle : 0.613 10.701 14586 Z= 0.330 Chirality : 0.043 0.218 1679 Planarity : 0.004 0.034 1310 Dihedral : 20.382 73.780 3082 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.25 % Allowed : 3.88 % Favored : 95.87 % Rotamer: Outliers : 3.43 % Allowed : 20.86 % Favored : 75.71 % 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: 0.28 (0.29), residues: 799 helix: 1.74 (0.28), residues: 365 sheet: -0.32 (0.38), residues: 157 loop : -1.64 (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 0.017 0.003 PHE A 102 TYR 0.028 0.002 TYR B 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 206 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 182 time to evaluate : 0.935 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 16 ASP cc_start: 0.7918 (t0) cc_final: 0.7686 (t0) REVERT: A 108 GLU cc_start: 0.8338 (mp0) cc_final: 0.8136 (mp0) REVERT: A 177 MET cc_start: 0.9123 (tpp) cc_final: 0.8637 (tpt) REVERT: A 221 ILE cc_start: 0.9033 (mt) cc_final: 0.8776 (mp) REVERT: A 244 LYS cc_start: 0.8721 (pttt) cc_final: 0.8445 (pttt) REVERT: A 283 ARG cc_start: 0.8719 (tpp-160) cc_final: 0.8494 (tpt170) REVERT: A 344 ASP cc_start: 0.8212 (t0) cc_final: 0.7954 (t70) REVERT: A 354 GLU cc_start: 0.7999 (OUTLIER) cc_final: 0.7268 (mp0) REVERT: A 377 ASN cc_start: 0.8273 (t0) cc_final: 0.7326 (p0) REVERT: B 82 LYS cc_start: 0.8449 (mmmm) cc_final: 0.8220 (mmmm) REVERT: B 242 ARG cc_start: 0.8360 (ptp-170) cc_final: 0.7448 (ptp-170) REVERT: B 254 ARG cc_start: 0.7950 (mtt90) cc_final: 0.7620 (mtp85) REVERT: B 312 MET cc_start: 0.8242 (mmm) cc_final: 0.8022 (mmp) REVERT: B 338 GLN cc_start: 0.8337 (mm110) cc_final: 0.8043 (mm110) REVERT: B 339 ASN cc_start: 0.8464 (t0) cc_final: 0.8078 (t0) REVERT: B 406 ARG cc_start: 0.6685 (mtp85) cc_final: 0.6331 (ttt90) outliers start: 24 outliers final: 10 residues processed: 192 average time/residue: 1.8049 time to fit residues: 363.4557 Evaluate side-chains 187 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 176 time to evaluate : 0.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 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 A residue 370 GLN Chi-restraints excluded: chain B residue 114 MET Chi-restraints excluded: chain B residue 160 LYS Chi-restraints excluded: chain B residue 239 THR Chi-restraints excluded: chain B residue 262 ILE Chi-restraints excluded: chain B residue 315 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 81 optimal weight: 0.8980 chunk 17 optimal weight: 0.8980 chunk 53 optimal weight: 10.0000 chunk 22 optimal weight: 1.9990 chunk 90 optimal weight: 9.9990 chunk 75 optimal weight: 2.9990 chunk 42 optimal weight: 10.0000 chunk 7 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 47 optimal weight: 10.0000 chunk 87 optimal weight: 0.7980 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 ASN 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: 0.8172 moved from start: 0.2450 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= 0.179 Angle : 0.515 10.248 14586 Z= 0.282 Chirality : 0.037 0.209 1679 Planarity : 0.003 0.033 1310 Dihedral : 20.241 73.738 3080 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.25 % Allowed : 3.50 % Favored : 96.25 % Rotamer: Outliers : 2.14 % Allowed : 22.86 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.65 (0.30), residues: 799 helix: 2.10 (0.28), residues: 364 sheet: -0.14 (0.38), residues: 157 loop : -1.52 (0.34), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 43 HIS 0.003 0.001 HIS B 72 PHE 0.015 0.001 PHE A 389 TYR 0.014 0.001 TYR A 351 ARG 0.006 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 196 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 181 time to evaluate : 0.860 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 16 ASP cc_start: 0.7881 (t0) cc_final: 0.7635 (t70) REVERT: A 105 TYR cc_start: 0.9175 (m-80) cc_final: 0.8849 (m-80) REVERT: A 221 ILE cc_start: 0.9009 (mt) cc_final: 0.8758 (mp) REVERT: A 242 ARG cc_start: 0.8331 (ptp90) cc_final: 0.7720 (ptp90) REVERT: A 244 LYS cc_start: 0.8633 (pttt) cc_final: 0.8355 (pttt) REVERT: A 264 MET cc_start: 0.8406 (mtt) cc_final: 0.8010 (mtp) REVERT: A 266 ARG cc_start: 0.8088 (mtp85) cc_final: 0.7737 (mtt180) REVERT: A 288 GLU cc_start: 0.7467 (mt-10) cc_final: 0.6920 (mt-10) REVERT: A 344 ASP cc_start: 0.7996 (t0) cc_final: 0.7704 (t70) REVERT: A 354 GLU cc_start: 0.7971 (OUTLIER) cc_final: 0.7204 (mp0) REVERT: A 377 ASN cc_start: 0.8138 (t0) cc_final: 0.7234 (p0) REVERT: B 11 LYS cc_start: 0.8941 (OUTLIER) cc_final: 0.8690 (pttt) REVERT: B 242 ARG cc_start: 0.8465 (ptp-170) cc_final: 0.7816 (ptp-170) REVERT: B 338 GLN cc_start: 0.8323 (mm110) cc_final: 0.8066 (mm110) REVERT: B 339 ASN cc_start: 0.8451 (t0) cc_final: 0.8121 (t0) outliers start: 15 outliers final: 7 residues processed: 186 average time/residue: 1.8680 time to fit residues: 364.7221 Evaluate side-chains 184 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 175 time to evaluate : 0.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 ASP 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 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 10 optimal weight: 4.9990 chunk 51 optimal weight: 10.0000 chunk 66 optimal weight: 5.9990 chunk 76 optimal weight: 5.9990 chunk 50 optimal weight: 10.0000 chunk 90 optimal weight: 10.0000 chunk 56 optimal weight: 8.9990 chunk 55 optimal weight: 10.0000 chunk 41 optimal weight: 6.9990 chunk 36 optimal weight: 5.9990 chunk 54 optimal weight: 8.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 ASN B 194 HIS B 199 ASN B 399 ASN B 412 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.2515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.070 10291 Z= 0.507 Angle : 0.664 10.594 14586 Z= 0.356 Chirality : 0.046 0.227 1679 Planarity : 0.005 0.052 1310 Dihedral : 20.418 73.891 3080 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.25 % Allowed : 4.88 % Favored : 94.87 % Rotamer: Outliers : 3.43 % Allowed : 22.57 % Favored : 74.00 % 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: 0.26 (0.29), residues: 799 helix: 1.72 (0.28), residues: 364 sheet: -0.31 (0.37), residues: 157 loop : -1.66 (0.34), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 43 HIS 0.008 0.002 HIS A 238 PHE 0.020 0.003 PHE A 102 TYR 0.022 0.002 TYR A 351 ARG 0.013 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 202 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 178 time to evaluate : 0.889 Fit side-chains revert: symmetry clash REVERT: A 16 ASP cc_start: 0.7954 (t0) cc_final: 0.7684 (t70) REVERT: A 177 MET cc_start: 0.9141 (tpp) cc_final: 0.8777 (tpt) REVERT: A 244 LYS cc_start: 0.8713 (pttt) cc_final: 0.8437 (pttt) REVERT: A 344 ASP cc_start: 0.8198 (t0) cc_final: 0.7952 (t70) REVERT: A 354 GLU cc_start: 0.8061 (OUTLIER) cc_final: 0.7159 (mp0) REVERT: A 355 GLU cc_start: 0.8528 (OUTLIER) cc_final: 0.8315 (mt-10) REVERT: B 1 MET cc_start: 0.5613 (mmt) cc_final: 0.5391 (tpt) REVERT: B 187 VAL cc_start: 0.8454 (OUTLIER) cc_final: 0.8221 (m) REVERT: B 316 MET cc_start: 0.8474 (mmm) cc_final: 0.8218 (mmm) REVERT: B 338 GLN cc_start: 0.8348 (mm110) cc_final: 0.8085 (mm110) REVERT: B 339 ASN cc_start: 0.8471 (t0) cc_final: 0.8154 (t0) outliers start: 24 outliers final: 10 residues processed: 188 average time/residue: 1.7669 time to fit residues: 348.6536 Evaluate side-chains 189 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 176 time to evaluate : 0.840 ------------------------------------------------------------------------------- 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 354 GLU Chi-restraints excluded: chain A residue 355 GLU 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 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: 6.9990 chunk 17 optimal weight: 0.8980 chunk 57 optimal weight: 3.9990 chunk 61 optimal weight: 6.9990 chunk 44 optimal weight: 4.9990 chunk 8 optimal weight: 0.7980 chunk 71 optimal weight: 0.9980 chunk 82 optimal weight: 4.9990 chunk 86 optimal weight: 8.9990 chunk 79 optimal weight: 1.9990 chunk 84 optimal weight: 0.7980 overall best weight: 1.0982 ------------------------------------------------------------------------------- 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 199 ASN 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: 0.8165 moved from start: 0.2669 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= 0.166 Angle : 0.532 10.290 14586 Z= 0.291 Chirality : 0.037 0.220 1679 Planarity : 0.003 0.036 1310 Dihedral : 20.229 73.846 3080 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.25 % Allowed : 3.00 % Favored : 96.75 % Rotamer: Outliers : 2.00 % Allowed : 25.29 % 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: 0.60 (0.30), residues: 799 helix: 2.02 (0.28), residues: 365 sheet: -0.14 (0.38), residues: 157 loop : -1.53 (0.34), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 17 HIS 0.002 0.001 HIS B 72 PHE 0.015 0.001 PHE A 389 TYR 0.014 0.001 TYR A 351 ARG 0.007 0.000 ARG B 25 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1598 Ramachandran restraints generated. 799 Oldfield, 0 Emsley, 799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1598 Ramachandran restraints generated. 799 Oldfield, 0 Emsley, 799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 177 time to evaluate : 0.873 Fit side-chains revert: symmetry clash REVERT: A 16 ASP cc_start: 0.7880 (t0) cc_final: 0.7657 (t70) REVERT: A 105 TYR cc_start: 0.9189 (m-80) cc_final: 0.8846 (m-80) REVERT: A 177 MET cc_start: 0.9068 (tpp) cc_final: 0.8653 (tpt) REVERT: A 221 ILE cc_start: 0.8995 (mt) cc_final: 0.8770 (mp) REVERT: A 244 LYS cc_start: 0.8650 (pttt) cc_final: 0.8359 (pttt) REVERT: A 312 MET cc_start: 0.8497 (tpp) cc_final: 0.8144 (mpp) REVERT: A 344 ASP cc_start: 0.7970 (t0) cc_final: 0.7677 (t70) REVERT: A 354 GLU cc_start: 0.8008 (OUTLIER) cc_final: 0.7797 (mp0) REVERT: A 377 ASN cc_start: 0.8291 (t0) cc_final: 0.7628 (p0) REVERT: B 1 MET cc_start: 0.5616 (mmt) cc_final: 0.5407 (tpt) REVERT: B 11 LYS cc_start: 0.8988 (OUTLIER) cc_final: 0.8731 (pttt) REVERT: B 107 LYS cc_start: 0.8623 (mmmm) cc_final: 0.8255 (mmmm) REVERT: B 170 ARG cc_start: 0.7789 (ptm-80) cc_final: 0.7496 (ptm-80) REVERT: B 242 ARG cc_start: 0.8508 (ptp-170) cc_final: 0.7882 (ptp-170) REVERT: B 254 ARG cc_start: 0.7800 (mtt90) cc_final: 0.7535 (mtp85) REVERT: B 338 GLN cc_start: 0.8261 (mm110) cc_final: 0.7910 (mm110) REVERT: B 339 ASN cc_start: 0.8431 (t0) cc_final: 0.8086 (t0) REVERT: B 407 ASN cc_start: 0.7355 (m-40) cc_final: 0.6801 (m110) outliers start: 14 outliers final: 7 residues processed: 180 average time/residue: 1.8049 time to fit residues: 340.6702 Evaluate side-chains 184 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 175 time to evaluate : 0.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 86 optimal weight: 7.9990 chunk 50 optimal weight: 10.0000 chunk 36 optimal weight: 1.9990 chunk 66 optimal weight: 4.9990 chunk 25 optimal weight: 9.9990 chunk 76 optimal weight: 5.9990 chunk 79 optimal weight: 7.9990 chunk 84 optimal weight: 4.9990 chunk 55 optimal weight: 10.0000 chunk 89 optimal weight: 7.9990 chunk 54 optimal weight: 8.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 ASN B 399 ASN B 412 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.2624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.061 10291 Z= 0.446 Angle : 0.645 11.045 14586 Z= 0.346 Chirality : 0.044 0.229 1679 Planarity : 0.005 0.066 1310 Dihedral : 20.349 73.801 3080 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.25 % Allowed : 4.88 % Favored : 94.87 % Rotamer: Outliers : 1.86 % Allowed : 26.14 % Favored : 72.00 % 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: 0.38 (0.29), residues: 799 helix: 1.79 (0.28), residues: 364 sheet: -0.19 (0.37), residues: 157 loop : -1.59 (0.34), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 17 HIS 0.007 0.002 HIS A 72 PHE 0.016 0.003 PHE A 102 TYR 0.034 0.002 TYR B 351 ARG 0.014 0.001 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 190 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 177 time to evaluate : 0.815 Fit side-chains revert: symmetry clash REVERT: A 16 ASP cc_start: 0.7949 (t0) cc_final: 0.7680 (t70) REVERT: A 18 LYS cc_start: 0.8068 (ttmt) cc_final: 0.7693 (mtpp) REVERT: A 121 ARG cc_start: 0.8442 (ttp-110) cc_final: 0.8228 (ptm160) REVERT: A 138 ASN cc_start: 0.7348 (p0) cc_final: 0.7131 (p0) REVERT: A 177 MET cc_start: 0.9124 (tpp) cc_final: 0.8777 (tpt) REVERT: A 221 ILE cc_start: 0.9018 (mt) cc_final: 0.8786 (mp) REVERT: A 234 MET cc_start: 0.9000 (mtm) cc_final: 0.8700 (mtp) REVERT: A 244 LYS cc_start: 0.8733 (pttt) cc_final: 0.8435 (pttt) REVERT: A 344 ASP cc_start: 0.8213 (t0) cc_final: 0.7956 (t70) REVERT: A 354 GLU cc_start: 0.8094 (OUTLIER) cc_final: 0.7183 (mp0) REVERT: A 377 ASN cc_start: 0.8300 (t0) cc_final: 0.7617 (p0) REVERT: B 1 MET cc_start: 0.5787 (mmt) cc_final: 0.5526 (tpt) REVERT: B 11 LYS cc_start: 0.8985 (OUTLIER) cc_final: 0.8784 (pttt) REVERT: B 170 ARG cc_start: 0.7838 (ptm-80) cc_final: 0.7576 (ptm-80) REVERT: B 338 GLN cc_start: 0.8341 (mm110) cc_final: 0.8075 (mm110) REVERT: B 339 ASN cc_start: 0.8465 (t0) cc_final: 0.8158 (t0) outliers start: 13 outliers final: 7 residues processed: 180 average time/residue: 1.8083 time to fit residues: 341.6386 Evaluate side-chains 183 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 174 time to evaluate : 0.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 315 LYS 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: 0.9990 chunk 93 optimal weight: 0.2980 chunk 86 optimal weight: 3.9990 chunk 74 optimal weight: 6.9990 chunk 7 optimal weight: 0.8980 chunk 57 optimal weight: 5.9990 chunk 45 optimal weight: 7.9990 chunk 59 optimal weight: 0.7980 chunk 79 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.2795 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= 0.173 Angle : 0.548 10.148 14586 Z= 0.298 Chirality : 0.037 0.219 1679 Planarity : 0.004 0.057 1310 Dihedral : 20.216 73.889 3080 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.25 % Allowed : 3.00 % Favored : 96.75 % Rotamer: Outliers : 1.29 % Allowed : 26.71 % Favored : 72.00 % 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: 0.77 (0.30), residues: 799 helix: 2.14 (0.28), residues: 363 sheet: -0.07 (0.39), residues: 155 loop : -1.36 (0.35), residues: 281 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 340 HIS 0.003 0.001 HIS B 72 PHE 0.016 0.001 PHE A 389 TYR 0.014 0.001 TYR A 351 ARG 0.014 0.001 ARG A 121 ********************** 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: 9 poor density : 176 time to evaluate : 0.827 Fit side-chains revert: symmetry clash REVERT: A 16 ASP cc_start: 0.7887 (t0) cc_final: 0.7606 (t70) REVERT: A 105 TYR cc_start: 0.9201 (m-80) cc_final: 0.8886 (m-80) REVERT: A 121 ARG cc_start: 0.8485 (ttp-110) cc_final: 0.8260 (ptm160) REVERT: A 177 MET cc_start: 0.9057 (tpp) cc_final: 0.8645 (tpt) REVERT: A 221 ILE cc_start: 0.8998 (mt) cc_final: 0.8771 (mp) REVERT: A 234 MET cc_start: 0.8955 (mtm) cc_final: 0.8673 (mtp) REVERT: A 244 LYS cc_start: 0.8700 (pttt) cc_final: 0.8376 (pttt) REVERT: A 264 MET cc_start: 0.8455 (mtt) cc_final: 0.8027 (mtp) REVERT: A 344 ASP cc_start: 0.7949 (t0) cc_final: 0.7675 (t0) REVERT: A 354 GLU cc_start: 0.8033 (OUTLIER) cc_final: 0.7198 (mp0) REVERT: A 377 ASN cc_start: 0.8273 (t0) cc_final: 0.7661 (p0) REVERT: B 11 LYS cc_start: 0.8965 (OUTLIER) cc_final: 0.8686 (pttt) REVERT: B 242 ARG cc_start: 0.8519 (ptp-170) cc_final: 0.7919 (ptp-170) REVERT: B 254 ARG cc_start: 0.7801 (mtt90) cc_final: 0.7560 (mtp85) REVERT: B 338 GLN cc_start: 0.8254 (mm110) cc_final: 0.7934 (mm110) REVERT: B 339 ASN cc_start: 0.8439 (t0) cc_final: 0.8092 (t0) REVERT: B 407 ASN cc_start: 0.7265 (m-40) cc_final: 0.6746 (m110) outliers start: 9 outliers final: 6 residues processed: 180 average time/residue: 1.8276 time to fit residues: 345.3900 Evaluate side-chains 183 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 175 time to evaluate : 0.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 68 optimal weight: 8.9990 chunk 11 optimal weight: 0.9990 chunk 20 optimal weight: 6.9990 chunk 74 optimal weight: 1.9990 chunk 31 optimal weight: 5.9990 chunk 76 optimal weight: 1.9990 chunk 9 optimal weight: 6.9990 chunk 13 optimal weight: 3.9990 chunk 65 optimal weight: 4.9990 chunk 4 optimal weight: 1.9990 chunk 53 optimal weight: 10.0000 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 ASN B 399 ASN B 412 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.120663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.098550 restraints weight = 14786.452| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 1.75 r_work: 0.3115 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2971 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.2755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 10291 Z= 0.230 Angle : 0.565 12.287 14586 Z= 0.304 Chirality : 0.038 0.207 1679 Planarity : 0.004 0.059 1310 Dihedral : 20.230 73.744 3080 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.25 % Allowed : 3.75 % Favored : 95.99 % Rotamer: Outliers : 1.57 % Allowed : 26.29 % 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: 0.75 (0.30), residues: 799 helix: 2.13 (0.27), residues: 364 sheet: -0.07 (0.39), residues: 157 loop : -1.41 (0.35), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 340 HIS 0.004 0.001 HIS A 72 PHE 0.015 0.002 PHE A 389 TYR 0.031 0.002 TYR B 351 ARG 0.014 0.001 ARG A 121 =============================================================================== Job complete usr+sys time: 4989.21 seconds wall clock time: 89 minutes 31.44 seconds (5371.44 seconds total)