Starting phenix.real_space_refine on Sun Nov 17 13:49:13 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8snx_40641/11_2024/8snx_40641_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8snx_40641/11_2024/8snx_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8snx_40641/11_2024/8snx_40641.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8snx_40641/11_2024/8snx_40641.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8snx_40641/11_2024/8snx_40641_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8snx_40641/11_2024/8snx_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-5513/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: 7.37, per 1000 atoms: 0.54 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: 3.68 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: 1.67 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: 5.19 Time building geometry restraints manager: 4.17 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: 0.420 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.010 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.500 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 32.480 Find NCS groups from input model: 0.190 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:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.880 ------------------------------------------------------------------------------- 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= 0.198 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 *********************** 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 : 1.917 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: 0.2739 time to fit residues: 115.0655 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 : 1.580 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 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= 0.157 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 *********************** 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 : 1.620 Fit side-chains revert: symmetry clash REVERT: A 861 TYR cc_start: 0.8902 (p90) cc_final: 0.8591 (p90) REVERT: A 872 THR cc_start: 0.7963 (OUTLIER) cc_final: 0.7758 (t) REVERT: A 874 GLN cc_start: 0.7690 (tm-30) cc_final: 0.6790 (tm-30) REVERT: A 912 THR cc_start: 0.9387 (p) cc_final: 0.9168 (p) REVERT: A 1304 ASN cc_start: 0.8526 (t0) cc_final: 0.8291 (t0) outliers start: 20 outliers final: 14 residues processed: 258 average time/residue: 0.2775 time to fit residues: 105.0280 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 : 1.617 ------------------------------------------------------------------------------- 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 83 optimal weight: 8.9990 chunk 46 optimal weight: 0.2980 chunk 125 optimal weight: 9.9990 chunk 102 optimal weight: 8.9990 chunk 41 optimal weight: 3.9990 chunk 151 optimal weight: 7.9990 chunk 163 optimal weight: 3.9990 chunk 134 optimal weight: 9.9990 chunk 149 optimal weight: 10.0000 chunk 51 optimal weight: 5.9990 chunk 121 optimal weight: 0.8980 overall best weight: 3.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 640 GLN A 734 HIS A 812 ASN A 895 ASN A1022 HIS A1049 ASN A1120 HIS B 150 HIS E 189 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.1461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 14000 Z= 0.346 Angle : 0.554 7.262 18960 Z= 0.290 Chirality : 0.042 0.178 2205 Planarity : 0.004 0.049 2354 Dihedral : 8.166 73.730 1982 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 2.28 % Allowed : 12.07 % Favored : 85.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.28 (0.21), residues: 1657 helix: 1.92 (0.17), residues: 956 sheet: -1.15 (0.59), residues: 66 loop : -0.57 (0.24), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 480 HIS 0.005 0.001 HIS A 206 PHE 0.021 0.002 PHE A 629 TYR 0.016 0.002 TYR A 221 ARG 0.003 0.000 ARG B 174 *********************** 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 253 residues out of total 1533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 218 time to evaluate : 1.644 Fit side-chains revert: symmetry clash REVERT: A 13 TYR cc_start: 0.8541 (m-80) cc_final: 0.7835 (m-80) REVERT: A 511 ARG cc_start: 0.7428 (tpp80) cc_final: 0.7039 (tpp-160) REVERT: A 640 GLN cc_start: 0.9015 (OUTLIER) cc_final: 0.8642 (tm130) REVERT: A 861 TYR cc_start: 0.8908 (p90) cc_final: 0.8513 (p90) REVERT: A 872 THR cc_start: 0.8355 (OUTLIER) cc_final: 0.8085 (t) REVERT: A 906 GLU cc_start: 0.8278 (mm-30) cc_final: 0.7828 (mt-10) REVERT: A 1287 ASP cc_start: 0.7539 (m-30) cc_final: 0.7323 (m-30) REVERT: A 1304 ASN cc_start: 0.8584 (t0) cc_final: 0.8279 (t0) REVERT: B 144 GLU cc_start: 0.7260 (mt-10) cc_final: 0.6889 (tt0) outliers start: 35 outliers final: 25 residues processed: 237 average time/residue: 0.2785 time to fit residues: 97.6504 Evaluate side-chains 238 residues out of total 1533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 211 time to evaluate : 1.555 ------------------------------------------------------------------------------- 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 640 GLN Chi-restraints excluded: chain A residue 692 ILE Chi-restraints excluded: chain A residue 809 ASN 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 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 138 ILE 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 149 optimal weight: 4.9990 chunk 113 optimal weight: 0.9990 chunk 78 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 72 optimal weight: 4.9990 chunk 101 optimal weight: 3.9990 chunk 151 optimal weight: 9.9990 chunk 160 optimal weight: 5.9990 chunk 79 optimal weight: 1.9990 chunk 143 optimal weight: 6.9990 chunk 43 optimal weight: 0.7980 overall best weight: 2.1588 ------------------------------------------------------------------------------- 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 E 189 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.1566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 14000 Z= 0.260 Angle : 0.508 7.161 18960 Z= 0.267 Chirality : 0.040 0.170 2205 Planarity : 0.003 0.049 2354 Dihedral : 8.042 73.689 1982 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.22 % Allowed : 14.02 % Favored : 83.76 % 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: 1.30 (0.21), residues: 1657 helix: 1.93 (0.16), residues: 956 sheet: -1.23 (0.59), residues: 66 loop : -0.54 (0.25), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 932 HIS 0.003 0.001 HIS A 206 PHE 0.017 0.002 PHE A 629 TYR 0.014 0.001 TYR A 221 ARG 0.005 0.000 ARG E 197 *********************** 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 256 residues out of total 1533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 222 time to evaluate : 1.631 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 13 TYR cc_start: 0.8550 (m-80) cc_final: 0.7822 (m-80) REVERT: A 861 TYR cc_start: 0.8898 (p90) cc_final: 0.8509 (p90) REVERT: A 872 THR cc_start: 0.8441 (OUTLIER) cc_final: 0.8190 (m) REVERT: A 906 GLU cc_start: 0.8175 (mm-30) cc_final: 0.7847 (mt-10) REVERT: A 1304 ASN cc_start: 0.8508 (t0) cc_final: 0.8171 (t0) REVERT: A 1396 MET cc_start: 0.7948 (OUTLIER) cc_final: 0.7734 (mtp) REVERT: E 139 ASP cc_start: 0.7708 (t0) cc_final: 0.7469 (t0) REVERT: E 146 LEU cc_start: 0.8208 (OUTLIER) cc_final: 0.7863 (mm) outliers start: 34 outliers final: 25 residues processed: 240 average time/residue: 0.2820 time to fit residues: 99.7778 Evaluate side-chains 234 residues out of total 1533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 206 time to evaluate : 1.722 ------------------------------------------------------------------------------- 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 872 THR Chi-restraints excluded: chain A residue 897 ILE Chi-restraints excluded: chain A residue 1072 ILE Chi-restraints excluded: chain A residue 1173 ILE Chi-restraints excluded: chain A residue 1347 CYS Chi-restraints excluded: chain A residue 1384 VAL Chi-restraints excluded: chain A residue 1396 MET Chi-restraints excluded: chain A residue 1454 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain C residue 149 LEU Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain D residue 146 LEU Chi-restraints excluded: chain D residue 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 146 LEU 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 133 optimal weight: 6.9990 chunk 91 optimal weight: 0.6980 chunk 2 optimal weight: 3.9990 chunk 119 optimal weight: 9.9990 chunk 66 optimal weight: 4.9990 chunk 136 optimal weight: 3.9990 chunk 110 optimal weight: 0.4980 chunk 0 optimal weight: 8.9990 chunk 81 optimal weight: 0.9980 chunk 144 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- 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 809 ASN A 812 ASN A 895 ASN A1022 HIS E 189 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.1558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 14000 Z= 0.164 Angle : 0.462 6.897 18960 Z= 0.244 Chirality : 0.038 0.164 2205 Planarity : 0.003 0.054 2354 Dihedral : 7.810 73.544 1982 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.48 % Allowed : 14.68 % Favored : 82.84 % 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: 1.52 (0.21), residues: 1657 helix: 2.12 (0.17), residues: 951 sheet: -1.10 (0.60), residues: 66 loop : -0.45 (0.25), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 932 HIS 0.002 0.000 HIS A 748 PHE 0.015 0.001 PHE A 629 TYR 0.013 0.001 TYR A 861 ARG 0.009 0.000 ARG B 134 *********************** 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 272 residues out of total 1533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 234 time to evaluate : 1.808 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 348 GLU cc_start: 0.8383 (mm-30) cc_final: 0.8127 (mm-30) REVERT: A 861 TYR cc_start: 0.8876 (p90) cc_final: 0.8482 (p90) REVERT: A 872 THR cc_start: 0.8353 (OUTLIER) cc_final: 0.8139 (m) REVERT: A 1304 ASN cc_start: 0.8344 (t0) cc_final: 0.8010 (t0) REVERT: E 139 ASP cc_start: 0.7631 (t0) cc_final: 0.7428 (t0) REVERT: E 146 LEU cc_start: 0.8118 (OUTLIER) cc_final: 0.7785 (mm) outliers start: 38 outliers final: 28 residues processed: 256 average time/residue: 0.2905 time to fit residues: 109.8241 Evaluate side-chains 245 residues out of total 1533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 215 time to evaluate : 1.713 ------------------------------------------------------------------------------- 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 809 ASN 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 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 149 LEU Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain D residue 146 LEU Chi-restraints excluded: chain D residue 152 LEU Chi-restraints excluded: chain D residue 177 MET Chi-restraints excluded: chain D residue 187 MET Chi-restraints excluded: chain E residue 136 ASP Chi-restraints excluded: chain E residue 146 LEU 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 53 optimal weight: 9.9990 chunk 144 optimal weight: 0.5980 chunk 31 optimal weight: 0.4980 chunk 94 optimal weight: 6.9990 chunk 39 optimal weight: 0.8980 chunk 160 optimal weight: 3.9990 chunk 133 optimal weight: 3.9990 chunk 74 optimal weight: 4.9990 chunk 13 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 154 optimal weight: 10.0000 overall best weight: 1.5984 ------------------------------------------------------------------------------- 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 895 ASN A1011 HIS A1022 HIS E 189 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.1628 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= 0.210 Angle : 0.480 7.119 18960 Z= 0.252 Chirality : 0.039 0.174 2205 Planarity : 0.003 0.053 2354 Dihedral : 7.781 73.555 1982 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.15 % Allowed : 15.59 % 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: 1.49 (0.21), residues: 1657 helix: 2.10 (0.17), residues: 951 sheet: -1.09 (0.60), residues: 66 loop : -0.47 (0.25), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 932 HIS 0.002 0.001 HIS A 206 PHE 0.018 0.001 PHE A 868 TYR 0.013 0.001 TYR A 221 ARG 0.008 0.000 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3314 Ramachandran restraints generated. 1657 Oldfield, 0 Emsley, 1657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3314 Ramachandran restraints generated. 1657 Oldfield, 0 Emsley, 1657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 224 time to evaluate : 1.689 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 13 TYR cc_start: 0.8530 (m-80) cc_final: 0.7796 (m-80) REVERT: A 473 PHE cc_start: 0.9167 (OUTLIER) cc_final: 0.8668 (m-80) REVERT: A 520 ARG cc_start: 0.8064 (mtm-85) cc_final: 0.7583 (mtm180) REVERT: A 629 PHE cc_start: 0.8154 (p90) cc_final: 0.7949 (p90) REVERT: A 861 TYR cc_start: 0.8876 (p90) cc_final: 0.8469 (p90) REVERT: A 872 THR cc_start: 0.8451 (OUTLIER) cc_final: 0.8234 (m) REVERT: A 875 HIS cc_start: 0.7446 (OUTLIER) cc_final: 0.6552 (p90) REVERT: A 1304 ASN cc_start: 0.8357 (t0) cc_final: 0.7995 (t0) REVERT: E 139 ASP cc_start: 0.7782 (t0) cc_final: 0.7467 (t0) REVERT: E 146 LEU cc_start: 0.8168 (OUTLIER) cc_final: 0.7714 (mm) REVERT: E 148 MET cc_start: 0.8091 (ppp) cc_final: 0.7835 (ppp) outliers start: 33 outliers final: 27 residues processed: 244 average time/residue: 0.2379 time to fit residues: 86.7832 Evaluate side-chains 247 residues out of total 1533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 216 time to evaluate : 1.031 ------------------------------------------------------------------------------- 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 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 B residue 146 LEU Chi-restraints excluded: chain C residue 149 LEU Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain D residue 146 LEU Chi-restraints excluded: chain D residue 152 LEU Chi-restraints excluded: chain D residue 177 MET Chi-restraints excluded: chain E residue 136 ASP Chi-restraints excluded: chain E residue 146 LEU 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 18 optimal weight: 5.9990 chunk 91 optimal weight: 0.8980 chunk 117 optimal weight: 4.9990 chunk 90 optimal weight: 20.0000 chunk 135 optimal weight: 4.9990 chunk 89 optimal weight: 2.9990 chunk 159 optimal weight: 6.9990 chunk 100 optimal weight: 0.7980 chunk 97 optimal weight: 3.9990 chunk 73 optimal weight: 5.9990 chunk 98 optimal weight: 3.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.1799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 14000 Z= 0.296 Angle : 0.532 10.146 18960 Z= 0.276 Chirality : 0.041 0.178 2205 Planarity : 0.004 0.064 2354 Dihedral : 7.850 73.662 1982 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 2.87 % Allowed : 15.46 % Favored : 81.67 % 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: 1.34 (0.21), residues: 1657 helix: 1.96 (0.16), residues: 956 sheet: -1.25 (0.59), residues: 66 loop : -0.52 (0.25), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 932 HIS 0.004 0.001 HIS A 206 PHE 0.019 0.002 PHE A 629 TYR 0.015 0.001 TYR A 221 ARG 0.011 0.000 ARG B 134 *********************** 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 263 residues out of total 1533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 219 time to evaluate : 1.788 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 13 TYR cc_start: 0.8576 (m-80) cc_final: 0.7844 (m-80) REVERT: A 348 GLU cc_start: 0.8371 (mm-30) cc_final: 0.8164 (mm-30) REVERT: A 473 PHE cc_start: 0.9244 (OUTLIER) cc_final: 0.8630 (m-80) REVERT: A 520 ARG cc_start: 0.8085 (mtm-85) cc_final: 0.7614 (mtm180) REVERT: A 628 MET cc_start: 0.8069 (mmt) cc_final: 0.7655 (mmt) REVERT: A 861 TYR cc_start: 0.8924 (p90) cc_final: 0.8480 (p90) REVERT: A 872 THR cc_start: 0.8550 (OUTLIER) cc_final: 0.8333 (m) REVERT: A 1304 ASN cc_start: 0.8516 (t0) cc_final: 0.8119 (t0) REVERT: C 146 LEU cc_start: 0.8078 (OUTLIER) cc_final: 0.7716 (mm) REVERT: E 139 ASP cc_start: 0.7812 (t0) cc_final: 0.7526 (t0) REVERT: E 146 LEU cc_start: 0.8231 (OUTLIER) cc_final: 0.7907 (mm) REVERT: E 148 MET cc_start: 0.8070 (ppp) cc_final: 0.7733 (tmm) outliers start: 44 outliers final: 30 residues processed: 247 average time/residue: 0.2616 time to fit residues: 95.7952 Evaluate side-chains 242 residues out of total 1533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 208 time to evaluate : 1.654 ------------------------------------------------------------------------------- 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 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 851 ILE Chi-restraints excluded: chain A residue 872 THR Chi-restraints excluded: chain A residue 894 ILE Chi-restraints excluded: chain A residue 897 ILE Chi-restraints excluded: chain A residue 955 ILE Chi-restraints excluded: chain A residue 1072 ILE Chi-restraints excluded: chain A residue 1173 ILE Chi-restraints excluded: chain A residue 1347 CYS Chi-restraints excluded: chain A residue 1384 VAL Chi-restraints excluded: chain A residue 1454 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 149 LEU Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain D residue 146 LEU Chi-restraints excluded: chain 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 146 LEU 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 63 optimal weight: 2.9990 chunk 95 optimal weight: 5.9990 chunk 48 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 30 optimal weight: 0.9980 chunk 101 optimal weight: 2.9990 chunk 109 optimal weight: 8.9990 chunk 79 optimal weight: 6.9990 chunk 14 optimal weight: 0.9980 chunk 125 optimal weight: 6.9990 chunk 145 optimal weight: 0.1980 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 255 HIS A 640 GLN A 812 ASN A 895 ASN A1049 ASN E 189 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.1819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14000 Z= 0.216 Angle : 0.508 9.494 18960 Z= 0.264 Chirality : 0.039 0.173 2205 Planarity : 0.004 0.054 2354 Dihedral : 7.778 73.602 1982 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.54 % Allowed : 16.31 % Favored : 81.15 % 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: 1.98 (0.16), residues: 952 sheet: -1.16 (0.61), residues: 64 loop : -0.50 (0.25), residues: 641 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 932 HIS 0.002 0.001 HIS A 206 PHE 0.018 0.002 PHE A 868 TYR 0.013 0.001 TYR A 221 ARG 0.011 0.000 ARG B 134 *********************** 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 260 residues out of total 1533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 221 time to evaluate : 1.718 Fit side-chains revert: symmetry clash REVERT: A 13 TYR cc_start: 0.8549 (m-80) cc_final: 0.7814 (m-80) REVERT: A 473 PHE cc_start: 0.9232 (OUTLIER) cc_final: 0.8684 (m-80) REVERT: A 629 PHE cc_start: 0.8206 (p90) cc_final: 0.7959 (p90) REVERT: A 861 TYR cc_start: 0.8912 (p90) cc_final: 0.8455 (p90) REVERT: A 872 THR cc_start: 0.8557 (OUTLIER) cc_final: 0.8325 (m) REVERT: A 1265 SER cc_start: 0.9080 (t) cc_final: 0.8692 (m) REVERT: A 1304 ASN cc_start: 0.8356 (t0) cc_final: 0.8020 (t0) REVERT: B 144 GLU cc_start: 0.7243 (OUTLIER) cc_final: 0.6380 (mt-10) REVERT: C 146 LEU cc_start: 0.8017 (OUTLIER) cc_final: 0.7685 (mm) REVERT: E 139 ASP cc_start: 0.7794 (t0) cc_final: 0.7564 (t0) outliers start: 39 outliers final: 29 residues processed: 247 average time/residue: 0.2707 time to fit residues: 98.9019 Evaluate side-chains 247 residues out of total 1533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 214 time to evaluate : 1.713 ------------------------------------------------------------------------------- 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 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 B residue 144 GLU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 149 LEU Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain D residue 146 LEU Chi-restraints excluded: chain D residue 152 LEU Chi-restraints excluded: chain E residue 136 ASP Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 156 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 153 optimal weight: 5.9990 chunk 139 optimal weight: 1.9990 chunk 149 optimal weight: 0.9980 chunk 89 optimal weight: 0.9980 chunk 64 optimal weight: 0.7980 chunk 117 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 134 optimal weight: 6.9990 chunk 141 optimal weight: 1.9990 chunk 148 optimal weight: 3.9990 chunk 97 optimal weight: 0.9980 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 640 GLN A 809 ASN A 812 ASN A 895 ASN A1049 ASN A1069 GLN E 189 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.1790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14000 Z= 0.181 Angle : 0.502 9.723 18960 Z= 0.260 Chirality : 0.039 0.176 2205 Planarity : 0.003 0.056 2354 Dihedral : 7.707 73.533 1982 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 2.48 % Allowed : 16.50 % 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: 1.44 (0.21), residues: 1657 helix: 2.05 (0.17), residues: 951 sheet: -1.15 (0.60), residues: 66 loop : -0.46 (0.25), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 932 HIS 0.003 0.001 HIS A 734 PHE 0.018 0.001 PHE A 629 TYR 0.013 0.001 TYR A 221 ARG 0.011 0.000 ARG B 134 *********************** 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 264 residues out of total 1533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 226 time to evaluate : 1.639 Fit side-chains revert: symmetry clash REVERT: A 473 PHE cc_start: 0.9195 (OUTLIER) cc_final: 0.8712 (m-80) REVERT: A 511 ARG cc_start: 0.7083 (tpp80) cc_final: 0.6647 (tpp80) REVERT: A 861 TYR cc_start: 0.8904 (p90) cc_final: 0.8462 (p90) REVERT: A 1265 SER cc_start: 0.9056 (t) cc_final: 0.8666 (m) REVERT: A 1304 ASN cc_start: 0.8264 (t0) cc_final: 0.7973 (t0) REVERT: B 144 GLU cc_start: 0.7153 (OUTLIER) cc_final: 0.6141 (mt-10) REVERT: C 146 LEU cc_start: 0.8048 (OUTLIER) cc_final: 0.7752 (mm) REVERT: E 148 MET cc_start: 0.8496 (tmm) cc_final: 0.8284 (ppp) REVERT: E 197 ARG cc_start: 0.8112 (ttp80) cc_final: 0.7881 (ttp80) outliers start: 38 outliers final: 30 residues processed: 251 average time/residue: 0.2695 time to fit residues: 99.7436 Evaluate side-chains 249 residues out of total 1533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 216 time to evaluate : 1.652 ------------------------------------------------------------------------------- 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 453 TYR 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 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 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 1361 TYR Chi-restraints excluded: chain A residue 1384 VAL Chi-restraints excluded: chain A residue 1454 THR Chi-restraints excluded: chain B residue 144 GLU 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 157 optimal weight: 1.9990 chunk 96 optimal weight: 0.1980 chunk 74 optimal weight: 5.9990 chunk 109 optimal weight: 0.4980 chunk 165 optimal weight: 10.0000 chunk 152 optimal weight: 3.9990 chunk 131 optimal weight: 0.9980 chunk 13 optimal weight: 3.9990 chunk 101 optimal weight: 7.9990 chunk 80 optimal weight: 2.9990 chunk 104 optimal weight: 0.7980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 640 GLN A 812 ASN A 895 ASN A1049 ASN A1404 ASN E 189 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.1816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.114 14000 Z= 0.211 Angle : 0.736 59.185 18960 Z= 0.431 Chirality : 0.039 0.413 2205 Planarity : 0.004 0.059 2354 Dihedral : 7.719 73.535 1982 Min Nonbonded Distance : 1.828 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 2.41 % Allowed : 16.70 % Favored : 80.89 % 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: 2.05 (0.17), residues: 951 sheet: -1.15 (0.60), residues: 66 loop : -0.47 (0.25), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 932 HIS 0.003 0.000 HIS A 734 PHE 0.019 0.001 PHE A 629 TYR 0.013 0.001 TYR A 221 ARG 0.011 0.000 ARG B 134 ********************** 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 256 residues out of total 1533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 219 time to evaluate : 1.563 Fit side-chains revert: symmetry clash REVERT: A 473 PHE cc_start: 0.9196 (OUTLIER) cc_final: 0.8710 (m-80) REVERT: A 511 ARG cc_start: 0.7060 (tpp80) cc_final: 0.6603 (tpp80) REVERT: A 861 TYR cc_start: 0.8904 (p90) cc_final: 0.8460 (p90) REVERT: A 1049 ASN cc_start: 0.7381 (OUTLIER) cc_final: 0.7172 (p0) REVERT: A 1265 SER cc_start: 0.9052 (t) cc_final: 0.8665 (m) REVERT: A 1304 ASN cc_start: 0.8269 (t0) cc_final: 0.7971 (t0) REVERT: B 144 GLU cc_start: 0.7151 (OUTLIER) cc_final: 0.6068 (mt-10) REVERT: C 146 LEU cc_start: 0.8044 (OUTLIER) cc_final: 0.7752 (mm) REVERT: E 148 MET cc_start: 0.8500 (tmm) cc_final: 0.8292 (ppp) REVERT: E 197 ARG cc_start: 0.8108 (ttp80) cc_final: 0.7881 (ttp80) outliers start: 37 outliers final: 31 residues processed: 242 average time/residue: 0.2737 time to fit residues: 99.5175 Evaluate side-chains 253 residues out of total 1533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 218 time to evaluate : 1.719 ------------------------------------------------------------------------------- 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 453 TYR 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 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 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 1361 TYR 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 144 GLU Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 149 LEU Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain D residue 146 LEU Chi-restraints excluded: chain D residue 152 LEU Chi-restraints excluded: chain E residue 136 ASP Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 156 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 140 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 121 optimal weight: 5.9990 chunk 19 optimal weight: 7.9990 chunk 36 optimal weight: 3.9990 chunk 131 optimal weight: 0.9980 chunk 55 optimal weight: 1.9990 chunk 135 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 chunk 24 optimal weight: 2.9990 chunk 115 optimal weight: 5.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 640 GLN A 812 ASN A 895 ASN ** A1049 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 189 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.119105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.094914 restraints weight = 19297.557| |-----------------------------------------------------------------------------| r_work (start): 0.2941 rms_B_bonded: 1.85 r_work: 0.2815 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2673 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2673 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2667 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2667 r_free = 0.2667 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2667 r_free = 0.2667 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2667 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.1813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.458 14000 Z= 0.421 Angle : 0.670 46.074 18960 Z= 0.464 Chirality : 0.038 0.168 2205 Planarity : 0.006 0.245 2354 Dihedral : 7.719 73.535 1982 Min Nonbonded Distance : 1.828 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 2.35 % Allowed : 16.76 % Favored : 80.89 % Cbeta Deviations : 0.06 % 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: 2.05 (0.17), residues: 951 sheet: -1.15 (0.60), residues: 66 loop : -0.47 (0.25), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 932 HIS 0.003 0.000 HIS A 734 PHE 0.019 0.001 PHE A 629 TYR 0.013 0.001 TYR A 221 ARG 0.011 0.000 ARG B 134 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3064.44 seconds wall clock time: 63 minutes 12.64 seconds (3792.64 seconds total)