Starting phenix.real_space_refine on Thu Aug 6 05:53:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8snx_40641/08_2026/8snx_40641_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8snx_40641/08_2026/8snx_40641.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8snx_40641/08_2026/8snx_40641_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8snx_40641/08_2026/8snx_40641_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8snx_40641/08_2026/8snx_40641.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8snx_40641/08_2026/8snx_40641.map" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- 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= 0.000 sd= 0.006 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: 5 Type Number sf(0) Gaussians P 9 5.49 5 S 75 5.16 5 C 8728 2.51 5 N 2332 2.21 5 O 2597 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 13741 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 11300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1386, 11300 Classifications: {'peptide': 1386} Link IDs: {'PTRANS': 47, 'TRANS': 1338} Chain breaks: 3 Chain: "B" Number of atoms: 452 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 452 Classifications: {'peptide': 59} Link IDs: {'PTRANS': 1, 'TRANS': 57} Chain: "C" Number of atoms: 430 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 430 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 1, 'TRANS': 54} Chain: "D" Number of atoms: 479 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 479 Classifications: {'peptide': 61} Link IDs: {'TRANS': 60} Chain breaks: 1 Chain: "E" Number of atoms: 877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 877 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 2, 'TRANS': 110} Chain: "T" Number of atoms: 203 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 203 Classifications: {'RNA': 10} Modifications used: {'5*END': 1, 'rna2p_pyr': 2, 'rna3p_pur': 2, 'rna3p_pyr': 6} Link IDs: {'rna2p': 2, 'rna3p': 7} Time building chain proxies: 2.47, per 1000 atoms: 0.18 Number of scatterers: 13741 At special positions: 0 Unit cell: (97.3363, 117.438, 122.728, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 75 16.00 P 9 15.00 O 2597 8.00 N 2332 7.00 C 8728 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.10 Conformation dependent library (CDL) restraints added in 542.0 milliseconds 3314 Ramachandran restraints generated. 1657 Oldfield, 0 Emsley, 1657 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3208 Finding SS restraints... Secondary structure from input PDB file: 77 helices and 10 sheets defined 62.0% alpha, 3.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.25 Creating SS restraints... Processing helix chain 'A' and resid 24 through 37 removed outlier: 3.640A pdb=" N CYS A 28 " --> pdb=" O SER A 24 " (cutoff:3.500A) Processing helix chain 'A' and resid 44 through 53 removed outlier: 4.211A pdb=" N LEU A 48 " --> pdb=" O ASP A 44 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 63 Processing helix chain 'A' and resid 64 through 76 Processing helix chain 'A' and resid 83 through 93 Processing helix chain 'A' and resid 98 through 132 removed outlier: 4.015A pdb=" N VAL A 122 " --> pdb=" O GLU A 118 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N LYS A 123 " --> pdb=" O ILE A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 197 Processing helix chain 'A' and resid 201 through 228 Processing helix chain 'A' and resid 265 through 296 removed outlier: 3.761A pdb=" N LEU A 295 " --> pdb=" O CYS A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 325 Processing helix chain 'A' and resid 327 through 334 removed outlier: 4.277A pdb=" N ILE A 331 " --> pdb=" O GLU A 327 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N GLU A 334 " --> pdb=" O TYR A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 348 removed outlier: 3.682A pdb=" N PHE A 338 " --> pdb=" O GLU A 334 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ILE A 346 " --> pdb=" O LEU A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 379 Processing helix chain 'A' and resid 389 through 395 removed outlier: 4.341A pdb=" N ILE A 393 " --> pdb=" O SER A 389 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ASN A 394 " --> pdb=" O ASP A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 413 removed outlier: 3.649A pdb=" N LEU A 400 " --> pdb=" O ARG A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 422 Processing helix chain 'A' and resid 424 through 429 removed outlier: 3.612A pdb=" N PHE A 429 " --> pdb=" O LEU A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 435 through 448 Processing helix chain 'A' and resid 455 through 478 Processing helix chain 'A' and resid 490 through 499 removed outlier: 3.582A pdb=" N TYR A 496 " --> pdb=" O ARG A 492 " (cutoff:3.500A) Processing helix chain 'A' and resid 509 through 517 Processing helix chain 'A' and resid 532 through 537 Processing helix chain 'A' and resid 545 through 552 removed outlier: 5.158A pdb=" N TRP A 550 " --> pdb=" O ASN A 547 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N SER A 552 " --> pdb=" O ILE A 549 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 571 removed outlier: 4.249A pdb=" N LEU A 571 " --> pdb=" O GLU A 567 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 588 Processing helix chain 'A' and resid 596 through 604 Processing helix chain 'A' and resid 633 through 650 Processing helix chain 'A' and resid 651 through 655 Processing helix chain 'A' and resid 667 through 674 removed outlier: 3.629A pdb=" N LYS A 674 " --> pdb=" O ILE A 670 " (cutoff:3.500A) Processing helix chain 'A' and resid 709 through 714 Processing helix chain 'A' and resid 716 through 724 removed outlier: 3.700A pdb=" N LEU A 720 " --> pdb=" O CYS A 716 " (cutoff:3.500A) Processing helix chain 'A' and resid 732 through 737 Processing helix chain 'A' and resid 781 through 801 Processing helix chain 'A' and resid 832 through 852 Processing helix chain 'A' and resid 882 through 887 removed outlier: 3.780A pdb=" N LYS A 886 " --> pdb=" O ALA A 882 " (cutoff:3.500A) Processing helix chain 'A' and resid 900 through 920 removed outlier: 3.659A pdb=" N GLU A 914 " --> pdb=" O SER A 910 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N LEU A 915 " --> pdb=" O LEU A 911 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLU A 920 " --> pdb=" O GLU A 916 " (cutoff:3.500A) Processing helix chain 'A' and resid 921 through 939 Processing helix chain 'A' and resid 940 through 944 Processing helix chain 'A' and resid 949 through 966 Processing helix chain 'A' and resid 970 through 980 Processing helix chain 'A' and resid 982 through 986 Processing helix chain 'A' and resid 992 through 997 Processing helix chain 'A' and resid 1003 through 1020 removed outlier: 4.156A pdb=" N GLU A1007 " --> pdb=" O ASP A1003 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N TYR A1018 " --> pdb=" O PHE A1014 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N TYR A1019 " --> pdb=" O ILE A1015 " (cutoff:3.500A) Processing helix chain 'A' and resid 1034 through 1043 Processing helix chain 'A' and resid 1052 through 1060 Processing helix chain 'A' and resid 1072 through 1087 removed outlier: 3.599A pdb=" N ILE A1076 " --> pdb=" O ILE A1072 " (cutoff:3.500A) removed outlier: 5.204A pdb=" N LEU A1079 " --> pdb=" O GLU A1075 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N ALA A1080 " --> pdb=" O ILE A1076 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N THR A1087 " --> pdb=" O GLU A1083 " (cutoff:3.500A) Processing helix chain 'A' and resid 1090 through 1099 Processing helix chain 'A' and resid 1099 through 1111 removed outlier: 4.447A pdb=" N MET A1111 " --> pdb=" O LEU A1107 " (cutoff:3.500A) Processing helix chain 'A' and resid 1118 through 1129 Processing helix chain 'A' and resid 1130 through 1143 removed outlier: 3.846A pdb=" N ALA A1134 " --> pdb=" O PRO A1130 " (cutoff:3.500A) Processing helix chain 'A' and resid 1149 through 1153 removed outlier: 4.153A pdb=" N LYS A1153 " --> pdb=" O ILE A1150 " (cutoff:3.500A) Processing helix chain 'A' and resid 1159 through 1174 Processing helix chain 'A' and resid 1175 through 1180 Processing helix chain 'A' and resid 1198 through 1212 Processing helix chain 'A' and resid 1223 through 1227 Processing helix chain 'A' and resid 1282 through 1299 Processing helix chain 'A' and resid 1304 through 1317 Processing helix chain 'A' and resid 1320 through 1326 removed outlier: 3.797A pdb=" N LYS A1326 " --> pdb=" O GLU A1322 " (cutoff:3.500A) Processing helix chain 'A' and resid 1354 through 1359 removed outlier: 3.649A pdb=" N THR A1358 " --> pdb=" O PRO A1354 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N THR A1359 " --> pdb=" O ALA A1355 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1354 through 1359' Processing helix chain 'A' and resid 1365 through 1375 Processing helix chain 'A' and resid 1384 through 1404 removed outlier: 3.574A pdb=" N CYS A1388 " --> pdb=" O VAL A1384 " (cutoff:3.500A) Processing helix chain 'A' and resid 1432 through 1443 Processing helix chain 'A' and resid 1452 through 1457 Processing helix chain 'A' and resid 1458 through 1461 removed outlier: 3.730A pdb=" N LEU A1461 " --> pdb=" O GLU A1458 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1458 through 1461' Processing helix chain 'B' and resid 130 through 157 removed outlier: 3.610A pdb=" N ALA B 157 " --> pdb=" O VAL B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 157 through 164 removed outlier: 3.547A pdb=" N ALA B 162 " --> pdb=" O GLY B 158 " (cutoff:3.500A) Processing helix chain 'B' and resid 166 through 172 Processing helix chain 'B' and resid 174 through 187 Processing helix chain 'C' and resid 129 through 157 removed outlier: 4.041A pdb=" N GLU C 140 " --> pdb=" O ASP C 136 " (cutoff:3.500A) Processing helix chain 'C' and resid 161 through 183 removed outlier: 3.777A pdb=" N GLY C 165 " --> pdb=" O SER C 161 " (cutoff:3.500A) Processing helix chain 'D' and resid 130 through 157 Processing helix chain 'D' and resid 171 through 200 Processing helix chain 'E' and resid 130 through 151 removed outlier: 4.017A pdb=" N ARG E 137 " --> pdb=" O ALA E 133 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ILE E 138 " --> pdb=" O ARG E 134 " (cutoff:3.500A) Processing helix chain 'E' and resid 174 through 183 Processing helix chain 'E' and resid 190 through 199 Processing helix chain 'E' and resid 203 through 210 Processing helix chain 'E' and resid 217 through 228 Processing sheet with id=AA1, first strand: chain 'A' and resid 11 through 12 Processing sheet with id=AA2, first strand: chain 'A' and resid 80 through 81 removed outlier: 6.567A pdb=" N LYS A 80 " --> pdb=" O ILE A 261 " (cutoff:3.500A) removed outlier: 9.288A pdb=" N VAL A 263 " --> pdb=" O LYS A 80 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA4, first strand: chain 'A' and resid 617 through 618 Processing sheet with id=AA5, first strand: chain 'A' and resid 691 through 694 Processing sheet with id=AA6, first strand: chain 'A' and resid 812 through 815 Processing sheet with id=AA7, first strand: chain 'A' and resid 741 through 743 Processing sheet with id=AA8, first strand: chain 'A' and resid 873 through 875 removed outlier: 3.843A pdb=" N ILE A 873 " --> pdb=" O TYR A 880 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 1228 through 1231 Processing sheet with id=AB1, first strand: chain 'A' and resid 1271 through 1272 removed outlier: 3.785A pdb=" N GLN A1330 " --> pdb=" O THR A1272 " (cutoff:3.500A) 740 hydrogen bonds defined for protein. 2151 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.13 Time building geometry restraints manager: 1.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2377 1.32 - 1.45: 3507 1.45 - 1.57: 7971 1.57 - 1.69: 18 1.69 - 1.82: 127 Bond restraints: 14000 Sorted by residual: bond pdb=" CA ARG A 555 " pdb=" C ARG A 555 " ideal model delta sigma weight residual 1.524 1.478 0.046 1.26e-02 6.30e+03 1.31e+01 bond pdb=" CA SER A 658 " pdb=" CB SER A 658 " ideal model delta sigma weight residual 1.527 1.480 0.047 1.30e-02 5.92e+03 1.30e+01 bond pdb=" C HIS A 325 " pdb=" O HIS A 325 " ideal model delta sigma weight residual 1.238 1.201 0.037 1.02e-02 9.61e+03 1.30e+01 bond pdb=" CA SER A 658 " pdb=" C SER A 658 " ideal model delta sigma weight residual 1.525 1.481 0.044 1.28e-02 6.10e+03 1.19e+01 bond pdb=" C GLU A 569 " pdb=" N LYS A 570 " ideal model delta sigma weight residual 1.334 1.290 0.044 1.27e-02 6.20e+03 1.19e+01 ... (remaining 13995 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.98: 18864 2.98 - 5.95: 86 5.95 - 8.93: 8 8.93 - 11.90: 1 11.90 - 14.88: 1 Bond angle restraints: 18960 Sorted by residual: angle pdb=" N THR A 660 " pdb=" CA THR A 660 " pdb=" C THR A 660 " ideal model delta sigma weight residual 113.30 98.42 14.88 1.34e+00 5.57e-01 1.23e+02 angle pdb=" N GLU A 672 " pdb=" CA GLU A 672 " pdb=" C GLU A 672 " ideal model delta sigma weight residual 112.89 105.65 7.24 1.24e+00 6.50e-01 3.41e+01 angle pdb=" N LEU A 673 " pdb=" CA LEU A 673 " pdb=" C LEU A 673 " ideal model delta sigma weight residual 111.28 105.07 6.21 1.09e+00 8.42e-01 3.25e+01 angle pdb=" N LYS A 570 " pdb=" CA LYS A 570 " pdb=" C LYS A 570 " ideal model delta sigma weight residual 111.03 105.47 5.56 1.11e+00 8.12e-01 2.50e+01 angle pdb=" N ALA A 675 " pdb=" CA ALA A 675 " pdb=" C ALA A 675 " ideal model delta sigma weight residual 110.68 104.67 6.01 1.39e+00 5.18e-01 1.87e+01 ... (remaining 18955 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.86: 7590 17.86 - 35.71: 794 35.71 - 53.57: 154 53.57 - 71.42: 34 71.42 - 89.28: 14 Dihedral angle restraints: 8586 sinusoidal: 3644 harmonic: 4942 Sorted by residual: dihedral pdb=" O4' U T 1 " pdb=" C1' U T 1 " pdb=" N1 U T 1 " pdb=" C2 U T 1 " ideal model delta sinusoidal sigma weight residual -160.00 -74.83 -85.17 1 1.50e+01 4.44e-03 3.91e+01 dihedral pdb=" CA LEU A 499 " pdb=" C LEU A 499 " pdb=" N ASN A 500 " pdb=" CA ASN A 500 " ideal model delta harmonic sigma weight residual -180.00 -161.54 -18.46 0 5.00e+00 4.00e-02 1.36e+01 dihedral pdb=" C LEU A 422 " pdb=" N LEU A 422 " pdb=" CA LEU A 422 " pdb=" CB LEU A 422 " ideal model delta harmonic sigma weight residual -122.60 -131.52 8.92 0 2.50e+00 1.60e-01 1.27e+01 ... (remaining 8583 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.081: 2075 0.081 - 0.163: 124 0.163 - 0.244: 4 0.244 - 0.326: 0 0.326 - 0.407: 2 Chirality restraints: 2205 Sorted by residual: chirality pdb=" CA HIS A 325 " pdb=" N HIS A 325 " pdb=" C HIS A 325 " pdb=" CB HIS A 325 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.14e+00 chirality pdb=" CA LEU A 422 " pdb=" N LEU A 422 " pdb=" C LEU A 422 " pdb=" CB LEU A 422 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.66e+00 chirality pdb=" CA ALA A 675 " pdb=" N ALA A 675 " pdb=" C ALA A 675 " pdb=" CB ALA A 675 " both_signs ideal model delta sigma weight residual False 2.48 2.71 -0.23 2.00e-01 2.50e+01 1.27e+00 ... (remaining 2202 not shown) Planarity restraints: 2354 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU A 83 " -0.035 5.00e-02 4.00e+02 5.31e-02 4.52e+00 pdb=" N PRO A 84 " 0.092 5.00e-02 4.00e+02 pdb=" CA PRO A 84 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 84 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR A1154 " -0.010 2.00e-02 2.50e+03 2.00e-02 3.98e+00 pdb=" C THR A1154 " 0.035 2.00e-02 2.50e+03 pdb=" O THR A1154 " -0.013 2.00e-02 2.50e+03 pdb=" N SER A1155 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 657 " -0.009 2.00e-02 2.50e+03 1.91e-02 3.64e+00 pdb=" C GLU A 657 " 0.033 2.00e-02 2.50e+03 pdb=" O GLU A 657 " -0.012 2.00e-02 2.50e+03 pdb=" N SER A 658 " -0.011 2.00e-02 2.50e+03 ... (remaining 2351 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1278 2.74 - 3.28: 14253 3.28 - 3.82: 23745 3.82 - 4.36: 28496 4.36 - 4.90: 49084 Nonbonded interactions: 116856 Sorted by model distance: nonbonded pdb=" NH2 ARG A1357 " pdb=" OE2 GLU A1400 " model vdw 2.202 3.120 nonbonded pdb=" OH TYR A 834 " pdb=" O ASP E 212 " model vdw 2.251 3.040 nonbonded pdb=" NZ LYS A 403 " pdb=" OD2 ASP E 231 " model vdw 2.268 3.120 nonbonded pdb=" O ALA E 207 " pdb=" OG SER E 211 " model vdw 2.298 3.040 nonbonded pdb=" OH TYR A 598 " pdb=" OE1 GLU B 176 " model vdw 2.300 3.040 ... (remaining 116851 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 'B' and resid 129 through 183) selection = (chain 'C' and resid 129 through 183) } 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=0.20 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: 0.680 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: 0.300 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 11.160 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 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 : 0.003 0.047 14000 Z= 0.186 Angle : 0.565 14.877 18960 Z= 0.318 Chirality : 0.042 0.407 2205 Planarity : 0.003 0.053 2354 Dihedral : 15.099 89.279 5378 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 0.33 % Allowed : 0.39 % Favored : 99.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.44 (0.21), residues: 1657 helix: 2.09 (0.17), residues: 957 sheet: -0.93 (0.62), residues: 66 loop : -0.61 (0.24), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 197 TYR 0.013 0.001 TYR A 861 PHE 0.014 0.001 PHE A 426 TRP 0.031 0.002 TRP A 480 HIS 0.002 0.001 HIS A 561 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.19 (14000) covalent geometry : angle 0.56514 / 0.32 (18960) hydrogen bonds : bond 0.09912 / 6.36 ( 740) hydrogen bonds : angle 5.09137 / 3.57 ( 2151) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3314 Ramachandran restraints generated. 1657 Oldfield, 0 Emsley, 1657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3314 Ramachandran restraints generated. 1657 Oldfield, 0 Emsley, 1657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 1533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 281 time to evaluate : 0.540 Fit side-chains REVERT: A 861 TYR cc_start: 0.9089 (p90) cc_final: 0.8660 (p90) REVERT: A 912 THR cc_start: 0.9361 (p) cc_final: 0.9139 (p) outliers start: 5 outliers final: 1 residues processed: 286 average time/residue: 0.1189 time to fit residues: 50.6305 Evaluate side-chains 229 residues out of total 1533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 228 time to evaluate : 0.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 666 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 98 optimal weight: 0.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 10.0000 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 8.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 653 GLN A 812 ASN A 930 ASN A1022 HIS A1049 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.120437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.095955 restraints weight = 19517.568| |-----------------------------------------------------------------------------| r_work (start): 0.2940 rms_B_bonded: 1.87 r_work: 0.2809 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2665 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2665 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2630 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2630 r_free = 0.2630 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2630 r_free = 0.2630 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (8 function evaluations) r_final: 0.2630 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8677 moved from start: 0.0930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 14000 Z= 0.186 Angle : 0.551 13.473 18960 Z= 0.288 Chirality : 0.041 0.208 2205 Planarity : 0.004 0.053 2354 Dihedral : 8.521 75.388 1985 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 1.50 % Allowed : 9.39 % Favored : 89.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.37 (0.21), residues: 1657 helix: 2.02 (0.17), residues: 953 sheet: -1.03 (0.62), residues: 64 loop : -0.58 (0.24), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 137 TYR 0.014 0.001 TYR A 221 PHE 0.022 0.002 PHE A 629 TRP 0.020 0.002 TRP A 480 HIS 0.004 0.001 HIS A 206 Details of bonding type rmsd/Z covalent geometry : bond 0.00446 / 0.19 (14000) covalent geometry : angle 0.55149 / 0.29 (18960) hydrogen bonds : bond 0.03940 / 2.55 ( 740) hydrogen bonds : angle 4.43802 / 3.11 ( 2151) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3314 Ramachandran restraints generated. 1657 Oldfield, 0 Emsley, 1657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3314 Ramachandran restraints generated. 1657 Oldfield, 0 Emsley, 1657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 233 time to evaluate : 0.516 Fit side-chains revert: symmetry clash REVERT: A 861 TYR cc_start: 0.9166 (p90) cc_final: 0.8855 (p90) REVERT: A 872 THR cc_start: 0.8431 (OUTLIER) cc_final: 0.8092 (t) REVERT: A 906 GLU cc_start: 0.8851 (mm-30) cc_final: 0.8250 (mt-10) REVERT: A 1304 ASN cc_start: 0.8861 (t0) cc_final: 0.8613 (t0) REVERT: A 1332 LEU cc_start: 0.8750 (mt) cc_final: 0.8502 (mm) REVERT: B 164 ASP cc_start: 0.8755 (m-30) cc_final: 0.8458 (m-30) outliers start: 23 outliers final: 17 residues processed: 243 average time/residue: 0.1198 time to fit residues: 43.0615 Evaluate side-chains 235 residues out of total 1533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 217 time to evaluate : 0.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 ILE Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 499 LEU Chi-restraints excluded: chain A residue 517 SER Chi-restraints excluded: chain A residue 653 GLN Chi-restraints excluded: chain A residue 666 GLU Chi-restraints excluded: chain A residue 808 ILE Chi-restraints excluded: chain A residue 856 LYS Chi-restraints excluded: chain A residue 872 THR Chi-restraints excluded: chain A residue 897 ILE Chi-restraints excluded: chain A residue 1072 ILE Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain C residue 149 LEU Chi-restraints excluded: chain D residue 146 LEU Chi-restraints excluded: chain E residue 136 ASP Chi-restraints excluded: chain E residue 138 ILE Chi-restraints excluded: chain E residue 156 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 70 optimal weight: 1.9990 chunk 90 optimal weight: 3.9990 chunk 110 optimal weight: 6.9990 chunk 59 optimal weight: 3.9990 chunk 73 optimal weight: 1.9990 chunk 44 optimal weight: 0.0870 chunk 135 optimal weight: 5.9990 chunk 144 optimal weight: 0.9980 chunk 155 optimal weight: 4.9990 chunk 108 optimal weight: 0.9990 chunk 23 optimal weight: 7.9990 overall best weight: 1.2164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 476 ASN A 809 ASN A 812 ASN A1022 HIS A1049 ASN E 189 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.121533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.097396 restraints weight = 19462.421| |-----------------------------------------------------------------------------| r_work (start): 0.2941 rms_B_bonded: 1.86 r_work: 0.2814 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2671 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2671 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2697 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2697 r_free = 0.2697 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2697 r_free = 0.2697 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2697 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8659 moved from start: 0.1063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14000 Z= 0.126 Angle : 0.484 7.020 18960 Z= 0.257 Chirality : 0.039 0.192 2205 Planarity : 0.003 0.052 2354 Dihedral : 8.322 73.719 1985 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.63 % Allowed : 12.00 % Favored : 86.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.45 (0.21), residues: 1657 helix: 2.07 (0.17), residues: 953 sheet: -1.03 (0.60), residues: 64 loop : -0.52 (0.24), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 396 TYR 0.013 0.001 TYR A 861 PHE 0.029 0.001 PHE A 629 TRP 0.014 0.001 TRP A 932 HIS 0.002 0.001 HIS B 150 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.13 (14000) covalent geometry : angle 0.48436 / 0.26 (18960) hydrogen bonds : bond 0.03640 / 2.36 ( 740) hydrogen bonds : angle 4.25966 / 2.97 ( 2151) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3314 Ramachandran restraints generated. 1657 Oldfield, 0 Emsley, 1657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3314 Ramachandran restraints generated. 1657 Oldfield, 0 Emsley, 1657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 230 time to evaluate : 0.546 Fit side-chains revert: symmetry clash REVERT: A 511 ARG cc_start: 0.7561 (tpp80) cc_final: 0.7296 (tpp-160) REVERT: A 861 TYR cc_start: 0.9200 (p90) cc_final: 0.8840 (p90) REVERT: A 872 THR cc_start: 0.8239 (OUTLIER) cc_final: 0.8020 (t) REVERT: A 906 GLU cc_start: 0.8944 (mm-30) cc_final: 0.8326 (mt-10) REVERT: A 1304 ASN cc_start: 0.8855 (t0) cc_final: 0.8551 (t0) REVERT: A 1332 LEU cc_start: 0.8710 (mt) cc_final: 0.8494 (mm) REVERT: A 1370 ARG cc_start: 0.8015 (ttt-90) cc_final: 0.7544 (ttm-80) outliers start: 25 outliers final: 16 residues processed: 243 average time/residue: 0.1173 time to fit residues: 42.5842 Evaluate side-chains 237 residues out of total 1533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 220 time to evaluate : 0.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 499 LEU Chi-restraints excluded: chain A residue 517 SER Chi-restraints excluded: chain A residue 808 ILE Chi-restraints excluded: chain A residue 809 ASN Chi-restraints excluded: chain A residue 835 LEU Chi-restraints excluded: chain A residue 856 LYS Chi-restraints excluded: chain A residue 872 THR Chi-restraints excluded: chain A residue 1072 ILE Chi-restraints excluded: chain A residue 1173 ILE Chi-restraints excluded: chain A residue 1347 CYS Chi-restraints excluded: chain C residue 149 LEU Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain D residue 146 LEU Chi-restraints excluded: chain E residue 136 ASP Chi-restraints excluded: chain E residue 156 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 58 optimal weight: 5.9990 chunk 45 optimal weight: 6.9990 chunk 33 optimal weight: 0.7980 chunk 1 optimal weight: 1.9990 chunk 133 optimal weight: 3.9990 chunk 108 optimal weight: 0.0670 chunk 138 optimal weight: 2.9990 chunk 111 optimal weight: 9.9990 chunk 156 optimal weight: 4.9990 chunk 131 optimal weight: 0.9990 chunk 34 optimal weight: 2.9990 overall best weight: 1.3724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 640 GLN A 809 ASN A 812 ASN A1022 HIS A1049 ASN E 189 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.120677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.096330 restraints weight = 19420.698| |-----------------------------------------------------------------------------| r_work (start): 0.2916 rms_B_bonded: 1.87 r_work: 0.2788 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2644 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2644 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2632 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2632 r_free = 0.2632 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2632 r_free = 0.2632 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.2632 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8669 moved from start: 0.1175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14000 Z= 0.128 Angle : 0.468 7.168 18960 Z= 0.248 Chirality : 0.039 0.177 2205 Planarity : 0.003 0.051 2354 Dihedral : 8.100 73.583 1982 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 1.96 % Allowed : 13.24 % Favored : 84.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.52 (0.21), residues: 1657 helix: 2.13 (0.17), residues: 953 sheet: -1.04 (0.61), residues: 64 loop : -0.48 (0.24), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 163 TYR 0.013 0.001 TYR A 861 PHE 0.022 0.001 PHE A 629 TRP 0.014 0.001 TRP A 932 HIS 0.003 0.001 HIS A 206 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.13 (14000) covalent geometry : angle 0.46755 / 0.25 (18960) hydrogen bonds : bond 0.03554 / 2.31 ( 740) hydrogen bonds : angle 4.16011 / 2.90 ( 2151) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3314 Ramachandran restraints generated. 1657 Oldfield, 0 Emsley, 1657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3314 Ramachandran restraints generated. 1657 Oldfield, 0 Emsley, 1657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 229 time to evaluate : 0.618 Fit side-chains revert: symmetry clash REVERT: A 511 ARG cc_start: 0.7646 (tpp80) cc_final: 0.7405 (tpp-160) REVERT: A 640 GLN cc_start: 0.9164 (OUTLIER) cc_final: 0.8872 (tm130) REVERT: A 861 TYR cc_start: 0.9188 (p90) cc_final: 0.8841 (p90) REVERT: A 872 THR cc_start: 0.8282 (OUTLIER) cc_final: 0.7969 (t) REVERT: A 906 GLU cc_start: 0.9033 (mm-30) cc_final: 0.8437 (mt-10) REVERT: A 1304 ASN cc_start: 0.8805 (t0) cc_final: 0.8505 (t0) REVERT: A 1332 LEU cc_start: 0.8703 (mt) cc_final: 0.8490 (mm) REVERT: A 1370 ARG cc_start: 0.8022 (ttt-90) cc_final: 0.7541 (ttm-80) REVERT: B 144 GLU cc_start: 0.7977 (mt-10) cc_final: 0.7518 (tt0) outliers start: 30 outliers final: 24 residues processed: 245 average time/residue: 0.1181 time to fit residues: 43.3553 Evaluate side-chains 243 residues out of total 1533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 217 time to evaluate : 0.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 ILE Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 499 LEU Chi-restraints excluded: chain A residue 517 SER Chi-restraints excluded: chain A residue 640 GLN Chi-restraints excluded: chain A residue 692 ILE Chi-restraints excluded: chain A residue 808 ILE Chi-restraints excluded: chain A residue 824 MET Chi-restraints excluded: chain A residue 835 LEU Chi-restraints excluded: chain A residue 851 ILE Chi-restraints excluded: chain A residue 856 LYS Chi-restraints excluded: chain A residue 872 THR Chi-restraints excluded: chain A residue 897 ILE Chi-restraints excluded: chain A residue 1072 ILE Chi-restraints excluded: chain A residue 1173 ILE Chi-restraints excluded: chain A residue 1347 CYS Chi-restraints excluded: chain A residue 1384 VAL Chi-restraints excluded: chain A residue 1423 LYS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain C residue 149 LEU Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain D residue 146 LEU Chi-restraints excluded: chain E residue 136 ASP Chi-restraints excluded: chain E residue 156 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 1 optimal weight: 0.9990 chunk 10 optimal weight: 4.9990 chunk 122 optimal weight: 6.9990 chunk 14 optimal weight: 6.9990 chunk 11 optimal weight: 4.9990 chunk 153 optimal weight: 9.9990 chunk 155 optimal weight: 2.9990 chunk 83 optimal weight: 6.9990 chunk 24 optimal weight: 1.9990 chunk 79 optimal weight: 6.9990 chunk 97 optimal weight: 6.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 734 HIS A 812 ASN A1011 HIS A1022 HIS A1049 ASN E 189 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.117679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.093174 restraints weight = 19640.400| |-----------------------------------------------------------------------------| r_work (start): 0.2891 rms_B_bonded: 1.87 r_work: 0.2762 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2616 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2616 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2570 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2570 r_free = 0.2570 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2570 r_free = 0.2570 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.2570 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8719 moved from start: 0.1436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 14000 Z= 0.226 Angle : 0.536 7.217 18960 Z= 0.281 Chirality : 0.042 0.173 2205 Planarity : 0.004 0.050 2354 Dihedral : 8.131 73.721 1982 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 2.15 % Allowed : 14.94 % Favored : 82.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.34 (0.21), residues: 1657 helix: 1.97 (0.16), residues: 957 sheet: -1.13 (0.61), residues: 64 loop : -0.55 (0.24), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 174 TYR 0.015 0.001 TYR A 221 PHE 0.025 0.002 PHE A 629 TRP 0.016 0.002 TRP A 480 HIS 0.005 0.001 HIS A 206 Details of bonding type rmsd/Z covalent geometry : bond 0.00549 / 0.23 (14000) covalent geometry : angle 0.53627 / 0.28 (18960) hydrogen bonds : bond 0.04021 / 2.62 ( 740) hydrogen bonds : angle 4.24906 / 2.97 ( 2151) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3314 Ramachandran restraints generated. 1657 Oldfield, 0 Emsley, 1657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3314 Ramachandran restraints generated. 1657 Oldfield, 0 Emsley, 1657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 215 time to evaluate : 0.552 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 861 TYR cc_start: 0.9215 (p90) cc_final: 0.8870 (p90) REVERT: A 872 THR cc_start: 0.8327 (OUTLIER) cc_final: 0.8043 (t) REVERT: A 906 GLU cc_start: 0.9138 (mm-30) cc_final: 0.8604 (mt-10) REVERT: A 1304 ASN cc_start: 0.8849 (t0) cc_final: 0.8474 (t0) REVERT: A 1332 LEU cc_start: 0.8772 (mt) cc_final: 0.8571 (mm) REVERT: A 1370 ARG cc_start: 0.8037 (ttt-90) cc_final: 0.7573 (ttm-80) REVERT: A 1396 MET cc_start: 0.8442 (OUTLIER) cc_final: 0.8196 (mtp) outliers start: 33 outliers final: 26 residues processed: 233 average time/residue: 0.1186 time to fit residues: 41.0534 Evaluate side-chains 228 residues out of total 1533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 200 time to evaluate : 0.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 ILE Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 499 LEU Chi-restraints excluded: chain A residue 517 SER Chi-restraints excluded: chain A residue 692 ILE Chi-restraints excluded: chain A residue 808 ILE Chi-restraints excluded: chain A residue 824 MET Chi-restraints excluded: chain A residue 835 LEU Chi-restraints excluded: chain A residue 851 ILE Chi-restraints excluded: chain A residue 872 THR Chi-restraints excluded: chain A residue 897 ILE Chi-restraints excluded: chain A residue 1072 ILE Chi-restraints excluded: chain A residue 1173 ILE Chi-restraints excluded: chain A residue 1347 CYS Chi-restraints excluded: chain A residue 1384 VAL Chi-restraints excluded: chain A residue 1396 MET Chi-restraints excluded: chain A residue 1454 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain C residue 149 LEU Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain D residue 146 LEU Chi-restraints excluded: chain D residue 152 LEU Chi-restraints excluded: chain E residue 136 ASP Chi-restraints excluded: chain E residue 138 ILE Chi-restraints excluded: chain E residue 156 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 160 optimal weight: 6.9990 chunk 162 optimal weight: 8.9990 chunk 145 optimal weight: 0.9990 chunk 52 optimal weight: 0.7980 chunk 161 optimal weight: 8.9990 chunk 136 optimal weight: 1.9990 chunk 157 optimal weight: 0.7980 chunk 121 optimal weight: 0.9980 chunk 106 optimal weight: 0.8980 chunk 57 optimal weight: 0.7980 chunk 30 optimal weight: 0.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 640 GLN A 734 HIS A 812 ASN A1022 HIS A1049 ASN E 189 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.118830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.094282 restraints weight = 19432.634| |-----------------------------------------------------------------------------| r_work (start): 0.2903 rms_B_bonded: 1.87 r_work: 0.2777 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2633 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2633 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2658 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2658 r_free = 0.2658 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2658 r_free = 0.2658 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2658 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8675 moved from start: 0.1430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 14000 Z= 0.109 Angle : 0.470 6.961 18960 Z= 0.248 Chirality : 0.038 0.168 2205 Planarity : 0.003 0.052 2354 Dihedral : 7.964 73.596 1982 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.09 % Allowed : 15.00 % Favored : 82.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.50 (0.21), residues: 1657 helix: 2.10 (0.17), residues: 951 sheet: -0.99 (0.62), residues: 63 loop : -0.48 (0.25), residues: 643 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 134 TYR 0.013 0.001 TYR A 861 PHE 0.021 0.001 PHE A 629 TRP 0.015 0.001 TRP A 932 HIS 0.002 0.001 HIS A1120 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.11 (14000) covalent geometry : angle 0.47011 / 0.25 (18960) hydrogen bonds : bond 0.03536 / 2.31 ( 740) hydrogen bonds : angle 4.14516 / 2.90 ( 2151) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3314 Ramachandran restraints generated. 1657 Oldfield, 0 Emsley, 1657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3314 Ramachandran restraints generated. 1657 Oldfield, 0 Emsley, 1657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 225 time to evaluate : 0.607 Fit side-chains revert: symmetry clash REVERT: A 511 ARG cc_start: 0.7753 (tpp80) cc_final: 0.7480 (tpp-160) REVERT: A 861 TYR cc_start: 0.9147 (p90) cc_final: 0.8815 (p90) REVERT: A 872 THR cc_start: 0.8299 (OUTLIER) cc_final: 0.7961 (t) REVERT: A 906 GLU cc_start: 0.9061 (mm-30) cc_final: 0.8542 (mt-10) REVERT: A 1304 ASN cc_start: 0.8739 (t0) cc_final: 0.8381 (t0) REVERT: A 1332 LEU cc_start: 0.8738 (mt) cc_final: 0.8516 (mm) REVERT: A 1370 ARG cc_start: 0.7989 (ttt-90) cc_final: 0.7546 (ttm-80) REVERT: A 1396 MET cc_start: 0.8164 (OUTLIER) cc_final: 0.7912 (mtp) REVERT: C 142 LEU cc_start: 0.8921 (mm) cc_final: 0.8664 (mm) REVERT: C 146 LEU cc_start: 0.8133 (OUTLIER) cc_final: 0.7818 (mm) outliers start: 32 outliers final: 25 residues processed: 243 average time/residue: 0.1177 time to fit residues: 43.0900 Evaluate side-chains 237 residues out of total 1533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 209 time to evaluate : 0.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 ILE Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 499 LEU Chi-restraints excluded: chain A residue 517 SER Chi-restraints excluded: chain A residue 692 ILE Chi-restraints excluded: chain A residue 808 ILE Chi-restraints excluded: chain A residue 824 MET Chi-restraints excluded: chain A residue 835 LEU Chi-restraints excluded: chain A residue 844 LEU Chi-restraints excluded: chain A residue 856 LYS Chi-restraints excluded: chain A residue 872 THR Chi-restraints excluded: chain A residue 955 ILE Chi-restraints excluded: chain A residue 1072 ILE Chi-restraints excluded: chain A residue 1173 ILE Chi-restraints excluded: chain A residue 1347 CYS Chi-restraints excluded: chain A residue 1384 VAL Chi-restraints excluded: chain A residue 1396 MET Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 149 LEU Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain D residue 146 LEU Chi-restraints excluded: chain D residue 152 LEU Chi-restraints excluded: chain E residue 136 ASP Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 156 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 90 optimal weight: 6.9990 chunk 79 optimal weight: 7.9990 chunk 86 optimal weight: 0.6980 chunk 37 optimal weight: 1.9990 chunk 55 optimal weight: 6.9990 chunk 7 optimal weight: 10.0000 chunk 65 optimal weight: 0.9980 chunk 109 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 127 optimal weight: 3.9990 chunk 89 optimal weight: 0.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 640 GLN A 734 HIS A 812 ASN A1022 HIS E 189 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.119363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.094703 restraints weight = 19406.035| |-----------------------------------------------------------------------------| r_work (start): 0.2912 rms_B_bonded: 1.90 r_work: 0.2785 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2640 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2640 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2629 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2629 r_free = 0.2629 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2629 r_free = 0.2629 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2629 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8685 moved from start: 0.1489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 14000 Z= 0.136 Angle : 0.487 7.173 18960 Z= 0.257 Chirality : 0.039 0.178 2205 Planarity : 0.003 0.053 2354 Dihedral : 7.884 73.611 1982 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 2.48 % Allowed : 15.26 % Favored : 82.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.51 (0.21), residues: 1657 helix: 2.11 (0.17), residues: 952 sheet: -0.96 (0.62), residues: 63 loop : -0.48 (0.25), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 134 TYR 0.013 0.001 TYR A 221 PHE 0.020 0.002 PHE A 629 TRP 0.015 0.001 TRP A 932 HIS 0.003 0.001 HIS A 206 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.14 (14000) covalent geometry : angle 0.48697 / 0.26 (18960) hydrogen bonds : bond 0.03639 / 2.38 ( 740) hydrogen bonds : angle 4.14766 / 2.89 ( 2151) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3314 Ramachandran restraints generated. 1657 Oldfield, 0 Emsley, 1657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3314 Ramachandran restraints generated. 1657 Oldfield, 0 Emsley, 1657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 221 time to evaluate : 0.500 Fit side-chains revert: symmetry clash REVERT: A 511 ARG cc_start: 0.7759 (tpp80) cc_final: 0.7429 (tpp-160) REVERT: A 640 GLN cc_start: 0.9180 (OUTLIER) cc_final: 0.8871 (tm130) REVERT: A 861 TYR cc_start: 0.9145 (p90) cc_final: 0.8800 (p90) REVERT: A 872 THR cc_start: 0.8328 (OUTLIER) cc_final: 0.7981 (t) REVERT: A 906 GLU cc_start: 0.9025 (mm-30) cc_final: 0.8527 (mt-10) REVERT: A 1049 ASN cc_start: 0.7800 (p0) cc_final: 0.7598 (p0) REVERT: A 1304 ASN cc_start: 0.8716 (t0) cc_final: 0.8341 (t0) REVERT: A 1332 LEU cc_start: 0.8759 (mt) cc_final: 0.8536 (mm) REVERT: A 1370 ARG cc_start: 0.7984 (ttt-90) cc_final: 0.7532 (ttm-80) REVERT: C 142 LEU cc_start: 0.8921 (mm) cc_final: 0.8656 (mm) REVERT: C 146 LEU cc_start: 0.8151 (OUTLIER) cc_final: 0.7820 (mm) REVERT: E 139 ASP cc_start: 0.7767 (t0) cc_final: 0.7336 (t0) outliers start: 38 outliers final: 28 residues processed: 244 average time/residue: 0.1161 time to fit residues: 42.6657 Evaluate side-chains 240 residues out of total 1533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 209 time to evaluate : 0.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 ILE Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 499 LEU Chi-restraints excluded: chain A residue 517 SER Chi-restraints excluded: chain A residue 640 GLN Chi-restraints excluded: chain A residue 808 ILE Chi-restraints excluded: chain A residue 814 SER Chi-restraints excluded: chain A residue 824 MET Chi-restraints excluded: chain A residue 835 LEU Chi-restraints excluded: chain A residue 844 LEU Chi-restraints excluded: chain A residue 851 ILE Chi-restraints excluded: chain A residue 856 LYS Chi-restraints excluded: chain A residue 872 THR Chi-restraints excluded: chain A residue 897 ILE Chi-restraints excluded: chain A residue 955 ILE Chi-restraints excluded: chain A residue 1072 ILE Chi-restraints excluded: chain A residue 1173 ILE Chi-restraints excluded: chain A residue 1347 CYS Chi-restraints excluded: chain A residue 1384 VAL Chi-restraints excluded: chain A residue 1454 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 149 LEU Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain D residue 146 LEU Chi-restraints excluded: chain D residue 152 LEU Chi-restraints excluded: chain E residue 136 ASP Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 156 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 46 optimal weight: 0.9990 chunk 127 optimal weight: 2.9990 chunk 146 optimal weight: 20.0000 chunk 45 optimal weight: 0.7980 chunk 129 optimal weight: 10.0000 chunk 95 optimal weight: 5.9990 chunk 43 optimal weight: 0.6980 chunk 56 optimal weight: 10.0000 chunk 42 optimal weight: 0.9990 chunk 130 optimal weight: 0.0670 chunk 120 optimal weight: 6.9990 overall best weight: 0.7122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 640 GLN A 734 HIS A 812 ASN A1022 HIS E 189 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.120411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.096025 restraints weight = 19333.309| |-----------------------------------------------------------------------------| r_work (start): 0.2910 rms_B_bonded: 1.86 r_work: 0.2781 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2638 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2638 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2620 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2620 r_free = 0.2620 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2620 r_free = 0.2620 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2620 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8674 moved from start: 0.1500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 14000 Z= 0.105 Angle : 0.479 7.046 18960 Z= 0.250 Chirality : 0.038 0.189 2205 Planarity : 0.003 0.055 2354 Dihedral : 7.827 73.558 1982 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.22 % Allowed : 15.98 % Favored : 81.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.55 (0.21), residues: 1657 helix: 2.15 (0.17), residues: 950 sheet: -1.01 (0.61), residues: 65 loop : -0.45 (0.25), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 134 TYR 0.012 0.001 TYR A 221 PHE 0.018 0.001 PHE A 629 TRP 0.015 0.001 TRP A 932 HIS 0.002 0.000 HIS B 150 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.11 (14000) covalent geometry : angle 0.47895 / 0.25 (18960) hydrogen bonds : bond 0.03516 / 2.29 ( 740) hydrogen bonds : angle 4.12134 / 2.88 ( 2151) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3314 Ramachandran restraints generated. 1657 Oldfield, 0 Emsley, 1657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3314 Ramachandran restraints generated. 1657 Oldfield, 0 Emsley, 1657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 220 time to evaluate : 0.543 Fit side-chains revert: symmetry clash REVERT: A 365 THR cc_start: 0.9023 (p) cc_final: 0.8821 (p) REVERT: A 511 ARG cc_start: 0.7731 (tpp80) cc_final: 0.7405 (tpp-160) REVERT: A 653 GLN cc_start: 0.9204 (OUTLIER) cc_final: 0.8205 (pp30) REVERT: A 861 TYR cc_start: 0.9159 (p90) cc_final: 0.8814 (p90) REVERT: A 872 THR cc_start: 0.8340 (OUTLIER) cc_final: 0.7941 (m) REVERT: A 906 GLU cc_start: 0.8977 (mm-30) cc_final: 0.8503 (mt-10) REVERT: A 1304 ASN cc_start: 0.8695 (t0) cc_final: 0.8336 (t0) REVERT: A 1332 LEU cc_start: 0.8735 (mt) cc_final: 0.8510 (mm) REVERT: A 1370 ARG cc_start: 0.8009 (ttt-90) cc_final: 0.7528 (ttm-80) REVERT: C 142 LEU cc_start: 0.8885 (mm) cc_final: 0.8632 (mm) REVERT: C 146 LEU cc_start: 0.8173 (OUTLIER) cc_final: 0.7876 (mm) REVERT: E 139 ASP cc_start: 0.7688 (t0) cc_final: 0.7487 (t0) outliers start: 34 outliers final: 28 residues processed: 241 average time/residue: 0.1140 time to fit residues: 41.2228 Evaluate side-chains 238 residues out of total 1533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 207 time to evaluate : 0.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 ILE Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 499 LEU Chi-restraints excluded: chain A residue 517 SER Chi-restraints excluded: chain A residue 653 GLN Chi-restraints excluded: chain A residue 808 ILE Chi-restraints excluded: chain A residue 814 SER Chi-restraints excluded: chain A residue 824 MET Chi-restraints excluded: chain A residue 835 LEU Chi-restraints excluded: chain A residue 844 LEU Chi-restraints excluded: chain A residue 851 ILE Chi-restraints excluded: chain A residue 856 LYS Chi-restraints excluded: chain A residue 872 THR Chi-restraints excluded: chain A residue 897 ILE Chi-restraints excluded: chain A residue 955 ILE Chi-restraints excluded: chain A residue 1072 ILE Chi-restraints excluded: chain A residue 1173 ILE Chi-restraints excluded: chain A residue 1347 CYS Chi-restraints excluded: chain A residue 1384 VAL Chi-restraints excluded: chain A residue 1454 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 149 LEU Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain D residue 146 LEU Chi-restraints excluded: chain D residue 152 LEU Chi-restraints excluded: chain E residue 136 ASP Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 156 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 78 optimal weight: 0.0770 chunk 62 optimal weight: 8.9990 chunk 47 optimal weight: 3.9990 chunk 56 optimal weight: 10.0000 chunk 30 optimal weight: 3.9990 chunk 135 optimal weight: 1.9990 chunk 102 optimal weight: 5.9990 chunk 15 optimal weight: 4.9990 chunk 2 optimal weight: 4.9990 chunk 86 optimal weight: 0.9980 chunk 77 optimal weight: 4.9990 overall best weight: 2.2144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 640 GLN A 734 HIS A 812 ASN A1022 HIS A1049 ASN E 189 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.118287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.093716 restraints weight = 19621.478| |-----------------------------------------------------------------------------| r_work (start): 0.2895 rms_B_bonded: 1.87 r_work: 0.2764 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2620 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2620 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2579 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2579 r_free = 0.2579 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2579 r_free = 0.2579 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2579 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8701 moved from start: 0.1586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 14000 Z= 0.171 Angle : 0.517 7.206 18960 Z= 0.270 Chirality : 0.040 0.181 2205 Planarity : 0.004 0.053 2354 Dihedral : 7.833 73.648 1982 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 2.54 % Allowed : 16.05 % Favored : 81.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.45 (0.21), residues: 1657 helix: 2.07 (0.16), residues: 956 sheet: -1.06 (0.60), residues: 65 loop : -0.51 (0.25), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 134 TYR 0.014 0.001 TYR A 221 PHE 0.021 0.002 PHE A 629 TRP 0.014 0.002 TRP A 932 HIS 0.003 0.001 HIS A 206 Details of bonding type rmsd/Z covalent geometry : bond 0.00412 / 0.17 (14000) covalent geometry : angle 0.51693 / 0.27 (18960) hydrogen bonds : bond 0.03749 / 2.45 ( 740) hydrogen bonds : angle 4.18238 / 2.92 ( 2151) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3314 Ramachandran restraints generated. 1657 Oldfield, 0 Emsley, 1657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3314 Ramachandran restraints generated. 1657 Oldfield, 0 Emsley, 1657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 208 time to evaluate : 0.431 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 194 MET cc_start: 0.8699 (tpt) cc_final: 0.8462 (tpp) REVERT: A 640 GLN cc_start: 0.9212 (OUTLIER) cc_final: 0.8910 (tm130) REVERT: A 653 GLN cc_start: 0.9244 (OUTLIER) cc_final: 0.8321 (pp30) REVERT: A 861 TYR cc_start: 0.9122 (p90) cc_final: 0.8750 (p90) REVERT: A 872 THR cc_start: 0.8414 (OUTLIER) cc_final: 0.8036 (m) REVERT: A 906 GLU cc_start: 0.9035 (mm-30) cc_final: 0.8613 (mt-10) REVERT: A 1304 ASN cc_start: 0.8722 (t0) cc_final: 0.8330 (t0) REVERT: A 1332 LEU cc_start: 0.8756 (mt) cc_final: 0.8531 (mm) REVERT: A 1361 TYR cc_start: 0.8492 (m-80) cc_final: 0.8250 (m-80) REVERT: A 1370 ARG cc_start: 0.8024 (ttt-90) cc_final: 0.7529 (ttm-80) REVERT: A 1396 MET cc_start: 0.8258 (OUTLIER) cc_final: 0.7866 (mtp) REVERT: B 134 ARG cc_start: 0.8301 (mtp85) cc_final: 0.7933 (mtp85) REVERT: C 142 LEU cc_start: 0.8916 (mm) cc_final: 0.8652 (mm) REVERT: C 146 LEU cc_start: 0.8176 (OUTLIER) cc_final: 0.7823 (mm) REVERT: E 139 ASP cc_start: 0.7861 (t0) cc_final: 0.7605 (t0) REVERT: E 148 MET cc_start: 0.8340 (ppp) cc_final: 0.7922 (tmm) outliers start: 39 outliers final: 30 residues processed: 232 average time/residue: 0.1158 time to fit residues: 40.1456 Evaluate side-chains 243 residues out of total 1533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 208 time to evaluate : 0.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 ILE Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 499 LEU Chi-restraints excluded: chain A residue 517 SER Chi-restraints excluded: chain A residue 640 GLN Chi-restraints excluded: chain A residue 653 GLN Chi-restraints excluded: chain A residue 808 ILE Chi-restraints excluded: chain A residue 814 SER Chi-restraints excluded: chain A residue 824 MET Chi-restraints excluded: chain A residue 835 LEU Chi-restraints excluded: chain A residue 844 LEU Chi-restraints excluded: chain A residue 851 ILE Chi-restraints excluded: chain A residue 856 LYS Chi-restraints excluded: chain A residue 872 THR Chi-restraints excluded: chain A residue 897 ILE Chi-restraints excluded: chain A residue 955 ILE Chi-restraints excluded: chain A residue 1049 ASN Chi-restraints excluded: chain A residue 1072 ILE Chi-restraints excluded: chain A residue 1173 ILE Chi-restraints excluded: chain A residue 1347 CYS Chi-restraints excluded: chain A residue 1384 VAL Chi-restraints excluded: chain A residue 1396 MET Chi-restraints excluded: chain A residue 1454 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 149 LEU Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain D residue 146 LEU Chi-restraints excluded: chain D residue 152 LEU Chi-restraints excluded: chain E residue 136 ASP Chi-restraints excluded: chain E residue 138 ILE Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 156 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 133 optimal weight: 5.9990 chunk 52 optimal weight: 0.9990 chunk 59 optimal weight: 3.9990 chunk 129 optimal weight: 7.9990 chunk 25 optimal weight: 4.9990 chunk 104 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 103 optimal weight: 0.3980 chunk 81 optimal weight: 0.2980 chunk 113 optimal weight: 4.9990 chunk 126 optimal weight: 2.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 734 HIS A1022 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.118423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.093929 restraints weight = 19470.773| |-----------------------------------------------------------------------------| r_work (start): 0.2877 rms_B_bonded: 1.86 r_work: 0.2748 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2605 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2605 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2589 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2589 r_free = 0.2589 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2589 r_free = 0.2589 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2589 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8702 moved from start: 0.1601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.096 14000 Z= 0.192 Angle : 0.927 59.200 18960 Z= 0.560 Chirality : 0.043 0.578 2205 Planarity : 0.004 0.052 2354 Dihedral : 7.846 73.650 1982 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.22 % Allowed : 16.11 % Favored : 81.67 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.45 (0.21), residues: 1657 helix: 2.06 (0.17), residues: 956 sheet: -1.07 (0.60), residues: 65 loop : -0.51 (0.25), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 134 TYR 0.014 0.001 TYR A 221 PHE 0.021 0.002 PHE A 629 TRP 0.014 0.002 TRP A 932 HIS 0.003 0.001 HIS A 206 Details of bonding type rmsd/Z covalent geometry : bond 0.00408 / 0.19 (14000) covalent geometry : angle 0.92700 / 0.56 (18960) hydrogen bonds : bond 0.03710 / 2.43 ( 740) hydrogen bonds : angle 4.18597 / 2.92 ( 2151) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3314 Ramachandran restraints generated. 1657 Oldfield, 0 Emsley, 1657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3314 Ramachandran restraints generated. 1657 Oldfield, 0 Emsley, 1657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 209 time to evaluate : 0.540 Fit side-chains revert: symmetry clash REVERT: A 194 MET cc_start: 0.8689 (tpt) cc_final: 0.8454 (tpp) REVERT: A 511 ARG cc_start: 0.7723 (tpp80) cc_final: 0.7386 (tpp-160) REVERT: A 653 GLN cc_start: 0.9238 (OUTLIER) cc_final: 0.8316 (pp30) REVERT: A 861 TYR cc_start: 0.9122 (p90) cc_final: 0.8750 (p90) REVERT: A 872 THR cc_start: 0.8413 (OUTLIER) cc_final: 0.8038 (m) REVERT: A 906 GLU cc_start: 0.9037 (mm-30) cc_final: 0.8617 (mt-10) REVERT: A 1304 ASN cc_start: 0.8713 (t0) cc_final: 0.8324 (t0) REVERT: A 1332 LEU cc_start: 0.8748 (mt) cc_final: 0.8521 (mm) REVERT: A 1370 ARG cc_start: 0.8025 (ttt-90) cc_final: 0.7533 (ttm-80) REVERT: A 1396 MET cc_start: 0.8255 (OUTLIER) cc_final: 0.7867 (mtp) REVERT: B 134 ARG cc_start: 0.8294 (mtp85) cc_final: 0.7929 (mtp85) REVERT: B 144 GLU cc_start: 0.8027 (tt0) cc_final: 0.7546 (tt0) REVERT: C 142 LEU cc_start: 0.8934 (mm) cc_final: 0.8669 (mm) REVERT: C 146 LEU cc_start: 0.8189 (OUTLIER) cc_final: 0.7838 (mm) REVERT: E 139 ASP cc_start: 0.7865 (t0) cc_final: 0.7601 (t0) REVERT: E 148 MET cc_start: 0.8343 (ppp) cc_final: 0.7920 (tmm) outliers start: 34 outliers final: 29 residues processed: 229 average time/residue: 0.1175 time to fit residues: 40.1867 Evaluate side-chains 238 residues out of total 1533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 205 time to evaluate : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 ILE Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 499 LEU Chi-restraints excluded: chain A residue 517 SER Chi-restraints excluded: chain A residue 653 GLN Chi-restraints excluded: chain A residue 808 ILE Chi-restraints excluded: chain A residue 814 SER Chi-restraints excluded: chain A residue 824 MET Chi-restraints excluded: chain A residue 835 LEU Chi-restraints excluded: chain A residue 844 LEU Chi-restraints excluded: chain A residue 851 ILE Chi-restraints excluded: chain A residue 856 LYS Chi-restraints excluded: chain A residue 872 THR Chi-restraints excluded: chain A residue 897 ILE Chi-restraints excluded: chain A residue 955 ILE Chi-restraints excluded: chain A residue 1072 ILE Chi-restraints excluded: chain A residue 1173 ILE Chi-restraints excluded: chain A residue 1347 CYS Chi-restraints excluded: chain A residue 1384 VAL Chi-restraints excluded: chain A residue 1396 MET Chi-restraints excluded: chain A residue 1454 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 149 LEU Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain D residue 146 LEU Chi-restraints excluded: chain D residue 152 LEU Chi-restraints excluded: chain E residue 136 ASP Chi-restraints excluded: chain E residue 138 ILE Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 156 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 48 optimal weight: 2.9990 chunk 147 optimal weight: 10.0000 chunk 156 optimal weight: 0.9980 chunk 135 optimal weight: 0.7980 chunk 40 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 130 optimal weight: 0.8980 chunk 73 optimal weight: 0.9990 chunk 71 optimal weight: 2.9990 chunk 42 optimal weight: 0.0170 chunk 117 optimal weight: 0.8980 overall best weight: 0.7218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 734 HIS A 812 ASN A1022 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.118408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.093934 restraints weight = 19394.359| |-----------------------------------------------------------------------------| r_work (start): 0.2872 rms_B_bonded: 1.86 r_work: 0.2744 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2603 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2603 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2595 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2595 r_free = 0.2595 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2595 r_free = 0.2595 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.2595 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8698 moved from start: 0.1600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.096 14000 Z= 0.192 Angle : 0.927 59.200 18960 Z= 0.560 Chirality : 0.043 0.578 2205 Planarity : 0.004 0.052 2354 Dihedral : 7.846 73.650 1982 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.15 % Allowed : 16.11 % Favored : 81.74 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.45 (0.21), residues: 1657 helix: 2.06 (0.17), residues: 956 sheet: -1.07 (0.60), residues: 65 loop : -0.51 (0.25), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 134 TYR 0.014 0.001 TYR A 221 PHE 0.021 0.002 PHE A 629 TRP 0.014 0.002 TRP A 932 HIS 0.003 0.001 HIS A 206 Details of bonding type rmsd/Z covalent geometry : bond 0.00408 / 0.19 (14000) covalent geometry : angle 0.92700 / 0.56 (18960) hydrogen bonds : bond 0.03710 / 2.43 ( 740) hydrogen bonds : angle 4.18597 / 2.92 ( 2151) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3421.45 seconds wall clock time: 59 minutes 45.88 seconds (3585.88 seconds total)