Starting phenix.real_space_refine on Fri Jul 3 11:09:36 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8snx_40641/07_2026/8snx_40641_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8snx_40641/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8snx_40641/07_2026/8snx_40641.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8snx_40641/07_2026/8snx_40641.map" model { file = "/net/cci-nas-00/data/ceres_data/8snx_40641/07_2026/8snx_40641_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8snx_40641/07_2026/8snx_40641_neut.cif" } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/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: 2.86, per 1000 atoms: 0.21 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: 0.82 Conformation dependent library (CDL) restraints added in 580.9 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: 0.45 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: 2.36 Time building geometry restraints manager: 1.19 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: 18860 2.98 - 5.95: 90 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: 2070 0.081 - 0.163: 127 0.163 - 0.244: 6 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: 0.490 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: 0.000 Extract box with map and model: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 12.360 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 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:1.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.190 ------------------------------------------------------------------------------- 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= 0.183 Angle : 0.566 14.877 18960 Z= 0.319 Chirality : 0.043 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 / 0.18 (14000) covalent geometry : angle 0.56633 / 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 : 0.545 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: 0.1157 time to fit residues: 49.0387 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 : 0.540 ------------------------------------------------------------------------------- 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 812 ASN A 930 ASN A1022 HIS A1049 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.119943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.095572 restraints weight = 19539.521| |-----------------------------------------------------------------------------| r_work (start): 0.2909 rms_B_bonded: 1.86 r_work: 0.2774 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2629 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2629 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2622 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2622 r_free = 0.2622 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 = 0.2621 r_free = 0.2621 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (8 function evaluations) r_final: 0.2621 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8684 moved from start: 0.0936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 14000 Z= 0.187 Angle : 0.555 12.983 18960 Z= 0.289 Chirality : 0.041 0.183 2205 Planarity : 0.004 0.052 2354 Dihedral : 8.547 74.871 1985 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 1.50 % Allowed : 9.07 % Favored : 89.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.36 (0.21), residues: 1657 helix: 2.01 (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 0.004 0.000 ARG C 137 TYR 0.014 0.001 TYR A 861 PHE 0.021 0.002 PHE A 629 TRP 0.022 0.002 TRP A 480 HIS 0.004 0.001 HIS A1362 Details of bonding type rmsd/Z covalent geometry : bond 0.00448 / 0.19 (14000) covalent geometry : angle 0.55534 / 0.29 (18960) hydrogen bonds : bond 0.03972 / 2.56 ( 740) hydrogen bonds : angle 4.44264 / 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 255 residues out of total 1533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 232 time to evaluate : 0.553 Fit side-chains revert: symmetry clash REVERT: A 861 TYR cc_start: 0.9173 (p90) cc_final: 0.8853 (p90) REVERT: A 872 THR cc_start: 0.8413 (OUTLIER) cc_final: 0.8086 (t) REVERT: A 906 GLU cc_start: 0.8886 (mm-30) cc_final: 0.8295 (mt-10) REVERT: A 1232 TYR cc_start: 0.8747 (m-80) cc_final: 0.8528 (m-80) REVERT: A 1304 ASN cc_start: 0.8858 (t0) cc_final: 0.8608 (t0) REVERT: A 1332 LEU cc_start: 0.8747 (mt) cc_final: 0.8500 (mm) REVERT: B 149 LEU cc_start: 0.9003 (mt) cc_final: 0.8793 (mt) REVERT: B 164 ASP cc_start: 0.8762 (m-30) cc_final: 0.8446 (m-30) outliers start: 23 outliers final: 17 residues processed: 242 average time/residue: 0.1215 time to fit residues: 43.4361 Evaluate side-chains 233 residues out of total 1533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 215 time to evaluate : 0.523 ------------------------------------------------------------------------------- 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 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 A residue 1347 CYS 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: 4.9990 chunk 90 optimal weight: 2.9990 chunk 110 optimal weight: 0.0770 chunk 59 optimal weight: 0.1980 chunk 73 optimal weight: 3.9990 chunk 44 optimal weight: 6.9990 chunk 135 optimal weight: 3.9990 chunk 144 optimal weight: 0.6980 chunk 155 optimal weight: 2.9990 chunk 108 optimal weight: 0.9980 chunk 23 optimal weight: 6.9990 overall best weight: 0.9940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3320 r_free = 0.3320 target = 0.121596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.097355 restraints weight = 19476.734| |-----------------------------------------------------------------------------| r_work (start): 0.2942 rms_B_bonded: 1.87 r_work: 0.2816 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2672 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2672 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2654 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2654 r_free = 0.2654 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 = 0.2654 r_free = 0.2654 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2654 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8651 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 0.034 14000 Z= 0.113 Angle : 0.472 6.891 18960 Z= 0.251 Chirality : 0.038 0.184 2205 Planarity : 0.003 0.053 2354 Dihedral : 8.305 73.761 1985 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.63 % Allowed : 11.81 % Favored : 86.56 % 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: 1.47 (0.21), residues: 1657 helix: 2.10 (0.17), residues: 952 sheet: -1.07 (0.60), residues: 64 loop : -0.52 (0.24), residues: 641 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 396 TYR 0.013 0.001 TYR A 861 PHE 0.022 0.001 PHE A 629 TRP 0.014 0.001 TRP A 480 HIS 0.002 0.001 HIS B 150 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.11 (14000) covalent geometry : angle 0.47215 / 0.25 (18960) hydrogen bonds : bond 0.03581 / 2.32 ( 740) hydrogen bonds : angle 4.22325 / 2.95 ( 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 260 residues out of total 1533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 235 time to evaluate : 0.596 Fit side-chains revert: symmetry clash REVERT: A 511 ARG cc_start: 0.7574 (tpp80) cc_final: 0.7293 (tpp-160) REVERT: A 861 TYR cc_start: 0.9198 (p90) cc_final: 0.8829 (p90) REVERT: A 872 THR cc_start: 0.8215 (OUTLIER) cc_final: 0.7940 (t) REVERT: A 906 GLU cc_start: 0.8923 (mm-30) cc_final: 0.8305 (mt-10) REVERT: A 1304 ASN cc_start: 0.8828 (t0) cc_final: 0.8510 (t0) REVERT: A 1332 LEU cc_start: 0.8710 (mt) cc_final: 0.8497 (mm) REVERT: A 1370 ARG cc_start: 0.8016 (ttt-90) cc_final: 0.7542 (ttm-80) outliers start: 25 outliers final: 15 residues processed: 248 average time/residue: 0.1140 time to fit residues: 42.2264 Evaluate side-chains 234 residues out of total 1533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 218 time to evaluate : 0.526 ------------------------------------------------------------------------------- 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 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: 0.9990 chunk 45 optimal weight: 5.9990 chunk 33 optimal weight: 1.9990 chunk 1 optimal weight: 4.9990 chunk 133 optimal weight: 3.9990 chunk 108 optimal weight: 0.8980 chunk 138 optimal weight: 1.9990 chunk 111 optimal weight: 10.0000 chunk 156 optimal weight: 6.9990 chunk 131 optimal weight: 0.5980 chunk 34 optimal weight: 2.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 812 ASN A1022 HIS A1049 ASN E 189 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.120971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.096608 restraints weight = 19414.418| |-----------------------------------------------------------------------------| r_work (start): 0.2925 rms_B_bonded: 1.88 r_work: 0.2797 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2653 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2653 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2640 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2640 r_free = 0.2640 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2640 r_free = 0.2640 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.2640 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8661 moved from start: 0.1189 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= 0.124 Angle : 0.464 7.139 18960 Z= 0.247 Chirality : 0.038 0.178 2205 Planarity : 0.003 0.052 2354 Dihedral : 8.081 73.589 1982 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 1.70 % Allowed : 13.70 % Favored : 84.61 % 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: 1.53 (0.21), residues: 1657 helix: 2.16 (0.17), residues: 949 sheet: -1.05 (0.60), residues: 64 loop : -0.49 (0.24), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 396 TYR 0.013 0.001 TYR A 861 PHE 0.036 0.001 PHE A 629 TRP 0.013 0.001 TRP A 932 HIS 0.002 0.001 HIS A 206 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.12 (14000) covalent geometry : angle 0.46359 / 0.25 (18960) hydrogen bonds : bond 0.03523 / 2.29 ( 740) hydrogen bonds : angle 4.14324 / 2.89 ( 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 255 residues out of total 1533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 229 time to evaluate : 0.581 Fit side-chains revert: symmetry clash REVERT: A 511 ARG cc_start: 0.7644 (tpp80) cc_final: 0.7389 (tpp-160) REVERT: A 861 TYR cc_start: 0.9180 (p90) cc_final: 0.8823 (p90) REVERT: A 872 THR cc_start: 0.8202 (OUTLIER) cc_final: 0.7966 (t) REVERT: A 906 GLU cc_start: 0.9038 (mm-30) cc_final: 0.8430 (mt-10) REVERT: A 1304 ASN cc_start: 0.8798 (t0) cc_final: 0.8485 (t0) REVERT: A 1332 LEU cc_start: 0.8708 (mt) cc_final: 0.8493 (mm) REVERT: A 1370 ARG cc_start: 0.8015 (ttt-90) cc_final: 0.7536 (ttm-80) REVERT: B 144 GLU cc_start: 0.8030 (mt-10) cc_final: 0.7584 (tt0) outliers start: 26 outliers final: 22 residues processed: 241 average time/residue: 0.1159 time to fit residues: 41.6238 Evaluate side-chains 239 residues out of total 1533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 216 time to evaluate : 0.572 ------------------------------------------------------------------------------- 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 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 1072 ILE Chi-restraints excluded: chain A residue 1173 ILE 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 D residue 187 MET 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: 2.9990 chunk 10 optimal weight: 4.9990 chunk 122 optimal weight: 0.3980 chunk 14 optimal weight: 5.9990 chunk 11 optimal weight: 4.9990 chunk 153 optimal weight: 6.9990 chunk 155 optimal weight: 3.9990 chunk 83 optimal weight: 6.9990 chunk 24 optimal weight: 0.0770 chunk 79 optimal weight: 9.9990 chunk 97 optimal weight: 6.9990 overall best weight: 2.4944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 734 HIS A 809 ASN A 812 ASN A1011 HIS A1022 HIS A1049 ASN E 189 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.118567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.094212 restraints weight = 19618.658| |-----------------------------------------------------------------------------| r_work (start): 0.2890 rms_B_bonded: 1.86 r_work: 0.2762 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2618 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2618 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2584 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2584 r_free = 0.2584 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 = 0.2584 r_free = 0.2584 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: 0.2584 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8701 moved from start: 0.1394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 14000 Z= 0.184 Angle : 0.508 7.238 18960 Z= 0.267 Chirality : 0.040 0.170 2205 Planarity : 0.004 0.050 2354 Dihedral : 8.109 73.689 1982 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 2.22 % Allowed : 14.48 % Favored : 83.30 % 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: 1.42 (0.21), residues: 1657 helix: 2.05 (0.16), residues: 955 sheet: -0.98 (0.61), residues: 63 loop : -0.55 (0.24), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 137 TYR 0.015 0.001 TYR A 221 PHE 0.039 0.002 PHE A 629 TRP 0.015 0.002 TRP A 480 HIS 0.004 0.001 HIS A 206 Details of bonding type rmsd/Z covalent geometry : bond 0.00443 / 0.18 (14000) covalent geometry : angle 0.50794 / 0.27 (18960) hydrogen bonds : bond 0.03805 / 2.48 ( 740) hydrogen bonds : angle 4.21338 / 2.94 ( 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 255 residues out of total 1533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 221 time to evaluate : 0.556 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 861 TYR cc_start: 0.9197 (p90) cc_final: 0.8848 (p90) REVERT: A 872 THR cc_start: 0.8306 (OUTLIER) cc_final: 0.7993 (t) REVERT: A 906 GLU cc_start: 0.9088 (mm-30) cc_final: 0.8561 (mt-10) REVERT: A 1304 ASN cc_start: 0.8796 (t0) cc_final: 0.8429 (t0) REVERT: A 1370 ARG cc_start: 0.8030 (ttt-90) cc_final: 0.7571 (ttm-80) REVERT: A 1396 MET cc_start: 0.8263 (OUTLIER) cc_final: 0.7971 (mtp) outliers start: 34 outliers final: 27 residues processed: 237 average time/residue: 0.1182 time to fit residues: 41.4972 Evaluate side-chains 238 residues out of total 1533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 209 time to evaluate : 0.512 ------------------------------------------------------------------------------- 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 D residue 187 MET 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: 9.9990 chunk 162 optimal weight: 5.9990 chunk 145 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 161 optimal weight: 10.0000 chunk 136 optimal weight: 4.9990 chunk 157 optimal weight: 0.7980 chunk 121 optimal weight: 2.9990 chunk 106 optimal weight: 3.9990 chunk 57 optimal weight: 0.9980 chunk 30 optimal weight: 0.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 734 HIS A 812 ASN A1022 HIS A1049 ASN E 189 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.119294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.094818 restraints weight = 19428.470| |-----------------------------------------------------------------------------| r_work (start): 0.2938 rms_B_bonded: 1.88 r_work: 0.2811 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2668 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2668 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2655 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2655 r_free = 0.2655 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 = 0.2655 r_free = 0.2655 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: 0.2655 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8683 moved from start: 0.1443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 14000 Z= 0.135 Angle : 0.484 7.042 18960 Z= 0.254 Chirality : 0.039 0.167 2205 Planarity : 0.003 0.052 2354 Dihedral : 8.021 73.635 1982 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 2.28 % Allowed : 15.07 % Favored : 82.65 % 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: 1.46 (0.21), residues: 1657 helix: 2.07 (0.17), residues: 953 sheet: -0.97 (0.62), residues: 63 loop : -0.50 (0.25), residues: 641 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG B 134 TYR 0.013 0.001 TYR A 221 PHE 0.034 0.001 PHE A 629 TRP 0.015 0.001 TRP A 932 HIS 0.002 0.001 HIS A 206 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.14 (14000) covalent geometry : angle 0.48382 / 0.25 (18960) hydrogen bonds : bond 0.03631 / 2.37 ( 740) hydrogen bonds : angle 4.16645 / 2.91 ( 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 263 residues out of total 1533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 228 time to evaluate : 0.493 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 861 TYR cc_start: 0.9139 (p90) cc_final: 0.8799 (p90) REVERT: A 872 THR cc_start: 0.8288 (OUTLIER) cc_final: 0.7956 (t) REVERT: A 906 GLU cc_start: 0.9121 (mm-30) cc_final: 0.8614 (mt-10) REVERT: A 1304 ASN cc_start: 0.8732 (t0) cc_final: 0.8355 (t0) REVERT: A 1370 ARG cc_start: 0.8000 (ttt-90) cc_final: 0.7547 (ttm-80) REVERT: A 1396 MET cc_start: 0.8169 (OUTLIER) cc_final: 0.7855 (mtp) REVERT: C 146 LEU cc_start: 0.8119 (OUTLIER) cc_final: 0.7817 (mm) REVERT: E 139 ASP cc_start: 0.7761 (t0) cc_final: 0.7546 (t0) REVERT: E 148 MET cc_start: 0.8315 (ppp) cc_final: 0.7946 (tmm) outliers start: 35 outliers final: 27 residues processed: 247 average time/residue: 0.1101 time to fit residues: 40.8091 Evaluate side-chains 241 residues out of total 1533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 211 time to evaluate : 0.533 ------------------------------------------------------------------------------- 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 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 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 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 D residue 187 MET Chi-restraints excluded: chain E residue 136 ASP 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: 8.9990 chunk 86 optimal weight: 0.7980 chunk 37 optimal weight: 7.9990 chunk 55 optimal weight: 2.9990 chunk 7 optimal weight: 0.6980 chunk 65 optimal weight: 3.9990 chunk 109 optimal weight: 5.9990 chunk 66 optimal weight: 0.8980 chunk 127 optimal weight: 0.9980 chunk 89 optimal weight: 0.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 = 0.3302 r_free = 0.3302 target = 0.120355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.095953 restraints weight = 19426.585| |-----------------------------------------------------------------------------| r_work (start): 0.2909 rms_B_bonded: 1.87 r_work: 0.2781 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2637 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2637 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2622 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2622 r_free = 0.2622 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 = 0.2622 r_free = 0.2622 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: 0.2622 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8668 moved from start: 0.1451 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= 0.108 Angle : 0.474 6.995 18960 Z= 0.248 Chirality : 0.038 0.192 2205 Planarity : 0.003 0.065 2354 Dihedral : 7.890 73.559 1982 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 2.15 % Allowed : 15.79 % Favored : 82.06 % 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: 1.57 (0.21), residues: 1657 helix: 2.15 (0.17), residues: 951 sheet: -0.89 (0.62), residues: 63 loop : -0.45 (0.25), residues: 643 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 134 TYR 0.013 0.001 TYR A 861 PHE 0.032 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 0.00245 / 0.11 (14000) covalent geometry : angle 0.47390 / 0.25 (18960) hydrogen bonds : bond 0.03476 / 2.27 ( 740) hydrogen bonds : angle 4.09483 / 2.86 ( 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 264 residues out of total 1533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 231 time to evaluate : 0.536 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 640 GLN cc_start: 0.9110 (OUTLIER) cc_final: 0.8902 (tm130) REVERT: A 861 TYR cc_start: 0.9148 (p90) cc_final: 0.8803 (p90) REVERT: A 872 THR cc_start: 0.8299 (OUTLIER) cc_final: 0.7949 (t) REVERT: A 906 GLU cc_start: 0.8994 (mm-30) cc_final: 0.8501 (mt-10) REVERT: A 1304 ASN cc_start: 0.8696 (t0) cc_final: 0.8326 (t0) REVERT: A 1361 TYR cc_start: 0.8516 (m-80) cc_final: 0.8298 (m-80) REVERT: A 1370 ARG cc_start: 0.8009 (ttt-90) cc_final: 0.7524 (ttm-80) REVERT: A 1396 MET cc_start: 0.8155 (OUTLIER) cc_final: 0.7850 (mtp) REVERT: D 148 MET cc_start: 0.7898 (ttm) cc_final: 0.7624 (ttm) REVERT: E 139 ASP cc_start: 0.7790 (t0) cc_final: 0.7482 (t0) outliers start: 33 outliers final: 26 residues processed: 248 average time/residue: 0.1154 time to fit residues: 42.6964 Evaluate side-chains 239 residues out of total 1533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 210 time to evaluate : 0.564 ------------------------------------------------------------------------------- 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 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 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 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: 0.9980 chunk 127 optimal weight: 0.9990 chunk 146 optimal weight: 10.0000 chunk 45 optimal weight: 0.7980 chunk 129 optimal weight: 9.9990 chunk 95 optimal weight: 5.9990 chunk 43 optimal weight: 0.3980 chunk 56 optimal weight: 0.6980 chunk 42 optimal weight: 0.0470 chunk 130 optimal weight: 3.9990 chunk 120 optimal weight: 2.9990 overall best weight: 0.5878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 640 GLN A 734 HIS A 812 ASN A 895 ASN A1022 HIS E 189 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.121551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.097253 restraints weight = 19301.392| |-----------------------------------------------------------------------------| r_work (start): 0.2926 rms_B_bonded: 1.86 r_work: 0.2799 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2656 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2656 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2636 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2636 r_free = 0.2636 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2636 r_free = 0.2636 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (5 function evaluations) r_final: 0.2636 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8659 moved from start: 0.1483 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= 0.100 Angle : 0.466 7.066 18960 Z= 0.245 Chirality : 0.038 0.175 2205 Planarity : 0.003 0.061 2354 Dihedral : 7.825 73.542 1982 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 2.02 % Allowed : 16.44 % Favored : 81.54 % 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: 1.63 (0.21), residues: 1657 helix: 2.21 (0.17), residues: 950 sheet: -0.84 (0.61), residues: 63 loop : -0.44 (0.25), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 134 TYR 0.012 0.001 TYR A 861 PHE 0.031 0.001 PHE A 629 TRP 0.014 0.001 TRP A 932 HIS 0.002 0.000 HIS B 150 Details of bonding type rmsd/Z covalent geometry : bond 0.00222 / 0.10 (14000) covalent geometry : angle 0.46640 / 0.24 (18960) hydrogen bonds : bond 0.03421 / 2.22 ( 740) hydrogen bonds : angle 4.06347 / 2.84 ( 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 253 residues out of total 1533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 222 time to evaluate : 0.523 Fit side-chains revert: symmetry clash REVERT: A 511 ARG cc_start: 0.7738 (tpp80) cc_final: 0.7383 (tpp-160) REVERT: A 861 TYR cc_start: 0.9104 (p90) cc_final: 0.8732 (p90) REVERT: A 872 THR cc_start: 0.8248 (OUTLIER) cc_final: 0.7886 (m) REVERT: A 906 GLU cc_start: 0.8949 (mm-30) cc_final: 0.8487 (mt-10) REVERT: A 1304 ASN cc_start: 0.8629 (t0) cc_final: 0.8260 (t0) REVERT: A 1370 ARG cc_start: 0.8006 (ttt-90) cc_final: 0.7520 (ttm-80) REVERT: A 1396 MET cc_start: 0.8069 (OUTLIER) cc_final: 0.7748 (mtp) REVERT: C 146 LEU cc_start: 0.8175 (OUTLIER) cc_final: 0.7888 (mm) REVERT: E 139 ASP cc_start: 0.7841 (t0) cc_final: 0.7379 (t0) outliers start: 31 outliers final: 26 residues processed: 239 average time/residue: 0.1098 time to fit residues: 39.3755 Evaluate side-chains 239 residues out of total 1533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 210 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 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 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 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 D residue 187 MET 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: 8.9990 chunk 62 optimal weight: 4.9990 chunk 47 optimal weight: 2.9990 chunk 56 optimal weight: 10.0000 chunk 30 optimal weight: 0.9990 chunk 135 optimal weight: 4.9990 chunk 102 optimal weight: 6.9990 chunk 15 optimal weight: 5.9990 chunk 2 optimal weight: 4.9990 chunk 86 optimal weight: 0.9980 chunk 77 optimal weight: 4.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 640 GLN A 734 HIS A 812 ASN A1022 HIS A1049 ASN A1404 ASN E 189 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.116934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.092382 restraints weight = 19702.028| |-----------------------------------------------------------------------------| r_work (start): 0.2852 rms_B_bonded: 1.87 r_work: 0.2723 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2579 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2579 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2557 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2557 r_free = 0.2557 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2557 r_free = 0.2557 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2557 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8714 moved from start: 0.1655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 14000 Z= 0.219 Angle : 0.554 9.049 18960 Z= 0.288 Chirality : 0.042 0.198 2205 Planarity : 0.004 0.054 2354 Dihedral : 7.894 73.671 1982 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 2.67 % Allowed : 15.85 % Favored : 81.47 % 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: 2.01 (0.16), residues: 956 sheet: -1.05 (0.61), residues: 65 loop : -0.57 (0.24), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 134 TYR 0.016 0.002 TYR A 221 PHE 0.032 0.002 PHE A 629 TRP 0.014 0.002 TRP A 480 HIS 0.005 0.001 HIS A 206 Details of bonding type rmsd/Z covalent geometry : bond 0.00540 / 0.22 (14000) covalent geometry : angle 0.55406 / 0.29 (18960) hydrogen bonds : bond 0.03911 / 2.57 ( 740) hydrogen bonds : angle 4.20789 / 2.94 ( 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: 41 poor density : 206 time to evaluate : 0.545 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 13 TYR cc_start: 0.8773 (m-80) cc_final: 0.8125 (m-80) REVERT: A 194 MET cc_start: 0.8709 (tpt) cc_final: 0.8473 (tpp) REVERT: A 421 GLU cc_start: 0.8197 (OUTLIER) cc_final: 0.7971 (tp30) REVERT: A 861 TYR cc_start: 0.9111 (p90) cc_final: 0.8706 (p90) REVERT: A 872 THR cc_start: 0.8453 (OUTLIER) cc_final: 0.8077 (m) REVERT: A 906 GLU cc_start: 0.9054 (mm-30) cc_final: 0.8637 (mt-10) REVERT: A 1304 ASN cc_start: 0.8783 (t0) cc_final: 0.8419 (t0) REVERT: A 1370 ARG cc_start: 0.8009 (ttt-90) cc_final: 0.7528 (ttm-80) REVERT: A 1396 MET cc_start: 0.8427 (OUTLIER) cc_final: 0.8138 (mtp) REVERT: C 146 LEU cc_start: 0.8233 (OUTLIER) cc_final: 0.7858 (mm) REVERT: D 148 MET cc_start: 0.7978 (ttm) cc_final: 0.7727 (ttm) REVERT: E 139 ASP cc_start: 0.7786 (t0) cc_final: 0.7463 (t0) outliers start: 41 outliers final: 29 residues processed: 232 average time/residue: 0.1182 time to fit residues: 40.7450 Evaluate side-chains 236 residues out of total 1533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 203 time to evaluate : 0.522 ------------------------------------------------------------------------------- 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 421 GLU 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 814 SER 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 894 ILE 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 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: 0.8980 chunk 59 optimal weight: 0.3980 chunk 129 optimal weight: 9.9990 chunk 25 optimal weight: 2.9990 chunk 104 optimal weight: 0.8980 chunk 20 optimal weight: 5.9990 chunk 103 optimal weight: 1.9990 chunk 81 optimal weight: 0.0050 chunk 113 optimal weight: 3.9990 chunk 126 optimal weight: 0.6980 overall best weight: 0.5794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 640 GLN A 734 HIS A 812 ASN A1022 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.117386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.092911 restraints weight = 19504.519| |-----------------------------------------------------------------------------| r_work (start): 0.2865 rms_B_bonded: 1.86 r_work: 0.2736 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2592 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2592 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2568 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2568 r_free = 0.2568 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 = 0.2568 r_free = 0.2568 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: 0.2568 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8707 moved from start: 0.1661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.106 14000 Z= 0.191 Angle : 0.774 59.193 18960 Z= 0.449 Chirality : 0.041 0.442 2205 Planarity : 0.004 0.068 2354 Dihedral : 7.915 73.702 1982 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.09 % Allowed : 16.11 % 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: 1.38 (0.21), residues: 1657 helix: 2.01 (0.16), residues: 956 sheet: -1.07 (0.60), residues: 65 loop : -0.57 (0.25), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.000 ARG B 134 TYR 0.016 0.001 TYR A 221 PHE 0.025 0.002 PHE A 629 TRP 0.014 0.002 TRP A 932 HIS 0.004 0.001 HIS A 206 Details of bonding type rmsd/Z covalent geometry : bond 0.00431 / 0.19 (14000) covalent geometry : angle 0.77350 / 0.45 (18960) hydrogen bonds : bond 0.03838 / 2.52 ( 740) hydrogen bonds : angle 4.20932 / 2.94 ( 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 239 residues out of total 1533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 207 time to evaluate : 0.519 Fit side-chains revert: symmetry clash REVERT: A 13 TYR cc_start: 0.8768 (m-80) cc_final: 0.8113 (m-80) REVERT: A 194 MET cc_start: 0.8711 (tpt) cc_final: 0.8475 (tpp) REVERT: A 511 ARG cc_start: 0.7769 (tpp80) cc_final: 0.7504 (tpp80) REVERT: A 861 TYR cc_start: 0.9114 (p90) cc_final: 0.8711 (p90) REVERT: A 872 THR cc_start: 0.8444 (OUTLIER) cc_final: 0.8066 (m) REVERT: A 906 GLU cc_start: 0.9042 (mm-30) cc_final: 0.8625 (mt-10) REVERT: A 1304 ASN cc_start: 0.8775 (t0) cc_final: 0.8387 (t0) REVERT: A 1370 ARG cc_start: 0.8000 (ttt-90) cc_final: 0.7528 (ttm-80) REVERT: C 146 LEU cc_start: 0.8219 (OUTLIER) cc_final: 0.7839 (mm) REVERT: D 148 MET cc_start: 0.7974 (ttm) cc_final: 0.7718 (ttm) REVERT: E 139 ASP cc_start: 0.7774 (t0) cc_final: 0.7482 (t0) outliers start: 32 outliers final: 27 residues processed: 226 average time/residue: 0.1062 time to fit residues: 35.7603 Evaluate side-chains 232 residues out of total 1533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 203 time to evaluate : 0.516 ------------------------------------------------------------------------------- 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 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 851 ILE Chi-restraints excluded: chain A residue 872 THR Chi-restraints excluded: chain A residue 894 ILE 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 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: 4.9990 chunk 147 optimal weight: 7.9990 chunk 156 optimal weight: 5.9990 chunk 135 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 31 optimal weight: 0.7980 chunk 130 optimal weight: 10.0000 chunk 73 optimal weight: 0.4980 chunk 71 optimal weight: 0.7980 chunk 42 optimal weight: 1.9990 chunk 117 optimal weight: 3.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 640 GLN A 734 HIS A 812 ASN A1022 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.117391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.092980 restraints weight = 19425.980| |-----------------------------------------------------------------------------| r_work (start): 0.2866 rms_B_bonded: 1.85 r_work: 0.2736 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2592 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2592 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2566 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2566 r_free = 0.2566 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 = 0.2566 r_free = 0.2566 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 (26 function evaluations) r_final: 0.2566 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8706 moved from start: 0.1650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.106 14000 Z= 0.191 Angle : 0.774 59.193 18960 Z= 0.449 Chirality : 0.041 0.442 2205 Planarity : 0.004 0.068 2354 Dihedral : 7.915 73.702 1982 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 1.96 % Allowed : 16.11 % Favored : 81.93 % 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: 1.38 (0.21), residues: 1657 helix: 2.01 (0.16), residues: 956 sheet: -1.07 (0.60), residues: 65 loop : -0.57 (0.25), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.000 ARG B 134 TYR 0.016 0.001 TYR A 221 PHE 0.025 0.002 PHE A 629 TRP 0.014 0.002 TRP A 932 HIS 0.004 0.001 HIS A 206 Details of bonding type rmsd/Z covalent geometry : bond 0.00431 / 0.19 (14000) covalent geometry : angle 0.77350 / 0.45 (18960) hydrogen bonds : bond 0.03838 / 2.52 ( 740) hydrogen bonds : angle 4.20932 / 2.94 ( 2151) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3243.35 seconds wall clock time: 56 minutes 33.50 seconds (3393.50 seconds total)