Starting phenix.real_space_refine on Thu Jul 31 21:18:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8snx_40641/07_2025/8snx_40641_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8snx_40641/07_2025/8snx_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_2025/8snx_40641.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8snx_40641/07_2025/8snx_40641.map" model { file = "/net/cci-nas-00/data/ceres_data/8snx_40641/07_2025/8snx_40641_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8snx_40641/07_2025/8snx_40641_neut.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 7.80, per 1000 atoms: 0.57 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: 4.16 Conformation dependent library (CDL) restraints added in 1.7 seconds 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: 1.47 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: 4.49 Time building geometry restraints manager: 4.51 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: 0.650 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: 0.020 Extract box with map and model: 0.500 Check model and map are aligned: 0.080 Set scattering table: 0.120 Process input model: 32.470 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 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 : 10.24 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.44 (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 TRP 0.031 0.002 TRP A 480 HIS 0.002 0.001 HIS A 561 PHE 0.014 0.001 PHE A 426 TYR 0.013 0.001 TYR A 861 ARG 0.004 0.000 ARG E 197 Details of bonding type rmsd hydrogen bonds : bond 0.09912 ( 740) hydrogen bonds : angle 5.09137 ( 2151) covalent geometry : bond 0.00318 (14000) covalent geometry : angle 0.56633 (18960) *********************** 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 : 1.331 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: 0.2525 time to fit residues: 105.9957 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 : 1.508 ------------------------------------------------------------------------------- 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 140 optimal weight: 1.9990 chunk 125 optimal weight: 8.9990 chunk 69 optimal weight: 1.9990 chunk 42 optimal weight: 5.9990 chunk 84 optimal weight: 1.9990 chunk 67 optimal weight: 0.0040 chunk 130 optimal weight: 0.1980 chunk 50 optimal weight: 5.9990 chunk 79 optimal weight: 0.5980 chunk 96 optimal weight: 0.9990 chunk 150 optimal weight: 8.9990 overall best weight: 0.7596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 809 ASN A 812 ASN A 930 ASN A1022 HIS A1049 ASN A1330 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.123879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.099640 restraints weight = 19245.039| |-----------------------------------------------------------------------------| r_work (start): 0.2995 rms_B_bonded: 1.89 r_work: 0.2867 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2723 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2723 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2743 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2743 r_free = 0.2743 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2743 r_free = 0.2743 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2743 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.0945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 14000 Z= 0.109 Angle : 0.483 7.216 18960 Z= 0.255 Chirality : 0.039 0.158 2205 Planarity : 0.003 0.053 2354 Dihedral : 8.292 73.719 1985 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 1.30 % Allowed : 9.26 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.54 (0.21), residues: 1657 helix: 2.17 (0.17), residues: 949 sheet: -0.99 (0.62), residues: 64 loop : -0.51 (0.24), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 480 HIS 0.002 0.000 HIS A1434 PHE 0.016 0.001 PHE A 629 TYR 0.016 0.001 TYR A 861 ARG 0.003 0.000 ARG A 396 Details of bonding type rmsd hydrogen bonds : bond 0.03486 ( 740) hydrogen bonds : angle 4.22621 ( 2151) covalent geometry : bond 0.00245 (14000) covalent geometry : angle 0.48333 (18960) *********************** 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 268 residues out of total 1533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 248 time to evaluate : 1.612 Fit side-chains revert: symmetry clash REVERT: A 861 TYR cc_start: 0.9144 (p90) cc_final: 0.8817 (p90) REVERT: A 872 THR cc_start: 0.7982 (OUTLIER) cc_final: 0.7757 (t) REVERT: A 874 GLN cc_start: 0.7966 (tm-30) cc_final: 0.7034 (tm-30) REVERT: A 912 THR cc_start: 0.9509 (p) cc_final: 0.9302 (p) REVERT: A 1304 ASN cc_start: 0.8807 (t0) cc_final: 0.8565 (t0) outliers start: 20 outliers final: 14 residues processed: 258 average time/residue: 0.2595 time to fit residues: 97.9416 Evaluate side-chains 240 residues out of total 1533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 225 time to evaluate : 1.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 499 LEU Chi-restraints excluded: chain A residue 517 SER Chi-restraints excluded: chain A residue 809 ASN Chi-restraints excluded: chain A residue 824 MET 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 1330 GLN 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 D residue 177 MET Chi-restraints excluded: chain E residue 136 ASP 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 156 optimal weight: 0.6980 chunk 39 optimal weight: 0.5980 chunk 53 optimal weight: 5.9990 chunk 120 optimal weight: 7.9990 chunk 2 optimal weight: 3.9990 chunk 55 optimal weight: 6.9990 chunk 3 optimal weight: 4.9990 chunk 91 optimal weight: 0.6980 chunk 68 optimal weight: 5.9990 chunk 92 optimal weight: 0.8980 chunk 86 optimal weight: 0.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 812 ASN A 895 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 = 0.3351 r_free = 0.3351 target = 0.124023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.100164 restraints weight = 19272.604| |-----------------------------------------------------------------------------| r_work (start): 0.2975 rms_B_bonded: 1.85 r_work: 0.2850 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2707 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2707 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2693 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2693 r_free = 0.2693 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2694 r_free = 0.2694 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2694 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.1142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 14000 Z= 0.103 Angle : 0.455 7.088 18960 Z= 0.241 Chirality : 0.038 0.180 2205 Planarity : 0.003 0.053 2354 Dihedral : 7.992 73.544 1982 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.37 % Allowed : 11.35 % Favored : 87.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.61 (0.21), residues: 1657 helix: 2.23 (0.17), residues: 950 sheet: -0.88 (0.60), residues: 64 loop : -0.50 (0.24), residues: 643 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 480 HIS 0.002 0.000 HIS B 150 PHE 0.020 0.001 PHE A 629 TYR 0.012 0.001 TYR A 221 ARG 0.003 0.000 ARG B 163 Details of bonding type rmsd hydrogen bonds : bond 0.03322 ( 740) hydrogen bonds : angle 4.08852 ( 2151) covalent geometry : bond 0.00232 (14000) covalent geometry : angle 0.45467 (18960) *********************** 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 259 residues out of total 1533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 238 time to evaluate : 1.611 Fit side-chains revert: symmetry clash REVERT: A 861 TYR cc_start: 0.9120 (p90) cc_final: 0.8730 (p90) REVERT: A 872 THR cc_start: 0.8015 (OUTLIER) cc_final: 0.7732 (t) REVERT: A 874 GLN cc_start: 0.7797 (tm-30) cc_final: 0.6901 (tm-30) REVERT: A 906 GLU cc_start: 0.8988 (mm-30) cc_final: 0.8195 (mt-10) REVERT: A 912 THR cc_start: 0.9483 (p) cc_final: 0.9259 (p) REVERT: A 1304 ASN cc_start: 0.8792 (t0) cc_final: 0.8501 (t0) REVERT: A 1370 ARG cc_start: 0.7955 (ttt-90) cc_final: 0.7507 (ttm-80) REVERT: E 148 MET cc_start: 0.8321 (ppp) cc_final: 0.8066 (ppp) outliers start: 21 outliers final: 15 residues processed: 246 average time/residue: 0.3190 time to fit residues: 117.9042 Evaluate side-chains 242 residues out of total 1533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 226 time to evaluate : 2.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 824 MET 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 897 ILE Chi-restraints excluded: chain A residue 1072 ILE 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 177 MET 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 124 optimal weight: 4.9990 chunk 6 optimal weight: 6.9990 chunk 86 optimal weight: 3.9990 chunk 53 optimal weight: 5.9990 chunk 40 optimal weight: 5.9990 chunk 89 optimal weight: 0.9980 chunk 111 optimal weight: 9.9990 chunk 102 optimal weight: 8.9990 chunk 104 optimal weight: 6.9990 chunk 134 optimal weight: 0.4980 chunk 153 optimal weight: 10.0000 overall best weight: 3.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 640 GLN A 734 HIS A 812 ASN A 895 ASN A1011 HIS A1069 GLN A1120 HIS E 189 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.116129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.091665 restraints weight = 19535.043| |-----------------------------------------------------------------------------| r_work (start): 0.2847 rms_B_bonded: 1.85 r_work: 0.2718 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2576 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2576 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2600 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2600 r_free = 0.2600 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2601 r_free = 0.2601 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2601 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.1643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 14000 Z= 0.238 Angle : 0.569 7.253 18960 Z= 0.297 Chirality : 0.042 0.170 2205 Planarity : 0.004 0.047 2354 Dihedral : 8.096 73.763 1982 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 2.41 % Allowed : 12.79 % Favored : 84.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.25 (0.21), residues: 1657 helix: 1.88 (0.16), residues: 958 sheet: -1.19 (0.59), residues: 66 loop : -0.57 (0.25), residues: 633 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 480 HIS 0.005 0.001 HIS A 206 PHE 0.025 0.002 PHE A 629 TYR 0.017 0.002 TYR A 586 ARG 0.007 0.001 ARG B 134 Details of bonding type rmsd hydrogen bonds : bond 0.04178 ( 740) hydrogen bonds : angle 4.30532 ( 2151) covalent geometry : bond 0.00574 (14000) covalent geometry : angle 0.56945 (18960) *********************** 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 257 residues out of total 1533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 220 time to evaluate : 1.724 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 13 TYR cc_start: 0.8792 (m-80) cc_final: 0.8118 (m-80) REVERT: A 861 TYR cc_start: 0.9111 (p90) cc_final: 0.8709 (p90) REVERT: A 872 THR cc_start: 0.8483 (OUTLIER) cc_final: 0.8133 (m) REVERT: A 906 GLU cc_start: 0.9105 (mm-30) cc_final: 0.8427 (mt-10) REVERT: A 1287 ASP cc_start: 0.8284 (m-30) cc_final: 0.8052 (m-30) REVERT: A 1304 ASN cc_start: 0.8836 (t0) cc_final: 0.8436 (t0) REVERT: A 1332 LEU cc_start: 0.8739 (mt) cc_final: 0.8528 (mm) REVERT: D 177 MET cc_start: 0.7968 (OUTLIER) cc_final: 0.7754 (ptm) REVERT: E 139 ASP cc_start: 0.7869 (t0) cc_final: 0.7495 (t0) REVERT: E 182 ARG cc_start: 0.8701 (ttp-170) cc_final: 0.8316 (ttp-170) outliers start: 37 outliers final: 25 residues processed: 239 average time/residue: 0.4115 time to fit residues: 146.6735 Evaluate side-chains 235 residues out of total 1533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 208 time to evaluate : 1.843 ------------------------------------------------------------------------------- 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 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 897 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 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 149 LEU Chi-restraints excluded: chain D residue 177 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 118 optimal weight: 10.0000 chunk 11 optimal weight: 0.9990 chunk 158 optimal weight: 9.9990 chunk 75 optimal weight: 0.5980 chunk 134 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 94 optimal weight: 6.9990 chunk 157 optimal weight: 3.9990 chunk 148 optimal weight: 7.9990 chunk 101 optimal weight: 0.8980 chunk 119 optimal weight: 7.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 734 HIS A 809 ASN A 812 ASN A1022 HIS A1069 GLN E 189 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.118510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.094037 restraints weight = 19417.501| |-----------------------------------------------------------------------------| r_work (start): 0.2924 rms_B_bonded: 1.87 r_work: 0.2796 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2653 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2653 ------------------------------------------------------------------------------- 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: 2 | |-----------------------------------------------------------------------------| |-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 | |-----------------------------------------------------------------------------| r_final: 0.2654 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.1603 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= 0.134 Angle : 0.482 6.966 18960 Z= 0.255 Chirality : 0.039 0.163 2205 Planarity : 0.003 0.051 2354 Dihedral : 7.866 73.654 1982 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.22 % Allowed : 14.68 % Favored : 83.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.38 (0.21), residues: 1657 helix: 1.99 (0.17), residues: 952 sheet: -1.19 (0.60), residues: 66 loop : -0.49 (0.25), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 932 HIS 0.004 0.001 HIS B 150 PHE 0.015 0.001 PHE A 704 TYR 0.013 0.001 TYR A 221 ARG 0.005 0.000 ARG E 197 Details of bonding type rmsd hydrogen bonds : bond 0.03645 ( 740) hydrogen bonds : angle 4.14165 ( 2151) covalent geometry : bond 0.00316 (14000) covalent geometry : angle 0.48200 (18960) *********************** 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 257 residues out of total 1533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 223 time to evaluate : 2.495 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 861 TYR cc_start: 0.9128 (p90) cc_final: 0.8730 (p90) REVERT: A 872 THR cc_start: 0.8484 (OUTLIER) cc_final: 0.8085 (m) REVERT: A 906 GLU cc_start: 0.9083 (mm-30) cc_final: 0.8449 (mt-10) REVERT: A 1304 ASN cc_start: 0.8728 (t0) cc_final: 0.8355 (t0) REVERT: A 1370 ARG cc_start: 0.8020 (ttt-90) cc_final: 0.7555 (ttm-80) REVERT: B 149 LEU cc_start: 0.9124 (mt) cc_final: 0.8898 (mt) REVERT: E 139 ASP cc_start: 0.7756 (t0) cc_final: 0.7490 (t0) outliers start: 34 outliers final: 25 residues processed: 242 average time/residue: 0.3244 time to fit residues: 116.3208 Evaluate side-chains 237 residues out of total 1533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 211 time to evaluate : 2.041 ------------------------------------------------------------------------------- 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 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 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 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 177 MET Chi-restraints excluded: chain E residue 136 ASP 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 133 optimal weight: 7.9990 chunk 47 optimal weight: 3.9990 chunk 146 optimal weight: 7.9990 chunk 24 optimal weight: 9.9990 chunk 9 optimal weight: 8.9990 chunk 93 optimal weight: 0.7980 chunk 108 optimal weight: 4.9990 chunk 29 optimal weight: 6.9990 chunk 95 optimal weight: 9.9990 chunk 5 optimal weight: 0.7980 chunk 56 optimal weight: 9.9990 overall best weight: 3.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 640 GLN A 734 HIS A 812 ASN A 895 ASN A1022 HIS A1069 GLN E 189 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.114990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.090500 restraints weight = 19732.523| |-----------------------------------------------------------------------------| r_work (start): 0.2872 rms_B_bonded: 1.86 r_work: 0.2745 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2601 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2601 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2593 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2593 r_free = 0.2593 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 = 0.2593 r_free = 0.2593 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2593 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8557 moved from start: 0.1892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 14000 Z= 0.248 Angle : 0.569 6.867 18960 Z= 0.295 Chirality : 0.043 0.177 2205 Planarity : 0.004 0.049 2354 Dihedral : 7.983 73.706 1982 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 2.67 % Allowed : 15.07 % Favored : 82.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.12 (0.21), residues: 1657 helix: 1.78 (0.16), residues: 957 sheet: -1.32 (0.60), residues: 66 loop : -0.59 (0.25), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 932 HIS 0.005 0.001 HIS A 206 PHE 0.019 0.002 PHE A 704 TYR 0.016 0.002 TYR A 221 ARG 0.006 0.000 ARG C 137 Details of bonding type rmsd hydrogen bonds : bond 0.04212 ( 740) hydrogen bonds : angle 4.34364 ( 2151) covalent geometry : bond 0.00603 (14000) covalent geometry : angle 0.56867 (18960) *********************** 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 252 residues out of total 1533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 211 time to evaluate : 2.770 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 861 TYR cc_start: 0.9165 (p90) cc_final: 0.8746 (p90) REVERT: A 872 THR cc_start: 0.8647 (OUTLIER) cc_final: 0.8249 (m) REVERT: A 906 GLU cc_start: 0.9127 (mm-30) cc_final: 0.8648 (mt-10) REVERT: A 1287 ASP cc_start: 0.8305 (m-30) cc_final: 0.8067 (m-30) REVERT: A 1304 ASN cc_start: 0.8821 (t0) cc_final: 0.8394 (t0) REVERT: E 139 ASP cc_start: 0.7917 (t0) cc_final: 0.7616 (t0) outliers start: 41 outliers final: 29 residues processed: 232 average time/residue: 0.3347 time to fit residues: 115.6838 Evaluate side-chains 228 residues out of total 1533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 198 time to evaluate : 4.020 ------------------------------------------------------------------------------- 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 1368 ILE Chi-restraints excluded: chain A residue 1384 VAL Chi-restraints excluded: chain A residue 1454 THR Chi-restraints excluded: chain A residue 1457 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain C residue 149 LEU Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain D residue 146 LEU Chi-restraints excluded: chain D residue 152 LEU Chi-restraints excluded: chain E residue 136 ASP Chi-restraints excluded: chain E residue 138 ILE Chi-restraints excluded: chain E residue 156 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 3 optimal weight: 2.9990 chunk 142 optimal weight: 0.8980 chunk 160 optimal weight: 7.9990 chunk 137 optimal weight: 10.0000 chunk 13 optimal weight: 1.9990 chunk 118 optimal weight: 7.9990 chunk 50 optimal weight: 0.8980 chunk 129 optimal weight: 5.9990 chunk 152 optimal weight: 2.9990 chunk 98 optimal weight: 0.9980 chunk 54 optimal weight: 0.8980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 417 ASN A 640 GLN A 734 HIS A 812 ASN A 895 ASN A1022 HIS A1069 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.119200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.094921 restraints weight = 19422.319| |-----------------------------------------------------------------------------| r_work (start): 0.2880 rms_B_bonded: 1.85 r_work: 0.2750 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2607 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2607 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2594 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2594 r_free = 0.2594 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2594 r_free = 0.2594 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2594 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.1778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14000 Z= 0.123 Angle : 0.483 6.886 18960 Z= 0.254 Chirality : 0.039 0.173 2205 Planarity : 0.003 0.054 2354 Dihedral : 7.773 73.608 1982 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.22 % Allowed : 15.98 % Favored : 81.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.37 (0.21), residues: 1657 helix: 2.00 (0.17), residues: 952 sheet: -1.25 (0.59), residues: 66 loop : -0.50 (0.25), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 932 HIS 0.003 0.001 HIS B 150 PHE 0.044 0.001 PHE A 629 TYR 0.013 0.001 TYR A 221 ARG 0.007 0.000 ARG C 137 Details of bonding type rmsd hydrogen bonds : bond 0.03625 ( 740) hydrogen bonds : angle 4.15222 ( 2151) covalent geometry : bond 0.00286 (14000) covalent geometry : angle 0.48259 (18960) *********************** 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 255 residues out of total 1533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 221 time to evaluate : 1.715 Fit side-chains revert: symmetry clash REVERT: A 473 PHE cc_start: 0.9322 (OUTLIER) cc_final: 0.8772 (m-80) REVERT: A 861 TYR cc_start: 0.9152 (p90) cc_final: 0.8731 (p90) REVERT: A 872 THR cc_start: 0.8583 (OUTLIER) cc_final: 0.8179 (m) REVERT: A 906 GLU cc_start: 0.9067 (mm-30) cc_final: 0.8611 (mt-10) REVERT: A 1265 SER cc_start: 0.9093 (t) cc_final: 0.8732 (m) REVERT: A 1304 ASN cc_start: 0.8690 (t0) cc_final: 0.8314 (t0) REVERT: A 1370 ARG cc_start: 0.7994 (ttt-90) cc_final: 0.7513 (ttm-80) REVERT: B 149 LEU cc_start: 0.9127 (mt) cc_final: 0.8903 (mt) REVERT: C 146 LEU cc_start: 0.8118 (OUTLIER) cc_final: 0.7795 (mm) REVERT: E 139 ASP cc_start: 0.7942 (t0) cc_final: 0.7632 (t0) outliers start: 34 outliers final: 25 residues processed: 245 average time/residue: 0.2589 time to fit residues: 94.7028 Evaluate side-chains 235 residues out of total 1533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 207 time to evaluate : 1.714 ------------------------------------------------------------------------------- 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 473 PHE 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 844 LEU Chi-restraints excluded: chain A residue 856 LYS Chi-restraints excluded: chain A residue 872 THR Chi-restraints excluded: chain A residue 897 ILE Chi-restraints excluded: chain A residue 955 ILE Chi-restraints excluded: chain A residue 1072 ILE Chi-restraints excluded: chain A residue 1173 ILE Chi-restraints excluded: chain A residue 1347 CYS Chi-restraints excluded: chain A residue 1384 VAL Chi-restraints excluded: chain A residue 1454 THR Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 149 LEU Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain D residue 146 LEU Chi-restraints excluded: chain D residue 152 LEU Chi-restraints excluded: chain E residue 136 ASP Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 156 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 31 optimal weight: 4.9990 chunk 100 optimal weight: 0.8980 chunk 24 optimal weight: 5.9990 chunk 46 optimal weight: 0.9980 chunk 109 optimal weight: 0.8980 chunk 87 optimal weight: 3.9990 chunk 19 optimal weight: 4.9990 chunk 128 optimal weight: 2.9990 chunk 60 optimal weight: 9.9990 chunk 75 optimal weight: 6.9990 chunk 120 optimal weight: 4.9990 overall best weight: 1.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 640 GLN A 734 HIS A 812 ASN A 895 ASN A1022 HIS A1069 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.117477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.092986 restraints weight = 19459.032| |-----------------------------------------------------------------------------| r_work (start): 0.2915 rms_B_bonded: 1.86 r_work: 0.2786 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2642 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2642 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2633 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2633 r_free = 0.2633 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 = 0.2633 r_free = 0.2633 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2633 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.1860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 14000 Z= 0.161 Angle : 0.514 7.059 18960 Z= 0.270 Chirality : 0.040 0.173 2205 Planarity : 0.004 0.053 2354 Dihedral : 7.799 73.616 1982 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 2.41 % Allowed : 16.63 % Favored : 80.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.21), residues: 1657 helix: 1.92 (0.16), residues: 955 sheet: -1.28 (0.58), residues: 66 loop : -0.54 (0.25), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 932 HIS 0.003 0.001 HIS B 150 PHE 0.045 0.002 PHE A 629 TYR 0.014 0.001 TYR A 221 ARG 0.004 0.000 ARG A 520 Details of bonding type rmsd hydrogen bonds : bond 0.03865 ( 740) hydrogen bonds : angle 4.19555 ( 2151) covalent geometry : bond 0.00387 (14000) covalent geometry : angle 0.51378 (18960) *********************** 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 245 residues out of total 1533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 208 time to evaluate : 1.516 Fit side-chains revert: symmetry clash REVERT: A 473 PHE cc_start: 0.9331 (OUTLIER) cc_final: 0.8787 (m-80) REVERT: A 511 ARG cc_start: 0.7622 (tpp80) cc_final: 0.7266 (tpp80) REVERT: A 640 GLN cc_start: 0.9245 (OUTLIER) cc_final: 0.8967 (tm130) REVERT: A 861 TYR cc_start: 0.9172 (p90) cc_final: 0.8732 (p90) REVERT: A 872 THR cc_start: 0.8656 (OUTLIER) cc_final: 0.8212 (m) REVERT: A 906 GLU cc_start: 0.9045 (mm-30) cc_final: 0.8652 (mt-10) REVERT: A 1265 SER cc_start: 0.9097 (t) cc_final: 0.8756 (m) REVERT: A 1304 ASN cc_start: 0.8695 (t0) cc_final: 0.8335 (t0) REVERT: A 1370 ARG cc_start: 0.8027 (ttt-90) cc_final: 0.7557 (ttm-80) REVERT: C 146 LEU cc_start: 0.8179 (OUTLIER) cc_final: 0.7835 (mm) REVERT: E 139 ASP cc_start: 0.7961 (t0) cc_final: 0.7662 (t0) outliers start: 37 outliers final: 29 residues processed: 233 average time/residue: 0.2700 time to fit residues: 92.9980 Evaluate side-chains 234 residues out of total 1533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 201 time to evaluate : 1.640 ------------------------------------------------------------------------------- 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 473 PHE 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 875 HIS 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 C residue 146 LEU Chi-restraints excluded: chain C residue 149 LEU Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain D residue 146 LEU Chi-restraints excluded: chain D residue 152 LEU Chi-restraints excluded: chain E residue 136 ASP Chi-restraints excluded: chain E residue 138 ILE Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 156 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 109 optimal weight: 3.9990 chunk 22 optimal weight: 0.9980 chunk 40 optimal weight: 3.9990 chunk 158 optimal weight: 9.9990 chunk 132 optimal weight: 2.9990 chunk 119 optimal weight: 10.0000 chunk 92 optimal weight: 0.9990 chunk 57 optimal weight: 0.6980 chunk 35 optimal weight: 4.9990 chunk 146 optimal weight: 10.0000 chunk 5 optimal weight: 4.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 734 HIS A 812 ASN A 875 HIS A 895 ASN 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 = 0.117423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.093060 restraints weight = 19360.890| |-----------------------------------------------------------------------------| r_work (start): 0.2895 rms_B_bonded: 1.84 r_work: 0.2769 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2622 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2622 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2621 |-occupancy refinement: start-------------------------------------------------| | 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 | |-----------------------------------------------------------------------------| |-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 | |-----------------------------------------------------------------------------| r_final: 0.2621 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.1872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 14000 Z= 0.160 Angle : 0.514 6.912 18960 Z= 0.269 Chirality : 0.040 0.176 2205 Planarity : 0.004 0.054 2354 Dihedral : 7.792 73.614 1982 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 2.15 % Allowed : 16.63 % Favored : 81.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.21), residues: 1657 helix: 1.92 (0.16), residues: 952 sheet: -1.24 (0.58), residues: 66 loop : -0.53 (0.25), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 932 HIS 0.003 0.001 HIS A 875 PHE 0.042 0.002 PHE A 629 TYR 0.014 0.001 TYR A 221 ARG 0.005 0.000 ARG A 520 Details of bonding type rmsd hydrogen bonds : bond 0.03840 ( 740) hydrogen bonds : angle 4.19649 ( 2151) covalent geometry : bond 0.00384 (14000) covalent geometry : angle 0.51416 (18960) *********************** 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 240 residues out of total 1533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 207 time to evaluate : 1.710 Fit side-chains revert: symmetry clash REVERT: A 194 MET cc_start: 0.8629 (tpp) cc_final: 0.8424 (tpt) REVERT: A 473 PHE cc_start: 0.9331 (OUTLIER) cc_final: 0.8785 (m-80) REVERT: A 511 ARG cc_start: 0.7459 (tpp80) cc_final: 0.7115 (tpp80) REVERT: A 861 TYR cc_start: 0.9162 (p90) cc_final: 0.8719 (p90) REVERT: A 872 THR cc_start: 0.8635 (OUTLIER) cc_final: 0.8244 (m) REVERT: A 906 GLU cc_start: 0.9016 (mm-30) cc_final: 0.8668 (mt-10) REVERT: A 1265 SER cc_start: 0.9087 (t) cc_final: 0.8745 (m) REVERT: A 1304 ASN cc_start: 0.8688 (t0) cc_final: 0.8326 (t0) REVERT: C 146 LEU cc_start: 0.8156 (OUTLIER) cc_final: 0.7796 (mm) outliers start: 33 outliers final: 28 residues processed: 229 average time/residue: 0.2967 time to fit residues: 101.0798 Evaluate side-chains 233 residues out of total 1533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 202 time to evaluate : 1.963 ------------------------------------------------------------------------------- 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 473 PHE 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 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 C residue 146 LEU Chi-restraints excluded: chain C residue 149 LEU Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain D residue 146 LEU Chi-restraints excluded: chain D residue 152 LEU Chi-restraints excluded: chain E residue 136 ASP Chi-restraints excluded: chain E residue 138 ILE Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 156 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 27 optimal weight: 0.4980 chunk 158 optimal weight: 6.9990 chunk 111 optimal weight: 0.6980 chunk 117 optimal weight: 9.9990 chunk 73 optimal weight: 1.9990 chunk 104 optimal weight: 0.9980 chunk 95 optimal weight: 6.9990 chunk 85 optimal weight: 2.9990 chunk 160 optimal weight: 0.0010 chunk 1 optimal weight: 0.0020 chunk 17 optimal weight: 2.9990 overall best weight: 0.4394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 640 GLN A 734 HIS A 812 ASN A 895 ASN A1049 ASN A1069 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.121041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.096817 restraints weight = 19339.953| |-----------------------------------------------------------------------------| r_work (start): 0.2942 rms_B_bonded: 1.87 r_work: 0.2816 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2675 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2675 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2651 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2651 r_free = 0.2651 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 = 0.2651 r_free = 0.2651 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2651 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.1825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 14000 Z= 0.101 Angle : 0.481 10.498 18960 Z= 0.251 Chirality : 0.038 0.169 2205 Planarity : 0.003 0.058 2354 Dihedral : 7.651 73.496 1982 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 1.76 % Allowed : 17.22 % Favored : 81.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.48 (0.21), residues: 1657 helix: 2.07 (0.17), residues: 952 sheet: -0.89 (0.60), residues: 63 loop : -0.48 (0.25), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 932 HIS 0.003 0.000 HIS B 150 PHE 0.039 0.001 PHE A 629 TYR 0.013 0.001 TYR A 221 ARG 0.005 0.000 ARG E 197 Details of bonding type rmsd hydrogen bonds : bond 0.03398 ( 740) hydrogen bonds : angle 4.05718 ( 2151) covalent geometry : bond 0.00221 (14000) covalent geometry : angle 0.48089 (18960) ********************** 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 262 residues out of total 1533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 235 time to evaluate : 1.632 Fit side-chains REVERT: A 336 GLU cc_start: 0.8324 (mm-30) cc_final: 0.8095 (mm-30) REVERT: A 511 ARG cc_start: 0.7353 (tpp80) cc_final: 0.7085 (tpp80) REVERT: A 640 GLN cc_start: 0.9128 (OUTLIER) cc_final: 0.8815 (tm130) REVERT: A 861 TYR cc_start: 0.9142 (p90) cc_final: 0.8707 (p90) REVERT: A 872 THR cc_start: 0.8476 (OUTLIER) cc_final: 0.8096 (m) REVERT: A 906 GLU cc_start: 0.8846 (mm-30) cc_final: 0.8507 (mt-10) REVERT: A 1265 SER cc_start: 0.9090 (t) cc_final: 0.8737 (m) REVERT: A 1304 ASN cc_start: 0.8574 (t0) cc_final: 0.8252 (t0) REVERT: A 1370 ARG cc_start: 0.7924 (ttt-90) cc_final: 0.7492 (ttm-80) REVERT: B 180 LYS cc_start: 0.8682 (tppt) cc_final: 0.8410 (tttp) REVERT: C 146 LEU cc_start: 0.8137 (OUTLIER) cc_final: 0.7849 (mm) REVERT: E 187 MET cc_start: 0.6743 (mmm) cc_final: 0.6477 (ttp) outliers start: 27 outliers final: 22 residues processed: 251 average time/residue: 0.2594 time to fit residues: 96.7145 Evaluate side-chains 244 residues out of total 1533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 219 time to evaluate : 1.504 ------------------------------------------------------------------------------- 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 640 GLN Chi-restraints excluded: chain A residue 814 SER 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 897 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 1454 THR Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 149 LEU Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain D residue 146 LEU Chi-restraints excluded: chain D residue 152 LEU Chi-restraints excluded: chain E residue 136 ASP Chi-restraints excluded: chain E residue 156 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 116 optimal weight: 0.0670 chunk 130 optimal weight: 0.6980 chunk 138 optimal weight: 2.9990 chunk 114 optimal weight: 3.9990 chunk 163 optimal weight: 3.9990 chunk 122 optimal weight: 2.9990 chunk 36 optimal weight: 0.7980 chunk 109 optimal weight: 10.0000 chunk 81 optimal weight: 0.9990 chunk 87 optimal weight: 0.0070 chunk 142 optimal weight: 7.9990 overall best weight: 0.5138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 705 ASN A 734 HIS A 812 ASN A 895 ASN A1022 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.121493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.097258 restraints weight = 19440.114| |-----------------------------------------------------------------------------| r_work (start): 0.2923 rms_B_bonded: 1.87 r_work: 0.2797 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2654 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2654 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2710 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2710 r_free = 0.2710 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2710 r_free = 0.2710 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2710 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.1837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.270 14000 Z= 0.233 Angle : 0.830 59.200 18960 Z= 0.504 Chirality : 0.049 1.235 2205 Planarity : 0.005 0.182 2354 Dihedral : 7.658 73.496 1982 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 1.63 % Allowed : 17.81 % Favored : 80.56 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.46 (0.21), residues: 1657 helix: 2.05 (0.17), residues: 952 sheet: -0.88 (0.60), residues: 63 loop : -0.48 (0.25), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 932 HIS 0.003 0.000 HIS C 150 PHE 0.037 0.001 PHE A 629 TYR 0.012 0.001 TYR A 221 ARG 0.005 0.000 ARG E 197 Details of bonding type rmsd hydrogen bonds : bond 0.03420 ( 740) hydrogen bonds : angle 4.06010 ( 2151) covalent geometry : bond 0.00470 (14000) covalent geometry : angle 0.82955 (18960) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7702.75 seconds wall clock time: 140 minutes 7.81 seconds (8407.81 seconds total)