Starting phenix.real_space_refine on Tue May 13 15:50:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qgt_18390/05_2025/8qgt_18390.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qgt_18390/05_2025/8qgt_18390.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8qgt_18390/05_2025/8qgt_18390.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qgt_18390/05_2025/8qgt_18390.map" model { file = "/net/cci-nas-00/data/ceres_data/8qgt_18390/05_2025/8qgt_18390.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qgt_18390/05_2025/8qgt_18390.cif" } resolution = 2.8 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= 0.001 sd= 0.056 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 12 5.49 5 S 57 5.16 5 C 6797 2.51 5 N 1790 2.21 5 O 1979 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 10635 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 10376 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1289, 10376 Classifications: {'peptide': 1289} Link IDs: {'PTRANS': 41, 'TRANS': 1247} Chain breaks: 9 Chain: "C" Number of atoms: 259 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 259 Classifications: {'RNA': 12} Modifications used: {'rna2p_pur': 3, 'rna2p_pyr': 1, 'rna3p_pur': 5, 'rna3p_pyr': 3} Link IDs: {'rna2p': 3, 'rna3p': 8} Time building chain proxies: 6.55, per 1000 atoms: 0.62 Number of scatterers: 10635 At special positions: 0 Unit cell: (91.451, 104.036, 124.172, 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 57 16.00 P 12 15.00 O 1979 8.00 N 1790 7.00 C 6797 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: 2.75 Conformation dependent library (CDL) restraints added in 1.5 seconds 2538 Ramachandran restraints generated. 1269 Oldfield, 0 Emsley, 1269 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2458 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 12 sheets defined 60.7% alpha, 10.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.24 Creating SS restraints... Processing helix chain 'A' and resid 239 through 251 removed outlier: 3.727A pdb=" N LEU A 243 " --> pdb=" O ASN A 239 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 282 removed outlier: 3.591A pdb=" N ALA A 276 " --> pdb=" O ASN A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 323 Processing helix chain 'A' and resid 328 through 343 Processing helix chain 'A' and resid 345 through 353 Processing helix chain 'A' and resid 374 through 378 Processing helix chain 'A' and resid 379 through 391 Processing helix chain 'A' and resid 409 through 429 Processing helix chain 'A' and resid 450 through 463 removed outlier: 4.782A pdb=" N GLN A 460 " --> pdb=" O GLN A 456 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N LYS A 461 " --> pdb=" O ASN A 457 " (cutoff:3.500A) Processing helix chain 'A' and resid 463 through 468 Processing helix chain 'A' and resid 470 through 489 removed outlier: 3.871A pdb=" N HIS A 474 " --> pdb=" O THR A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 539 through 541 No H-bonds generated for 'chain 'A' and resid 539 through 541' Processing helix chain 'A' and resid 564 through 572 removed outlier: 3.611A pdb=" N ILE A 572 " --> pdb=" O LEU A 568 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 593 Processing helix chain 'A' and resid 597 through 614 Processing helix chain 'A' and resid 616 through 635 removed outlier: 3.580A pdb=" N ARG A 627 " --> pdb=" O PHE A 623 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N TYR A 628 " --> pdb=" O ASP A 624 " (cutoff:3.500A) Proline residue: A 631 - end of helix Processing helix chain 'A' and resid 639 through 649 Processing helix chain 'A' and resid 654 through 673 Processing helix chain 'A' and resid 712 through 725 removed outlier: 3.918A pdb=" N LEU A 716 " --> pdb=" O HIS A 712 " (cutoff:3.500A) Processing helix chain 'A' and resid 733 through 742 removed outlier: 4.233A pdb=" N HIS A 742 " --> pdb=" O GLU A 738 " (cutoff:3.500A) Processing helix chain 'A' and resid 742 through 759 Processing helix chain 'A' and resid 760 through 767 Processing helix chain 'A' and resid 769 through 777 Processing helix chain 'A' and resid 786 through 802 removed outlier: 3.951A pdb=" N VAL A 800 " --> pdb=" O GLU A 796 " (cutoff:3.500A) Processing helix chain 'A' and resid 804 through 814 Processing helix chain 'A' and resid 820 through 828 removed outlier: 3.666A pdb=" N SER A 823 " --> pdb=" O PRO A 820 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N GLN A 824 " --> pdb=" O TYR A 821 " (cutoff:3.500A) removed outlier: 5.713A pdb=" N THR A 825 " --> pdb=" O PHE A 822 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N ARG A 826 " --> pdb=" O SER A 823 " (cutoff:3.500A) Processing helix chain 'A' and resid 848 through 858 Processing helix chain 'A' and resid 864 through 873 Processing helix chain 'A' and resid 898 through 917 Processing helix chain 'A' and resid 928 through 947 removed outlier: 4.079A pdb=" N ILE A 932 " --> pdb=" O GLY A 928 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LEU A 933 " --> pdb=" O GLU A 929 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N SER A 947 " --> pdb=" O LEU A 943 " (cutoff:3.500A) Processing helix chain 'A' and resid 983 through 992 removed outlier: 4.137A pdb=" N ARG A 987 " --> pdb=" O ALA A 983 " (cutoff:3.500A) Processing helix chain 'A' and resid 999 through 1011 Processing helix chain 'A' and resid 1020 through 1030 removed outlier: 3.621A pdb=" N MET A1030 " --> pdb=" O TYR A1026 " (cutoff:3.500A) Processing helix chain 'A' and resid 1034 through 1042 Processing helix chain 'A' and resid 1061 through 1084 removed outlier: 3.564A pdb=" N SER A1065 " --> pdb=" O LEU A1061 " (cutoff:3.500A) Processing helix chain 'A' and resid 1113 through 1126 removed outlier: 3.625A pdb=" N LEU A1118 " --> pdb=" O THR A1114 " (cutoff:3.500A) Processing helix chain 'A' and resid 1128 through 1135 removed outlier: 3.637A pdb=" N SER A1133 " --> pdb=" O HIS A1130 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ASN A1135 " --> pdb=" O PHE A1132 " (cutoff:3.500A) Processing helix chain 'A' and resid 1137 through 1153 removed outlier: 3.860A pdb=" N SER A1141 " --> pdb=" O GLU A1137 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLY A1153 " --> pdb=" O ILE A1149 " (cutoff:3.500A) Processing helix chain 'A' and resid 1169 through 1179 Processing helix chain 'A' and resid 1184 through 1192 removed outlier: 3.836A pdb=" N ILE A1188 " --> pdb=" O PRO A1184 " (cutoff:3.500A) Processing helix chain 'A' and resid 1200 through 1219 Processing helix chain 'A' and resid 1221 through 1241 Processing helix chain 'A' and resid 1249 through 1253 Processing helix chain 'A' and resid 1272 through 1280 Processing helix chain 'A' and resid 1282 through 1299 Processing helix chain 'A' and resid 1301 through 1320 removed outlier: 4.280A pdb=" N ILE A1307 " --> pdb=" O SER A1303 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N LEU A1308 " --> pdb=" O MET A1304 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLY A1309 " --> pdb=" O LEU A1305 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LEU A1310 " --> pdb=" O TYR A1306 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N PHE A1311 " --> pdb=" O ILE A1307 " (cutoff:3.500A) Processing helix chain 'A' and resid 1354 through 1365 Processing helix chain 'A' and resid 1366 through 1370 Processing helix chain 'A' and resid 1375 through 1388 removed outlier: 4.371A pdb=" N ILE A1381 " --> pdb=" O ASP A1377 " (cutoff:3.500A) Processing helix chain 'A' and resid 1389 through 1396 Processing helix chain 'A' and resid 1402 through 1412 removed outlier: 4.210A pdb=" N PHE A1406 " --> pdb=" O LEU A1402 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ARG A1407 " --> pdb=" O GLN A1403 " (cutoff:3.500A) Processing helix chain 'A' and resid 1425 through 1439 Processing helix chain 'A' and resid 1444 through 1457 Processing helix chain 'A' and resid 1463 through 1470 removed outlier: 3.699A pdb=" N PHE A1467 " --> pdb=" O ALA A1463 " (cutoff:3.500A) Processing helix chain 'A' and resid 1503 through 1512 Processing helix chain 'A' and resid 1514 through 1525 Processing helix chain 'A' and resid 1527 through 1529 No H-bonds generated for 'chain 'A' and resid 1527 through 1529' Processing helix chain 'A' and resid 1530 through 1545 Processing helix chain 'A' and resid 1552 through 1560 removed outlier: 3.591A pdb=" N MET A1556 " --> pdb=" O LEU A1552 " (cutoff:3.500A) Processing helix chain 'A' and resid 1581 through 1592 Processing sheet with id=AA1, first strand: chain 'A' and resid 260 through 261 Processing sheet with id=AA2, first strand: chain 'A' and resid 296 through 297 Processing sheet with id=AA3, first strand: chain 'A' and resid 499 through 503 removed outlier: 5.378A pdb=" N THR A 529 " --> pdb=" O SER A 557 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 499 through 503 Processing sheet with id=AA5, first strand: chain 'A' and resid 701 through 702 Processing sheet with id=AA6, first strand: chain 'A' and resid 832 through 837 removed outlier: 5.037A pdb=" N SER A 834 " --> pdb=" O SER A 846 " (cutoff:3.500A) removed outlier: 5.707A pdb=" N SER A 846 " --> pdb=" O SER A 834 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N GLN A 836 " --> pdb=" O SER A 844 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 893 through 897 removed outlier: 7.040A pdb=" N ALA A 877 " --> pdb=" O ASP A1016 " (cutoff:3.500A) removed outlier: 7.837A pdb=" N PHE A1018 " --> pdb=" O ALA A 877 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N ALA A 879 " --> pdb=" O PHE A1018 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 949 through 952 Processing sheet with id=AA9, first strand: chain 'A' and resid 949 through 952 removed outlier: 3.537A pdb=" N THR A1163 " --> pdb=" O SER A 970 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 1417 through 1419 Processing sheet with id=AB2, first strand: chain 'A' and resid 1474 through 1476 removed outlier: 4.758A pdb=" N THR A1598 " --> pdb=" O ILE A1476 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 1486 through 1489 594 hydrogen bonds defined for protein. 1701 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: 3.95 Time building geometry restraints manager: 3.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2240 1.33 - 1.45: 2542 1.45 - 1.57: 5995 1.57 - 1.69: 23 1.69 - 1.81: 95 Bond restraints: 10895 Sorted by residual: bond pdb=" N ILE A1372 " pdb=" CA ILE A1372 " ideal model delta sigma weight residual 1.456 1.493 -0.036 8.70e-03 1.32e+04 1.76e+01 bond pdb=" N ASP A1112 " pdb=" CA ASP A1112 " ideal model delta sigma weight residual 1.457 1.493 -0.036 1.29e-02 6.01e+03 7.80e+00 bond pdb=" N ILE A1333 " pdb=" CA ILE A1333 " ideal model delta sigma weight residual 1.464 1.495 -0.031 1.13e-02 7.83e+03 7.53e+00 bond pdb=" N PHE A1330 " pdb=" CA PHE A1330 " ideal model delta sigma weight residual 1.454 1.486 -0.032 1.17e-02 7.31e+03 7.50e+00 bond pdb=" N ILE A1371 " pdb=" CA ILE A1371 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.25e-02 6.40e+03 7.39e+00 ... (remaining 10890 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.29: 14621 2.29 - 4.57: 131 4.57 - 6.86: 19 6.86 - 9.14: 3 9.14 - 11.43: 1 Bond angle restraints: 14775 Sorted by residual: angle pdb=" C3' A C 8 " pdb=" O3' A C 8 " pdb=" P G C 9 " ideal model delta sigma weight residual 120.20 108.77 11.43 1.50e+00 4.44e-01 5.80e+01 angle pdb=" C3' U C 7 " pdb=" O3' U C 7 " pdb=" P A C 8 " ideal model delta sigma weight residual 120.20 111.31 8.89 1.50e+00 4.44e-01 3.52e+01 angle pdb=" N PRO A 978 " pdb=" CA PRO A 978 " pdb=" C PRO A 978 " ideal model delta sigma weight residual 114.20 107.89 6.31 1.20e+00 6.94e-01 2.76e+01 angle pdb=" N SER A 252 " pdb=" CA SER A 252 " pdb=" C SER A 252 " ideal model delta sigma weight residual 113.28 108.84 4.44 1.22e+00 6.72e-01 1.33e+01 angle pdb=" CA THR A 328 " pdb=" C THR A 328 " pdb=" O THR A 328 " ideal model delta sigma weight residual 121.08 117.99 3.09 8.90e-01 1.26e+00 1.21e+01 ... (remaining 14770 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.25: 6243 32.25 - 64.50: 272 64.50 - 96.75: 17 96.75 - 129.00: 1 129.00 - 161.26: 1 Dihedral angle restraints: 6534 sinusoidal: 2742 harmonic: 3792 Sorted by residual: dihedral pdb=" O4' U C 7 " pdb=" C1' U C 7 " pdb=" N1 U C 7 " pdb=" C2 U C 7 " ideal model delta sinusoidal sigma weight residual 200.00 38.74 161.26 1 1.50e+01 4.44e-03 8.31e+01 dihedral pdb=" CA LEU A1152 " pdb=" C LEU A1152 " pdb=" N GLY A1153 " pdb=" CA GLY A1153 " ideal model delta harmonic sigma weight residual 180.00 160.75 19.25 0 5.00e+00 4.00e-02 1.48e+01 dihedral pdb=" CB GLU A 909 " pdb=" CG GLU A 909 " pdb=" CD GLU A 909 " pdb=" OE1 GLU A 909 " ideal model delta sinusoidal sigma weight residual 0.00 -85.52 85.52 1 3.00e+01 1.11e-03 9.83e+00 ... (remaining 6531 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 1553 0.082 - 0.164: 93 0.164 - 0.246: 6 0.246 - 0.328: 0 0.328 - 0.409: 3 Chirality restraints: 1655 Sorted by residual: chirality pdb=" P U C 7 " pdb=" OP1 U C 7 " pdb=" OP2 U C 7 " pdb=" O5' U C 7 " both_signs ideal model delta sigma weight residual True 2.41 -2.82 -0.41 2.00e-01 2.50e+01 4.19e+00 chirality pdb=" P A C 8 " pdb=" OP1 A C 8 " pdb=" OP2 A C 8 " pdb=" O5' A C 8 " both_signs ideal model delta sigma weight residual True 2.41 -2.78 -0.37 2.00e-01 2.50e+01 3.40e+00 chirality pdb=" P G C 9 " pdb=" OP1 G C 9 " pdb=" OP2 G C 9 " pdb=" O5' G C 9 " both_signs ideal model delta sigma weight residual True 2.41 -2.76 -0.35 2.00e-01 2.50e+01 3.08e+00 ... (remaining 1652 not shown) Planarity restraints: 1813 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 286 " 0.166 9.50e-02 1.11e+02 7.42e-02 3.42e+00 pdb=" NE ARG A 286 " -0.009 2.00e-02 2.50e+03 pdb=" CZ ARG A 286 " -0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG A 286 " -0.000 2.00e-02 2.50e+03 pdb=" NH2 ARG A 286 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A1467 " -0.009 2.00e-02 2.50e+03 1.32e-02 3.06e+00 pdb=" CG PHE A1467 " 0.030 2.00e-02 2.50e+03 pdb=" CD1 PHE A1467 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 PHE A1467 " -0.011 2.00e-02 2.50e+03 pdb=" CE1 PHE A1467 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A1467 " -0.000 2.00e-02 2.50e+03 pdb=" CZ PHE A1467 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 253 " -0.142 9.50e-02 1.11e+02 6.36e-02 2.48e+00 pdb=" NE ARG A 253 " 0.009 2.00e-02 2.50e+03 pdb=" CZ ARG A 253 " 0.001 2.00e-02 2.50e+03 pdb=" NH1 ARG A 253 " 0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG A 253 " -0.005 2.00e-02 2.50e+03 ... (remaining 1810 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1402 2.75 - 3.29: 10249 3.29 - 3.83: 18362 3.83 - 4.36: 22568 4.36 - 4.90: 37901 Nonbonded interactions: 90482 Sorted by model distance: nonbonded pdb=" O ILE A 717 " pdb=" OG1 THR A 721 " model vdw 2.214 3.040 nonbonded pdb=" O GLU A 765 " pdb=" OH TYR A 785 " model vdw 2.215 3.040 nonbonded pdb=" OH TYR A1306 " pdb=" OD1 ASN A1434 " model vdw 2.224 3.040 nonbonded pdb=" OE2 GLU A 738 " pdb=" OG SER A1020 " model vdw 2.229 3.040 nonbonded pdb=" OG SER A 297 " pdb=" O ARG A 532 " model vdw 2.235 3.040 ... (remaining 90477 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.380 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 26.580 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 10895 Z= 0.202 Angle : 0.562 11.428 14775 Z= 0.331 Chirality : 0.044 0.409 1655 Planarity : 0.004 0.074 1813 Dihedral : 16.976 161.255 4076 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 0.88 % Allowed : 21.42 % Favored : 77.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.23), residues: 1269 helix: 1.53 (0.19), residues: 703 sheet: 0.22 (0.49), residues: 103 loop : -0.57 (0.29), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 976 HIS 0.005 0.001 HIS A1413 PHE 0.030 0.002 PHE A1467 TYR 0.012 0.001 TYR A 912 ARG 0.008 0.000 ARG A 707 Details of bonding type rmsd hydrogen bonds : bond 0.14887 ( 580) hydrogen bonds : angle 5.75603 ( 1701) covalent geometry : bond 0.00370 (10895) covalent geometry : angle 0.56170 (14775) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2538 Ramachandran restraints generated. 1269 Oldfield, 0 Emsley, 1269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2538 Ramachandran restraints generated. 1269 Oldfield, 0 Emsley, 1269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 175 time to evaluate : 1.292 Fit side-chains REVERT: A 299 ILE cc_start: 0.7738 (OUTLIER) cc_final: 0.7392 (mp) REVERT: A 520 VAL cc_start: 0.8177 (OUTLIER) cc_final: 0.7962 (t) REVERT: A 951 PHE cc_start: 0.8211 (m-80) cc_final: 0.7916 (m-80) REVERT: A 961 ARG cc_start: 0.7478 (ptm160) cc_final: 0.7216 (ttp80) outliers start: 10 outliers final: 5 residues processed: 183 average time/residue: 1.2046 time to fit residues: 239.1448 Evaluate side-chains 149 residues out of total 1139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 142 time to evaluate : 1.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain A residue 1118 LEU Chi-restraints excluded: chain A residue 1259 THR Chi-restraints excluded: chain A residue 1454 THR Chi-restraints excluded: chain A residue 1481 VAL Chi-restraints excluded: chain A residue 1524 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 108 optimal weight: 0.5980 chunk 97 optimal weight: 0.9980 chunk 54 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 4.9990 chunk 52 optimal weight: 0.9980 chunk 101 optimal weight: 4.9990 chunk 39 optimal weight: 0.9980 chunk 61 optimal weight: 2.9990 chunk 75 optimal weight: 0.5980 chunk 117 optimal weight: 6.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 457 ASN A 598 GLN A 842 HIS A1036 HIS ** A1249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1399 GLN A1413 HIS A1577 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.160978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.128385 restraints weight = 12238.335| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 1.31 r_work: 0.3170 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3059 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.2274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 10895 Z= 0.157 Angle : 0.512 6.339 14775 Z= 0.276 Chirality : 0.039 0.148 1655 Planarity : 0.004 0.042 1813 Dihedral : 9.968 146.969 1576 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 4.13 % Allowed : 20.90 % Favored : 74.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.23), residues: 1269 helix: 1.51 (0.19), residues: 721 sheet: 0.07 (0.50), residues: 104 loop : -0.65 (0.28), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 976 HIS 0.006 0.001 HIS A 861 PHE 0.019 0.002 PHE A1313 TYR 0.015 0.002 TYR A 912 ARG 0.007 0.001 ARG A 707 Details of bonding type rmsd hydrogen bonds : bond 0.04598 ( 580) hydrogen bonds : angle 4.40907 ( 1701) covalent geometry : bond 0.00355 (10895) covalent geometry : angle 0.51212 (14775) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2538 Ramachandran restraints generated. 1269 Oldfield, 0 Emsley, 1269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2538 Ramachandran restraints generated. 1269 Oldfield, 0 Emsley, 1269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 150 time to evaluate : 1.287 Fit side-chains REVERT: A 269 GLU cc_start: 0.7957 (mt-10) cc_final: 0.7664 (mm-30) REVERT: A 729 LYS cc_start: 0.8629 (OUTLIER) cc_final: 0.8318 (mttt) REVERT: A 761 GLU cc_start: 0.7775 (OUTLIER) cc_final: 0.7561 (tp30) REVERT: A 1010 LYS cc_start: 0.8254 (OUTLIER) cc_final: 0.8012 (mttt) REVERT: A 1275 GLU cc_start: 0.7707 (OUTLIER) cc_final: 0.7436 (mp0) REVERT: A 1287 ASN cc_start: 0.7864 (m-40) cc_final: 0.7525 (m-40) REVERT: A 1304 MET cc_start: 0.6983 (tmm) cc_final: 0.6694 (tmm) REVERT: A 1538 MET cc_start: 0.6412 (OUTLIER) cc_final: 0.6016 (mtm) outliers start: 47 outliers final: 11 residues processed: 182 average time/residue: 1.1952 time to fit residues: 235.0701 Evaluate side-chains 161 residues out of total 1139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 145 time to evaluate : 1.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 370 THR Chi-restraints excluded: chain A residue 376 SER Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain A residue 529 THR Chi-restraints excluded: chain A residue 545 THR Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain A residue 709 VAL Chi-restraints excluded: chain A residue 717 ILE Chi-restraints excluded: chain A residue 729 LYS Chi-restraints excluded: chain A residue 761 GLU Chi-restraints excluded: chain A residue 1010 LYS Chi-restraints excluded: chain A residue 1134 VAL Chi-restraints excluded: chain A residue 1275 GLU Chi-restraints excluded: chain A residue 1416 VAL Chi-restraints excluded: chain A residue 1538 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 23 optimal weight: 0.9980 chunk 107 optimal weight: 0.0060 chunk 110 optimal weight: 0.5980 chunk 42 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 chunk 71 optimal weight: 0.6980 chunk 33 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 67 optimal weight: 4.9990 chunk 95 optimal weight: 0.9980 chunk 120 optimal weight: 8.9990 overall best weight: 0.6196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 406 ASN A 457 ASN A 565 ASN ** A 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1036 HIS A1287 ASN A1413 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.160921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.127528 restraints weight = 12271.182| |-----------------------------------------------------------------------------| r_work (start): 0.3324 rms_B_bonded: 1.34 r_work: 0.3144 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3032 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 moved from start: 0.2623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10895 Z= 0.125 Angle : 0.464 6.240 14775 Z= 0.249 Chirality : 0.037 0.145 1655 Planarity : 0.004 0.043 1813 Dihedral : 9.886 146.581 1568 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 3.25 % Allowed : 21.16 % Favored : 75.59 % 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 (0.23), residues: 1269 helix: 1.80 (0.19), residues: 714 sheet: 0.09 (0.50), residues: 104 loop : -0.53 (0.29), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 473 HIS 0.005 0.001 HIS A 742 PHE 0.019 0.002 PHE A1313 TYR 0.012 0.001 TYR A 713 ARG 0.006 0.000 ARG A 961 Details of bonding type rmsd hydrogen bonds : bond 0.04197 ( 580) hydrogen bonds : angle 4.21709 ( 1701) covalent geometry : bond 0.00280 (10895) covalent geometry : angle 0.46375 (14775) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2538 Ramachandran restraints generated. 1269 Oldfield, 0 Emsley, 1269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2538 Ramachandran restraints generated. 1269 Oldfield, 0 Emsley, 1269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 142 time to evaluate : 1.158 Fit side-chains REVERT: A 761 GLU cc_start: 0.7877 (OUTLIER) cc_final: 0.7635 (tp30) REVERT: A 778 GLU cc_start: 0.7572 (OUTLIER) cc_final: 0.7144 (mp0) REVERT: A 1010 LYS cc_start: 0.8194 (OUTLIER) cc_final: 0.7902 (mttt) REVERT: A 1287 ASN cc_start: 0.7836 (m110) cc_final: 0.7528 (m-40) REVERT: A 1304 MET cc_start: 0.7110 (tmm) cc_final: 0.6782 (tmm) REVERT: A 1312 LYS cc_start: 0.7354 (OUTLIER) cc_final: 0.6733 (mmtt) REVERT: A 1538 MET cc_start: 0.6433 (OUTLIER) cc_final: 0.5979 (mtm) outliers start: 37 outliers final: 13 residues processed: 170 average time/residue: 1.2484 time to fit residues: 229.1193 Evaluate side-chains 152 residues out of total 1139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 134 time to evaluate : 1.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 370 THR Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain A residue 529 THR Chi-restraints excluded: chain A residue 545 THR Chi-restraints excluded: chain A residue 709 VAL Chi-restraints excluded: chain A residue 717 ILE Chi-restraints excluded: chain A residue 741 ILE Chi-restraints excluded: chain A residue 761 GLU Chi-restraints excluded: chain A residue 778 GLU Chi-restraints excluded: chain A residue 1010 LYS Chi-restraints excluded: chain A residue 1072 MET Chi-restraints excluded: chain A residue 1134 VAL Chi-restraints excluded: chain A residue 1312 LYS Chi-restraints excluded: chain A residue 1377 ASP Chi-restraints excluded: chain A residue 1416 VAL Chi-restraints excluded: chain A residue 1538 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 70 optimal weight: 4.9990 chunk 47 optimal weight: 0.9990 chunk 108 optimal weight: 0.2980 chunk 74 optimal weight: 0.9980 chunk 125 optimal weight: 10.0000 chunk 45 optimal weight: 0.9990 chunk 73 optimal weight: 0.9990 chunk 67 optimal weight: 4.9990 chunk 78 optimal weight: 0.7980 chunk 36 optimal weight: 0.5980 chunk 50 optimal weight: 1.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 565 ASN ** A 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1036 HIS A1122 GLN A1413 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.159865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.127326 restraints weight = 12194.888| |-----------------------------------------------------------------------------| r_work (start): 0.3323 rms_B_bonded: 1.36 r_work: 0.3123 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3012 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8585 moved from start: 0.2909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10895 Z= 0.138 Angle : 0.477 7.597 14775 Z= 0.255 Chirality : 0.038 0.144 1655 Planarity : 0.004 0.043 1813 Dihedral : 9.837 146.127 1568 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 3.34 % Allowed : 21.60 % Favored : 75.07 % 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: 1.24 (0.23), residues: 1269 helix: 1.82 (0.19), residues: 715 sheet: 0.02 (0.50), residues: 104 loop : -0.58 (0.29), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 473 HIS 0.004 0.001 HIS A 861 PHE 0.021 0.002 PHE A1313 TYR 0.014 0.001 TYR A 912 ARG 0.008 0.000 ARG A 961 Details of bonding type rmsd hydrogen bonds : bond 0.04219 ( 580) hydrogen bonds : angle 4.15945 ( 1701) covalent geometry : bond 0.00311 (10895) covalent geometry : angle 0.47724 (14775) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2538 Ramachandran restraints generated. 1269 Oldfield, 0 Emsley, 1269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2538 Ramachandran restraints generated. 1269 Oldfield, 0 Emsley, 1269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 136 time to evaluate : 1.217 Fit side-chains REVERT: A 761 GLU cc_start: 0.7856 (OUTLIER) cc_final: 0.7629 (tp30) REVERT: A 778 GLU cc_start: 0.7543 (OUTLIER) cc_final: 0.7130 (mp0) REVERT: A 831 LYS cc_start: 0.8446 (OUTLIER) cc_final: 0.7872 (mmmm) REVERT: A 1010 LYS cc_start: 0.8240 (OUTLIER) cc_final: 0.7965 (mttt) REVERT: A 1107 LEU cc_start: 0.8659 (OUTLIER) cc_final: 0.8326 (mt) REVERT: A 1287 ASN cc_start: 0.7813 (m110) cc_final: 0.7494 (m-40) REVERT: A 1304 MET cc_start: 0.7188 (OUTLIER) cc_final: 0.6717 (tmm) REVERT: A 1312 LYS cc_start: 0.7350 (OUTLIER) cc_final: 0.7147 (mmmt) REVERT: A 1538 MET cc_start: 0.6408 (OUTLIER) cc_final: 0.5884 (mtm) outliers start: 38 outliers final: 18 residues processed: 167 average time/residue: 1.1808 time to fit residues: 213.4984 Evaluate side-chains 154 residues out of total 1139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 128 time to evaluate : 1.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 370 THR Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain A residue 529 THR Chi-restraints excluded: chain A residue 545 THR Chi-restraints excluded: chain A residue 709 VAL Chi-restraints excluded: chain A residue 717 ILE Chi-restraints excluded: chain A residue 741 ILE Chi-restraints excluded: chain A residue 761 GLU Chi-restraints excluded: chain A residue 778 GLU Chi-restraints excluded: chain A residue 831 LYS Chi-restraints excluded: chain A residue 873 ARG Chi-restraints excluded: chain A residue 915 ILE Chi-restraints excluded: chain A residue 1010 LYS Chi-restraints excluded: chain A residue 1072 MET Chi-restraints excluded: chain A residue 1107 LEU Chi-restraints excluded: chain A residue 1134 VAL Chi-restraints excluded: chain A residue 1199 LEU Chi-restraints excluded: chain A residue 1227 LEU Chi-restraints excluded: chain A residue 1304 MET Chi-restraints excluded: chain A residue 1312 LYS Chi-restraints excluded: chain A residue 1416 VAL Chi-restraints excluded: chain A residue 1457 THR Chi-restraints excluded: chain A residue 1489 THR Chi-restraints excluded: chain A residue 1538 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 4 optimal weight: 1.9990 chunk 103 optimal weight: 4.9990 chunk 91 optimal weight: 0.6980 chunk 120 optimal weight: 0.3980 chunk 124 optimal weight: 9.9990 chunk 107 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 34 optimal weight: 0.4980 chunk 19 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 96 optimal weight: 0.9980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 565 ASN ** A 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1036 HIS A1413 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.159034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.126023 restraints weight = 12134.281| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 1.31 r_work: 0.3141 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3031 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8578 moved from start: 0.3110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 10895 Z= 0.157 Angle : 0.495 6.516 14775 Z= 0.265 Chirality : 0.039 0.148 1655 Planarity : 0.004 0.044 1813 Dihedral : 9.843 146.033 1568 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 3.86 % Allowed : 21.86 % Favored : 74.28 % 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: 1.17 (0.23), residues: 1269 helix: 1.72 (0.19), residues: 722 sheet: -0.05 (0.50), residues: 104 loop : -0.55 (0.29), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 976 HIS 0.004 0.001 HIS A 861 PHE 0.021 0.002 PHE A1313 TYR 0.014 0.002 TYR A 912 ARG 0.010 0.000 ARG A 961 Details of bonding type rmsd hydrogen bonds : bond 0.04481 ( 580) hydrogen bonds : angle 4.18997 ( 1701) covalent geometry : bond 0.00359 (10895) covalent geometry : angle 0.49487 (14775) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2538 Ramachandran restraints generated. 1269 Oldfield, 0 Emsley, 1269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2538 Ramachandran restraints generated. 1269 Oldfield, 0 Emsley, 1269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 130 time to evaluate : 1.249 Fit side-chains revert: symmetry clash REVERT: A 761 GLU cc_start: 0.7833 (OUTLIER) cc_final: 0.7614 (tp30) REVERT: A 778 GLU cc_start: 0.7498 (OUTLIER) cc_final: 0.7035 (mp0) REVERT: A 1107 LEU cc_start: 0.8590 (OUTLIER) cc_final: 0.8260 (mt) REVERT: A 1275 GLU cc_start: 0.7767 (OUTLIER) cc_final: 0.7567 (mp0) REVERT: A 1287 ASN cc_start: 0.7808 (m110) cc_final: 0.7489 (m-40) REVERT: A 1304 MET cc_start: 0.7182 (OUTLIER) cc_final: 0.6719 (tmm) REVERT: A 1312 LYS cc_start: 0.7315 (OUTLIER) cc_final: 0.7095 (mmmt) REVERT: A 1538 MET cc_start: 0.6449 (OUTLIER) cc_final: 0.5909 (mtm) outliers start: 44 outliers final: 17 residues processed: 164 average time/residue: 1.2117 time to fit residues: 215.0627 Evaluate side-chains 143 residues out of total 1139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 119 time to evaluate : 1.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 370 THR Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain A residue 529 THR Chi-restraints excluded: chain A residue 545 THR Chi-restraints excluded: chain A residue 709 VAL Chi-restraints excluded: chain A residue 717 ILE Chi-restraints excluded: chain A residue 741 ILE Chi-restraints excluded: chain A residue 761 GLU Chi-restraints excluded: chain A residue 778 GLU Chi-restraints excluded: chain A residue 886 GLN Chi-restraints excluded: chain A residue 915 ILE Chi-restraints excluded: chain A residue 1057 LEU Chi-restraints excluded: chain A residue 1072 MET Chi-restraints excluded: chain A residue 1107 LEU Chi-restraints excluded: chain A residue 1134 VAL Chi-restraints excluded: chain A residue 1275 GLU Chi-restraints excluded: chain A residue 1304 MET Chi-restraints excluded: chain A residue 1312 LYS Chi-restraints excluded: chain A residue 1416 VAL Chi-restraints excluded: chain A residue 1457 THR Chi-restraints excluded: chain A residue 1489 THR Chi-restraints excluded: chain A residue 1538 MET Chi-restraints excluded: chain A residue 1593 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 45 optimal weight: 0.6980 chunk 83 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 103 optimal weight: 4.9990 chunk 91 optimal weight: 0.9980 chunk 48 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 24 optimal weight: 0.5980 chunk 104 optimal weight: 4.9990 chunk 9 optimal weight: 3.9990 chunk 127 optimal weight: 0.7980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1036 HIS A1122 GLN A1413 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.158593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.125424 restraints weight = 12203.050| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 1.30 r_work: 0.3136 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3024 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8589 moved from start: 0.3214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 10895 Z= 0.167 Angle : 0.512 9.471 14775 Z= 0.274 Chirality : 0.040 0.229 1655 Planarity : 0.004 0.045 1813 Dihedral : 9.861 145.516 1568 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 3.60 % Allowed : 22.21 % Favored : 74.19 % 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 (0.23), residues: 1269 helix: 1.68 (0.19), residues: 722 sheet: -0.06 (0.49), residues: 106 loop : -0.59 (0.29), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 976 HIS 0.005 0.001 HIS A 861 PHE 0.017 0.002 PHE A1313 TYR 0.015 0.002 TYR A 912 ARG 0.011 0.001 ARG A 961 Details of bonding type rmsd hydrogen bonds : bond 0.04592 ( 580) hydrogen bonds : angle 4.20051 ( 1701) covalent geometry : bond 0.00387 (10895) covalent geometry : angle 0.51226 (14775) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2538 Ramachandran restraints generated. 1269 Oldfield, 0 Emsley, 1269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2538 Ramachandran restraints generated. 1269 Oldfield, 0 Emsley, 1269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 126 time to evaluate : 1.224 Fit side-chains REVERT: A 349 MET cc_start: 0.8733 (mmt) cc_final: 0.8506 (mmp) REVERT: A 761 GLU cc_start: 0.7820 (OUTLIER) cc_final: 0.7585 (tp30) REVERT: A 778 GLU cc_start: 0.7526 (OUTLIER) cc_final: 0.7068 (mp0) REVERT: A 831 LYS cc_start: 0.8361 (OUTLIER) cc_final: 0.7733 (mmmm) REVERT: A 1107 LEU cc_start: 0.8596 (OUTLIER) cc_final: 0.8254 (mt) REVERT: A 1287 ASN cc_start: 0.7810 (m110) cc_final: 0.7454 (m-40) REVERT: A 1304 MET cc_start: 0.7203 (OUTLIER) cc_final: 0.6676 (tmm) REVERT: A 1305 LEU cc_start: 0.6676 (OUTLIER) cc_final: 0.6383 (pp) REVERT: A 1538 MET cc_start: 0.6421 (OUTLIER) cc_final: 0.5852 (mtm) outliers start: 41 outliers final: 21 residues processed: 158 average time/residue: 1.1216 time to fit residues: 192.9291 Evaluate side-chains 149 residues out of total 1139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 121 time to evaluate : 1.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 363 GLN Chi-restraints excluded: chain A residue 370 THR Chi-restraints excluded: chain A residue 376 SER Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain A residue 529 THR Chi-restraints excluded: chain A residue 545 THR Chi-restraints excluded: chain A residue 709 VAL Chi-restraints excluded: chain A residue 717 ILE Chi-restraints excluded: chain A residue 741 ILE Chi-restraints excluded: chain A residue 761 GLU Chi-restraints excluded: chain A residue 770 MET Chi-restraints excluded: chain A residue 778 GLU Chi-restraints excluded: chain A residue 831 LYS Chi-restraints excluded: chain A residue 886 GLN Chi-restraints excluded: chain A residue 915 ILE Chi-restraints excluded: chain A residue 977 SER Chi-restraints excluded: chain A residue 1057 LEU Chi-restraints excluded: chain A residue 1072 MET Chi-restraints excluded: chain A residue 1107 LEU Chi-restraints excluded: chain A residue 1134 VAL Chi-restraints excluded: chain A residue 1304 MET Chi-restraints excluded: chain A residue 1305 LEU Chi-restraints excluded: chain A residue 1416 VAL Chi-restraints excluded: chain A residue 1457 THR Chi-restraints excluded: chain A residue 1489 THR Chi-restraints excluded: chain A residue 1538 MET Chi-restraints excluded: chain A residue 1593 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 9 optimal weight: 3.9990 chunk 58 optimal weight: 1.9990 chunk 109 optimal weight: 0.6980 chunk 125 optimal weight: 0.9980 chunk 128 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 100 optimal weight: 2.9990 chunk 85 optimal weight: 0.6980 chunk 84 optimal weight: 1.9990 chunk 62 optimal weight: 0.8980 chunk 11 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1036 HIS A1413 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.159158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.126030 restraints weight = 12287.296| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 1.27 r_work: 0.3145 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3033 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8579 moved from start: 0.3276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10895 Z= 0.149 Angle : 0.501 8.407 14775 Z= 0.267 Chirality : 0.039 0.154 1655 Planarity : 0.004 0.049 1813 Dihedral : 9.840 145.414 1568 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.81 % Allowed : 22.91 % Favored : 74.28 % 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: 1.23 (0.23), residues: 1269 helix: 1.76 (0.19), residues: 721 sheet: -0.02 (0.49), residues: 106 loop : -0.52 (0.29), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 976 HIS 0.004 0.001 HIS A1036 PHE 0.021 0.002 PHE A1467 TYR 0.015 0.001 TYR A 912 ARG 0.011 0.001 ARG A 961 Details of bonding type rmsd hydrogen bonds : bond 0.04358 ( 580) hydrogen bonds : angle 4.15789 ( 1701) covalent geometry : bond 0.00342 (10895) covalent geometry : angle 0.50116 (14775) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2538 Ramachandran restraints generated. 1269 Oldfield, 0 Emsley, 1269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2538 Ramachandran restraints generated. 1269 Oldfield, 0 Emsley, 1269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 127 time to evaluate : 1.068 Fit side-chains REVERT: A 349 MET cc_start: 0.8735 (mmt) cc_final: 0.8498 (mmp) REVERT: A 761 GLU cc_start: 0.7860 (OUTLIER) cc_final: 0.7604 (tp30) REVERT: A 778 GLU cc_start: 0.7543 (OUTLIER) cc_final: 0.7077 (mp0) REVERT: A 810 ASN cc_start: 0.7226 (m-40) cc_final: 0.6925 (m-40) REVERT: A 1107 LEU cc_start: 0.8584 (OUTLIER) cc_final: 0.8240 (mt) REVERT: A 1287 ASN cc_start: 0.7796 (m110) cc_final: 0.7491 (m-40) REVERT: A 1304 MET cc_start: 0.7283 (OUTLIER) cc_final: 0.6776 (tmm) REVERT: A 1305 LEU cc_start: 0.6697 (OUTLIER) cc_final: 0.6454 (pp) REVERT: A 1312 LYS cc_start: 0.7416 (OUTLIER) cc_final: 0.7196 (mmmt) REVERT: A 1369 ASP cc_start: 0.7506 (t0) cc_final: 0.7278 (t0) REVERT: A 1372 ILE cc_start: 0.7810 (OUTLIER) cc_final: 0.7367 (mt) REVERT: A 1538 MET cc_start: 0.6446 (OUTLIER) cc_final: 0.5862 (mtm) outliers start: 32 outliers final: 18 residues processed: 151 average time/residue: 1.1355 time to fit residues: 186.3050 Evaluate side-chains 149 residues out of total 1139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 123 time to evaluate : 1.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 370 THR Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 376 SER Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain A residue 529 THR Chi-restraints excluded: chain A residue 545 THR Chi-restraints excluded: chain A residue 709 VAL Chi-restraints excluded: chain A residue 717 ILE Chi-restraints excluded: chain A residue 741 ILE Chi-restraints excluded: chain A residue 761 GLU Chi-restraints excluded: chain A residue 778 GLU Chi-restraints excluded: chain A residue 915 ILE Chi-restraints excluded: chain A residue 1057 LEU Chi-restraints excluded: chain A residue 1072 MET Chi-restraints excluded: chain A residue 1107 LEU Chi-restraints excluded: chain A residue 1134 VAL Chi-restraints excluded: chain A residue 1304 MET Chi-restraints excluded: chain A residue 1305 LEU Chi-restraints excluded: chain A residue 1312 LYS Chi-restraints excluded: chain A residue 1372 ILE Chi-restraints excluded: chain A residue 1416 VAL Chi-restraints excluded: chain A residue 1457 THR Chi-restraints excluded: chain A residue 1489 THR Chi-restraints excluded: chain A residue 1538 MET Chi-restraints excluded: chain A residue 1593 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 54 optimal weight: 2.9990 chunk 121 optimal weight: 0.9980 chunk 74 optimal weight: 1.9990 chunk 108 optimal weight: 0.7980 chunk 95 optimal weight: 0.9990 chunk 97 optimal weight: 0.2980 chunk 73 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1036 HIS A1122 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.158081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.125359 restraints weight = 12098.982| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 1.29 r_work: 0.3118 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3005 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8613 moved from start: 0.3324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 10895 Z= 0.169 Angle : 0.526 9.583 14775 Z= 0.280 Chirality : 0.040 0.206 1655 Planarity : 0.004 0.053 1813 Dihedral : 9.873 145.017 1568 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 3.42 % Allowed : 22.56 % Favored : 74.01 % 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: 1.16 (0.23), residues: 1269 helix: 1.71 (0.19), residues: 721 sheet: -0.06 (0.49), residues: 106 loop : -0.55 (0.29), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 976 HIS 0.007 0.001 HIS A1413 PHE 0.017 0.002 PHE A1143 TYR 0.015 0.002 TYR A 912 ARG 0.013 0.001 ARG A 707 Details of bonding type rmsd hydrogen bonds : bond 0.04624 ( 580) hydrogen bonds : angle 4.20233 ( 1701) covalent geometry : bond 0.00391 (10895) covalent geometry : angle 0.52644 (14775) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2538 Ramachandran restraints generated. 1269 Oldfield, 0 Emsley, 1269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2538 Ramachandran restraints generated. 1269 Oldfield, 0 Emsley, 1269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 127 time to evaluate : 1.137 Fit side-chains REVERT: A 349 MET cc_start: 0.8763 (mmt) cc_final: 0.8539 (mmp) REVERT: A 761 GLU cc_start: 0.7868 (OUTLIER) cc_final: 0.7598 (tp30) REVERT: A 778 GLU cc_start: 0.7626 (OUTLIER) cc_final: 0.7167 (mp0) REVERT: A 810 ASN cc_start: 0.7268 (m-40) cc_final: 0.6972 (m-40) REVERT: A 831 LYS cc_start: 0.8353 (OUTLIER) cc_final: 0.7750 (mmmm) REVERT: A 1107 LEU cc_start: 0.8614 (OUTLIER) cc_final: 0.8268 (mt) REVERT: A 1287 ASN cc_start: 0.7815 (m110) cc_final: 0.7507 (m-40) REVERT: A 1304 MET cc_start: 0.7284 (OUTLIER) cc_final: 0.6762 (tmm) REVERT: A 1305 LEU cc_start: 0.6740 (OUTLIER) cc_final: 0.6514 (pp) REVERT: A 1369 ASP cc_start: 0.7587 (t0) cc_final: 0.7324 (t0) REVERT: A 1538 MET cc_start: 0.6423 (OUTLIER) cc_final: 0.5831 (mtm) outliers start: 39 outliers final: 24 residues processed: 158 average time/residue: 1.1396 time to fit residues: 195.5451 Evaluate side-chains 155 residues out of total 1139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 124 time to evaluate : 1.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 363 GLN Chi-restraints excluded: chain A residue 370 THR Chi-restraints excluded: chain A residue 376 SER Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain A residue 529 THR Chi-restraints excluded: chain A residue 545 THR Chi-restraints excluded: chain A residue 709 VAL Chi-restraints excluded: chain A residue 717 ILE Chi-restraints excluded: chain A residue 741 ILE Chi-restraints excluded: chain A residue 761 GLU Chi-restraints excluded: chain A residue 770 MET Chi-restraints excluded: chain A residue 778 GLU Chi-restraints excluded: chain A residue 831 LYS Chi-restraints excluded: chain A residue 886 GLN Chi-restraints excluded: chain A residue 915 ILE Chi-restraints excluded: chain A residue 977 SER Chi-restraints excluded: chain A residue 1057 LEU Chi-restraints excluded: chain A residue 1072 MET Chi-restraints excluded: chain A residue 1107 LEU Chi-restraints excluded: chain A residue 1134 VAL Chi-restraints excluded: chain A residue 1227 LEU Chi-restraints excluded: chain A residue 1304 MET Chi-restraints excluded: chain A residue 1305 LEU Chi-restraints excluded: chain A residue 1377 ASP Chi-restraints excluded: chain A residue 1416 VAL Chi-restraints excluded: chain A residue 1457 THR Chi-restraints excluded: chain A residue 1489 THR Chi-restraints excluded: chain A residue 1538 MET Chi-restraints excluded: chain A residue 1577 ASN Chi-restraints excluded: chain A residue 1593 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 88 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 57 optimal weight: 0.0970 chunk 13 optimal weight: 3.9990 chunk 7 optimal weight: 0.7980 chunk 125 optimal weight: 4.9990 chunk 24 optimal weight: 1.9990 chunk 43 optimal weight: 0.1980 chunk 116 optimal weight: 4.9990 chunk 91 optimal weight: 0.5980 chunk 77 optimal weight: 0.0070 overall best weight: 0.3396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1036 HIS A1413 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.162058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.129393 restraints weight = 12308.170| |-----------------------------------------------------------------------------| r_work (start): 0.3349 rms_B_bonded: 1.30 r_work: 0.3171 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3058 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8551 moved from start: 0.3393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 10895 Z= 0.105 Angle : 0.477 9.958 14775 Z= 0.251 Chirality : 0.037 0.175 1655 Planarity : 0.004 0.057 1813 Dihedral : 9.731 146.422 1568 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.11 % Allowed : 23.71 % Favored : 74.19 % 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 (0.23), residues: 1269 helix: 1.95 (0.19), residues: 721 sheet: 0.48 (0.53), residues: 94 loop : -0.45 (0.29), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 976 HIS 0.004 0.001 HIS A1036 PHE 0.026 0.001 PHE A1467 TYR 0.015 0.001 TYR A 713 ARG 0.015 0.001 ARG A 961 Details of bonding type rmsd hydrogen bonds : bond 0.03634 ( 580) hydrogen bonds : angle 4.00703 ( 1701) covalent geometry : bond 0.00225 (10895) covalent geometry : angle 0.47722 (14775) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2538 Ramachandran restraints generated. 1269 Oldfield, 0 Emsley, 1269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2538 Ramachandran restraints generated. 1269 Oldfield, 0 Emsley, 1269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 132 time to evaluate : 1.161 Fit side-chains REVERT: A 349 MET cc_start: 0.8707 (mmt) cc_final: 0.8486 (mmp) REVERT: A 810 ASN cc_start: 0.7205 (m-40) cc_final: 0.6918 (m-40) REVERT: A 831 LYS cc_start: 0.8273 (OUTLIER) cc_final: 0.7706 (mmmm) REVERT: A 1125 GLN cc_start: 0.8076 (pt0) cc_final: 0.7816 (mm110) REVERT: A 1287 ASN cc_start: 0.7778 (m110) cc_final: 0.7417 (m-40) REVERT: A 1304 MET cc_start: 0.7246 (tmm) cc_final: 0.6718 (tmm) REVERT: A 1369 ASP cc_start: 0.7541 (t0) cc_final: 0.7296 (t0) REVERT: A 1538 MET cc_start: 0.6340 (OUTLIER) cc_final: 0.5737 (mtm) outliers start: 24 outliers final: 13 residues processed: 150 average time/residue: 1.2512 time to fit residues: 202.7426 Evaluate side-chains 145 residues out of total 1139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 130 time to evaluate : 1.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain A residue 529 THR Chi-restraints excluded: chain A residue 545 THR Chi-restraints excluded: chain A residue 709 VAL Chi-restraints excluded: chain A residue 741 ILE Chi-restraints excluded: chain A residue 831 LYS Chi-restraints excluded: chain A residue 915 ILE Chi-restraints excluded: chain A residue 977 SER Chi-restraints excluded: chain A residue 1057 LEU Chi-restraints excluded: chain A residue 1072 MET Chi-restraints excluded: chain A residue 1134 VAL Chi-restraints excluded: chain A residue 1416 VAL Chi-restraints excluded: chain A residue 1457 THR Chi-restraints excluded: chain A residue 1538 MET Chi-restraints excluded: chain A residue 1577 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 33 optimal weight: 0.0970 chunk 17 optimal weight: 2.9990 chunk 91 optimal weight: 0.5980 chunk 4 optimal weight: 2.9990 chunk 51 optimal weight: 0.6980 chunk 19 optimal weight: 1.9990 chunk 3 optimal weight: 0.7980 chunk 5 optimal weight: 0.9980 chunk 56 optimal weight: 4.9990 chunk 32 optimal weight: 0.6980 chunk 24 optimal weight: 3.9990 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1036 HIS A1122 GLN A1413 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.160946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.128151 restraints weight = 12216.795| |-----------------------------------------------------------------------------| r_work (start): 0.3339 rms_B_bonded: 1.30 r_work: 0.3141 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3028 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8585 moved from start: 0.3394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10895 Z= 0.122 Angle : 0.494 9.790 14775 Z= 0.259 Chirality : 0.038 0.166 1655 Planarity : 0.004 0.061 1813 Dihedral : 9.761 146.381 1568 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.67 % Allowed : 24.06 % Favored : 74.28 % 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: 1.51 (0.23), residues: 1269 helix: 1.95 (0.19), residues: 721 sheet: 0.50 (0.53), residues: 94 loop : -0.42 (0.29), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 976 HIS 0.004 0.001 HIS A1036 PHE 0.017 0.001 PHE A1117 TYR 0.015 0.001 TYR A 912 ARG 0.014 0.001 ARG A 961 Details of bonding type rmsd hydrogen bonds : bond 0.03921 ( 580) hydrogen bonds : angle 4.02842 ( 1701) covalent geometry : bond 0.00274 (10895) covalent geometry : angle 0.49355 (14775) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2538 Ramachandran restraints generated. 1269 Oldfield, 0 Emsley, 1269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2538 Ramachandran restraints generated. 1269 Oldfield, 0 Emsley, 1269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 129 time to evaluate : 1.299 Fit side-chains REVERT: A 349 MET cc_start: 0.8739 (mmt) cc_final: 0.8527 (mmp) REVERT: A 831 LYS cc_start: 0.8259 (OUTLIER) cc_final: 0.7712 (mmmm) REVERT: A 1125 GLN cc_start: 0.8134 (pt0) cc_final: 0.7835 (mm-40) REVERT: A 1287 ASN cc_start: 0.7826 (m110) cc_final: 0.7437 (m-40) REVERT: A 1304 MET cc_start: 0.7251 (tmm) cc_final: 0.6719 (tmm) REVERT: A 1369 ASP cc_start: 0.7559 (t0) cc_final: 0.7310 (t0) REVERT: A 1538 MET cc_start: 0.6336 (OUTLIER) cc_final: 0.5733 (mtm) outliers start: 19 outliers final: 15 residues processed: 143 average time/residue: 1.2144 time to fit residues: 188.9079 Evaluate side-chains 147 residues out of total 1139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 130 time to evaluate : 1.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain A residue 529 THR Chi-restraints excluded: chain A residue 545 THR Chi-restraints excluded: chain A residue 709 VAL Chi-restraints excluded: chain A residue 717 ILE Chi-restraints excluded: chain A residue 741 ILE Chi-restraints excluded: chain A residue 770 MET Chi-restraints excluded: chain A residue 831 LYS Chi-restraints excluded: chain A residue 915 ILE Chi-restraints excluded: chain A residue 977 SER Chi-restraints excluded: chain A residue 1057 LEU Chi-restraints excluded: chain A residue 1072 MET Chi-restraints excluded: chain A residue 1134 VAL Chi-restraints excluded: chain A residue 1416 VAL Chi-restraints excluded: chain A residue 1457 THR Chi-restraints excluded: chain A residue 1538 MET Chi-restraints excluded: chain A residue 1577 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 21 optimal weight: 0.8980 chunk 56 optimal weight: 0.7980 chunk 106 optimal weight: 0.5980 chunk 116 optimal weight: 3.9990 chunk 80 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 60 optimal weight: 0.9980 chunk 76 optimal weight: 0.5980 chunk 73 optimal weight: 2.9990 chunk 112 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1036 HIS A1122 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.160336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.126868 restraints weight = 12139.811| |-----------------------------------------------------------------------------| r_work (start): 0.3317 rms_B_bonded: 1.30 r_work: 0.3145 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3031 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 moved from start: 0.3433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10895 Z= 0.141 Angle : 0.514 10.534 14775 Z= 0.269 Chirality : 0.039 0.151 1655 Planarity : 0.004 0.060 1813 Dihedral : 9.805 145.918 1568 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.02 % Allowed : 23.97 % Favored : 74.01 % 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: 1.42 (0.23), residues: 1269 helix: 1.89 (0.19), residues: 720 sheet: 0.48 (0.53), residues: 94 loop : -0.46 (0.29), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 976 HIS 0.005 0.001 HIS A1036 PHE 0.029 0.002 PHE A1467 TYR 0.015 0.001 TYR A 912 ARG 0.014 0.001 ARG A 961 Details of bonding type rmsd hydrogen bonds : bond 0.04218 ( 580) hydrogen bonds : angle 4.08320 ( 1701) covalent geometry : bond 0.00323 (10895) covalent geometry : angle 0.51356 (14775) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7723.42 seconds wall clock time: 133 minutes 46.17 seconds (8026.17 seconds total)