Starting phenix.real_space_refine on Fri Jul 3 00:33:11 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9lgc_63061/07_2026/9lgc_63061_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9lgc_63061/07_2026/9lgc_63061.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.95 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9lgc_63061/07_2026/9lgc_63061_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9lgc_63061/07_2026/9lgc_63061_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9lgc_63061/07_2026/9lgc_63061.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9lgc_63061/07_2026/9lgc_63061.map" } resolution = 2.95 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.102 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: 4 Type Number sf(0) Gaussians S 57 5.16 5 C 6991 2.51 5 N 1767 2.21 5 O 1909 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10724 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 10584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1333, 10584 Classifications: {'peptide': 1333} Link IDs: {'PTRANS': 49, 'TRANS': 1283} Chain breaks: 8 Chain: "A" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 140 Unusual residues: {'GSH': 1, 'R1Q': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 2.05, per 1000 atoms: 0.19 Number of scatterers: 10724 At special positions: 0 Unit cell: (81, 119, 150, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 57 16.00 O 1909 8.00 N 1767 7.00 C 6991 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.70 Conformation dependent library (CDL) restraints added in 286.1 milliseconds 2630 Ramachandran restraints generated. 1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2522 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 4 sheets defined 72.8% alpha, 5.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.35 Creating SS restraints... Processing helix chain 'A' and resid 17 through 22 removed outlier: 3.653A pdb=" N THR A 21 " --> pdb=" O GLU A 17 " (cutoff:3.500A) Processing helix chain 'A' and resid 30 through 60 removed outlier: 3.960A pdb=" N LEU A 38 " --> pdb=" O GLN A 34 " (cutoff:3.500A) removed outlier: 5.027A pdb=" N VAL A 39 " --> pdb=" O ASN A 35 " (cutoff:3.500A) Proline residue: A 42 - end of helix Proline residue: A 51 - end of helix removed outlier: 3.866A pdb=" N LEU A 55 " --> pdb=" O PRO A 51 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N TYR A 56 " --> pdb=" O PHE A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 68 through 94 removed outlier: 3.697A pdb=" N LEU A 89 " --> pdb=" O CYS A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 130 removed outlier: 3.578A pdb=" N VAL A 108 " --> pdb=" O PRO A 104 " (cutoff:3.500A) Proline residue: A 110 - end of helix Processing helix chain 'A' and resid 135 through 160 Processing helix chain 'A' and resid 171 through 191 removed outlier: 3.544A pdb=" N PHE A 175 " --> pdb=" O ARG A 171 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N PHE A 191 " --> pdb=" O VAL A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 220 Processing helix chain 'A' and resid 224 through 234 Processing helix chain 'A' and resid 249 through 267 Proline residue: A 255 - end of helix Processing helix chain 'A' and resid 312 through 321 Processing helix chain 'A' and resid 321 through 355 removed outlier: 4.360A pdb=" N MET A 327 " --> pdb=" O PRO A 323 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N SER A 328 " --> pdb=" O TYR A 324 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLY A 342 " --> pdb=" O MET A 338 " (cutoff:3.500A) Proline residue: A 343 - end of helix Processing helix chain 'A' and resid 359 through 410 removed outlier: 3.897A pdb=" N GLY A 363 " --> pdb=" O PRO A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 419 Processing helix chain 'A' and resid 420 through 441 removed outlier: 3.944A pdb=" N ASP A 430 " --> pdb=" O LEU A 426 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N ALA A 431 " --> pdb=" O MET A 427 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N TYR A 440 " --> pdb=" O ASP A 436 " (cutoff:3.500A) Processing helix chain 'A' and resid 442 through 463 Proline residue: A 448 - end of helix Processing helix chain 'A' and resid 465 through 510 removed outlier: 4.277A pdb=" N GLY A 469 " --> pdb=" O SER A 465 " (cutoff:3.500A) Proline residue: A 478 - end of helix Processing helix chain 'A' and resid 511 through 518 Processing helix chain 'A' and resid 520 through 572 Proline residue: A 557 - end of helix removed outlier: 3.846A pdb=" N ASP A 572 " --> pdb=" O TYR A 568 " (cutoff:3.500A) Processing helix chain 'A' and resid 578 through 621 removed outlier: 3.725A pdb=" N VAL A 584 " --> pdb=" O GLN A 580 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N SER A 585 " --> pdb=" O LYS A 581 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N PHE A 594 " --> pdb=" O ASN A 590 " (cutoff:3.500A) Proline residue: A 595 - end of helix Proline residue: A 600 - end of helix Processing helix chain 'A' and resid 626 through 630 removed outlier: 4.404A pdb=" N ILE A 630 " --> pdb=" O PRO A 627 " (cutoff:3.500A) Processing helix chain 'A' and resid 683 through 692 removed outlier: 3.551A pdb=" N LEU A 688 " --> pdb=" O LYS A 684 " (cutoff:3.500A) Processing helix chain 'A' and resid 721 through 728 Processing helix chain 'A' and resid 733 through 744 removed outlier: 4.370A pdb=" N GLU A 742 " --> pdb=" O LYS A 738 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ALA A 743 " --> pdb=" O ALA A 739 " (cutoff:3.500A) Processing helix chain 'A' and resid 746 through 753 Processing helix chain 'A' and resid 755 through 759 removed outlier: 3.659A pdb=" N ARG A 758 " --> pdb=" O SER A 755 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N THR A 759 " --> pdb=" O GLY A 756 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 755 through 759' Processing helix chain 'A' and resid 769 through 785 Processing helix chain 'A' and resid 799 through 810 Processing helix chain 'A' and resid 831 through 835 Processing helix chain 'A' and resid 851 through 859 Processing helix chain 'A' and resid 860 through 869 removed outlier: 4.015A pdb=" N TYR A 869 " --> pdb=" O PHE A 865 " (cutoff:3.500A) Processing helix chain 'A' and resid 958 through 970 removed outlier: 3.901A pdb=" N TYR A 962 " --> pdb=" O LYS A 958 " (cutoff:3.500A) Processing helix chain 'A' and resid 970 through 1000 Processing helix chain 'A' and resid 1011 through 1058 Processing helix chain 'A' and resid 1059 through 1066 removed outlier: 3.638A pdb=" N PHE A1063 " --> pdb=" O PRO A1059 " (cutoff:3.500A) Processing helix chain 'A' and resid 1067 through 1076 removed outlier: 3.610A pdb=" N LEU A1071 " --> pdb=" O PRO A1067 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N PHE A1075 " --> pdb=" O LEU A1071 " (cutoff:3.500A) Processing helix chain 'A' and resid 1077 through 1085 Processing helix chain 'A' and resid 1085 through 1111 removed outlier: 4.114A pdb=" N VAL A1100 " --> pdb=" O SER A1096 " (cutoff:3.500A) Processing helix chain 'A' and resid 1112 through 1116 Processing helix chain 'A' and resid 1117 through 1160 removed outlier: 4.825A pdb=" N GLN A1138 " --> pdb=" O ALA A1134 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N SER A1148 " --> pdb=" O SER A1144 " (cutoff:3.500A) Proline residue: A1149 - end of helix Processing helix chain 'A' and resid 1160 through 1167 Processing helix chain 'A' and resid 1169 through 1220 Proline residue: A1190 - end of helix Processing helix chain 'A' and resid 1221 through 1224 Processing helix chain 'A' and resid 1225 through 1264 removed outlier: 4.236A pdb=" N THR A1241 " --> pdb=" O LEU A1237 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N ASN A1244 " --> pdb=" O THR A1240 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N TRP A1245 " --> pdb=" O THR A1241 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N VAL A1258 " --> pdb=" O GLU A1254 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N ALA A1259 " --> pdb=" O THR A1255 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N VAL A1260 " --> pdb=" O ASN A1256 " (cutoff:3.500A) Processing helix chain 'A' and resid 1265 through 1268 removed outlier: 4.046A pdb=" N GLU A1268 " --> pdb=" O GLU A1265 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1265 through 1268' Processing helix chain 'A' and resid 1331 through 1340 removed outlier: 3.670A pdb=" N THR A1336 " --> pdb=" O LYS A1332 " (cutoff:3.500A) Processing helix chain 'A' and resid 1361 through 1368 Processing helix chain 'A' and resid 1382 through 1388 Processing helix chain 'A' and resid 1394 through 1405 Processing helix chain 'A' and resid 1407 through 1412 Processing helix chain 'A' and resid 1416 through 1420 removed outlier: 3.863A pdb=" N HIS A1420 " --> pdb=" O LYS A1417 " (cutoff:3.500A) Processing helix chain 'A' and resid 1430 through 1446 removed outlier: 3.638A pdb=" N LYS A1446 " --> pdb=" O ALA A1442 " (cutoff:3.500A) Processing helix chain 'A' and resid 1463 through 1474 removed outlier: 3.975A pdb=" N GLN A1474 " --> pdb=" O THR A1470 " (cutoff:3.500A) Processing helix chain 'A' and resid 1486 through 1493 removed outlier: 3.878A pdb=" N ILE A1490 " --> pdb=" O ARG A1486 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N ASP A1492 " --> pdb=" O ASN A1488 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N TYR A1493 " --> pdb=" O THR A1489 " (cutoff:3.500A) Processing helix chain 'A' and resid 1509 through 1514 Processing sheet with id=AA1, first strand: chain 'A' and resid 661 through 668 removed outlier: 7.038A pdb=" N HIS A 662 " --> pdb=" O THR A 650 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N THR A 650 " --> pdb=" O HIS A 662 " (cutoff:3.500A) removed outlier: 5.592A pdb=" N ILE A 664 " --> pdb=" O ASN A 648 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N VAL A 646 " --> pdb=" O VAL A 702 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N VAL A 702 " --> pdb=" O VAL A 646 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N ASN A 648 " --> pdb=" O GLY A 700 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLY A 700 " --> pdb=" O ASN A 648 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N THR A 650 " --> pdb=" O VAL A 698 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 708 through 711 removed outlier: 6.265A pdb=" N TYR A 789 " --> pdb=" O LEU A 823 " (cutoff:3.500A) removed outlier: 7.707A pdb=" N VAL A 825 " --> pdb=" O TYR A 789 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N LEU A 791 " --> pdb=" O VAL A 825 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N LEU A 673 " --> pdb=" O VAL A 837 " (cutoff:3.500A) removed outlier: 7.344A pdb=" N ILE A 839 " --> pdb=" O LEU A 673 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N ALA A 675 " --> pdb=" O ILE A 839 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1309 through 1316 removed outlier: 5.508A pdb=" N LYS A1310 " --> pdb=" O LEU A1299 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N LEU A1299 " --> pdb=" O LYS A1310 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N VAL A1314 " --> pdb=" O ARG A1295 " (cutoff:3.500A) removed outlier: 4.966A pdb=" N ARG A1295 " --> pdb=" O VAL A1314 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N ILE A1316 " --> pdb=" O GLU A1293 " (cutoff:3.500A) removed outlier: 5.197A pdb=" N GLU A1293 " --> pdb=" O ILE A1316 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1369 through 1372 removed outlier: 6.390A pdb=" N LEU A1450 " --> pdb=" O LEU A1481 " (cutoff:3.500A) removed outlier: 8.029A pdb=" N ILE A1483 " --> pdb=" O LEU A1450 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N LEU A1452 " --> pdb=" O ILE A1483 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N GLY A1323 " --> pdb=" O ILE A1497 " (cutoff:3.500A) removed outlier: 7.676A pdb=" N LEU A1499 " --> pdb=" O GLY A1323 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N VAL A1325 " --> pdb=" O LEU A1499 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N VAL A1496 " --> pdb=" O TRP A1507 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N TRP A1507 " --> pdb=" O VAL A1496 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N VAL A1498 " --> pdb=" O GLN A1505 " (cutoff:3.500A) 706 hydrogen bonds defined for protein. 2082 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: 1.58 Time building geometry restraints manager: 0.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 1681 1.30 - 1.43: 2924 1.43 - 1.56: 6275 1.56 - 1.69: 3 1.69 - 1.82: 92 Bond restraints: 10975 Sorted by residual: bond pdb=" N VAL A1289 " pdb=" CA VAL A1289 " ideal model delta sigma weight residual 1.456 1.493 -0.037 9.50e-03 1.11e+04 1.48e+01 bond pdb=" N PHE A 594 " pdb=" CA PHE A 594 " ideal model delta sigma weight residual 1.463 1.488 -0.025 6.90e-03 2.10e+04 1.32e+01 bond pdb=" N ILE A1355 " pdb=" CA ILE A1355 " ideal model delta sigma weight residual 1.458 1.496 -0.038 1.19e-02 7.06e+03 9.95e+00 bond pdb=" C31 R1Q A1602 " pdb=" C32 R1Q A1602 " ideal model delta sigma weight residual 1.568 1.507 0.061 2.00e-02 2.50e+03 9.37e+00 bond pdb=" N THR A 24 " pdb=" CA THR A 24 " ideal model delta sigma weight residual 1.454 1.493 -0.038 1.27e-02 6.20e+03 9.05e+00 ... (remaining 10970 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.15: 14853 4.15 - 8.30: 68 8.30 - 12.45: 7 12.45 - 16.61: 0 16.61 - 20.76: 2 Bond angle restraints: 14930 Sorted by residual: angle pdb=" C05 R1Q A1603 " pdb=" C04 R1Q A1603 " pdb=" N03 R1Q A1603 " ideal model delta sigma weight residual 118.51 97.75 20.76 3.00e+00 1.11e-01 4.79e+01 angle pdb=" C05 R1Q A1602 " pdb=" C04 R1Q A1602 " pdb=" N03 R1Q A1602 " ideal model delta sigma weight residual 118.51 98.06 20.45 3.00e+00 1.11e-01 4.65e+01 angle pdb=" N VAL A1289 " pdb=" CA VAL A1289 " pdb=" C VAL A1289 " ideal model delta sigma weight residual 113.53 108.32 5.21 9.80e-01 1.04e+00 2.83e+01 angle pdb=" N ASP A1285 " pdb=" CA ASP A1285 " pdb=" C ASP A1285 " ideal model delta sigma weight residual 112.58 107.63 4.95 1.22e+00 6.72e-01 1.64e+01 angle pdb=" N CYS A1208 " pdb=" CA CYS A1208 " pdb=" C CYS A1208 " ideal model delta sigma weight residual 111.36 107.13 4.23 1.09e+00 8.42e-01 1.50e+01 ... (remaining 14925 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.35: 6156 25.35 - 50.70: 449 50.70 - 76.05: 75 76.05 - 101.39: 12 101.39 - 126.74: 4 Dihedral angle restraints: 6696 sinusoidal: 2805 harmonic: 3891 Sorted by residual: dihedral pdb=" C45 R1Q A1603 " pdb=" C43 R1Q A1603 " pdb=" C44 R1Q A1603 " pdb=" C46 R1Q A1603 " ideal model delta sinusoidal sigma weight residual 176.67 49.93 126.74 1 3.00e+01 1.11e-03 1.70e+01 dihedral pdb=" C45 R1Q A1603 " pdb=" C43 R1Q A1603 " pdb=" C44 R1Q A1603 " pdb=" C53 R1Q A1603 " ideal model delta sinusoidal sigma weight residual 54.94 -70.58 125.52 1 3.00e+01 1.11e-03 1.69e+01 dihedral pdb=" C45 R1Q A1602 " pdb=" C43 R1Q A1602 " pdb=" C44 R1Q A1602 " pdb=" C46 R1Q A1602 " ideal model delta sinusoidal sigma weight residual 176.67 58.89 117.78 1 3.00e+01 1.11e-03 1.56e+01 ... (remaining 6693 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.087: 1497 0.087 - 0.173: 216 0.173 - 0.260: 17 0.260 - 0.346: 1 0.346 - 0.433: 2 Chirality restraints: 1733 Sorted by residual: chirality pdb=" C32 R1Q A1602 " pdb=" C31 R1Q A1602 " pdb=" C34 R1Q A1602 " pdb=" C38 R1Q A1602 " both_signs ideal model delta sigma weight residual False -2.87 -2.44 -0.43 2.00e-01 2.50e+01 4.68e+00 chirality pdb=" C32 R1Q A1603 " pdb=" C31 R1Q A1603 " pdb=" C34 R1Q A1603 " pdb=" C38 R1Q A1603 " both_signs ideal model delta sigma weight residual False -2.87 -2.44 -0.43 2.00e-01 2.50e+01 4.63e+00 chirality pdb=" C52 R1Q A1602 " pdb=" C22 R1Q A1602 " pdb=" C31 R1Q A1602 " pdb=" C51 R1Q A1602 " both_signs ideal model delta sigma weight residual False 3.01 2.69 0.32 2.00e-01 2.50e+01 2.64e+00 ... (remaining 1730 not shown) Planarity restraints: 1832 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C23 R1Q A1603 " 0.076 2.00e-02 2.50e+03 3.12e-01 1.22e+03 pdb=" C29 R1Q A1603 " -0.469 2.00e-02 2.50e+03 pdb=" C31 R1Q A1603 " 0.216 2.00e-02 2.50e+03 pdb=" N28 R1Q A1603 " -0.227 2.00e-02 2.50e+03 pdb=" O30 R1Q A1603 " 0.404 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG1 GSH A1601 " -0.146 2.00e-02 2.50e+03 2.95e-01 1.09e+03 pdb=" CD1 GSH A1601 " 0.080 2.00e-02 2.50e+03 pdb=" OE1 GSH A1601 " -0.116 2.00e-02 2.50e+03 pdb=" CA2 GSH A1601 " -0.343 2.00e-02 2.50e+03 pdb=" N2 GSH A1601 " 0.525 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 GSH A1601 " -0.082 2.00e-02 2.50e+03 1.71e-01 3.67e+02 pdb=" CA2 GSH A1601 " 0.161 2.00e-02 2.50e+03 pdb=" CA3 GSH A1601 " 0.210 2.00e-02 2.50e+03 pdb=" N3 GSH A1601 " -0.264 2.00e-02 2.50e+03 pdb=" O2 GSH A1601 " -0.025 2.00e-02 2.50e+03 ... (remaining 1829 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 3108 2.82 - 3.34: 11078 3.34 - 3.86: 18773 3.86 - 4.38: 21554 4.38 - 4.90: 36759 Nonbonded interactions: 91272 Sorted by model distance: nonbonded pdb=" O ALA A 566 " pdb=" OG1 THR A 570 " model vdw 2.299 3.040 nonbonded pdb=" OH TYR A 404 " pdb=" OG1 THR A1157 " model vdw 2.323 3.040 nonbonded pdb=" O33 R1Q A1602 " pdb=" O36 R1Q A1602 " model vdw 2.362 2.432 nonbonded pdb=" N ASN A 719 " pdb=" OE2 GLU A1156 " model vdw 2.379 3.120 nonbonded pdb=" O THR A 220 " pdb=" OG1 THR A 220 " model vdw 2.395 3.040 ... (remaining 91267 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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=1.00 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: 2.590 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 9.340 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 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 : 0.007 0.061 10975 Z= 0.443 Angle : 0.959 20.756 14930 Z= 0.604 Chirality : 0.060 0.433 1733 Planarity : 0.014 0.312 1832 Dihedral : 17.544 126.743 4174 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 0.17 % Allowed : 19.64 % Favored : 80.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.32 (0.23), residues: 1315 helix: 0.79 (0.17), residues: 891 sheet: -0.38 (0.57), residues: 70 loop : -0.96 (0.33), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 735 TYR 0.033 0.002 TYR A 318 PHE 0.028 0.002 PHE A 865 TRP 0.018 0.001 TRP A1197 HIS 0.005 0.001 HIS A 382 Details of bonding type rmsd/Z covalent geometry : bond 0.00666 / 0.44 (10975) covalent geometry : angle 0.95888 / 0.60 (14930) hydrogen bonds : bond 0.14190 / 9.02 ( 706) hydrogen bonds : angle 6.06792 / 4.40 ( 2082) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2630 Ramachandran restraints generated. 1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2630 Ramachandran restraints generated. 1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1171 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 194 time to evaluate : 0.420 Fit side-chains REVERT: A 128 ARG cc_start: 0.6929 (tmm-80) cc_final: 0.6456 (tmm-80) REVERT: A 240 ASP cc_start: 0.8626 (m-30) cc_final: 0.8417 (m-30) REVERT: A 327 MET cc_start: 0.8165 (mpp) cc_final: 0.7810 (mtp) REVERT: A 476 MET cc_start: 0.8441 (tpp) cc_final: 0.8236 (mmt) REVERT: A 723 ARG cc_start: 0.8002 (ttt-90) cc_final: 0.7682 (ttt180) REVERT: A 751 GLU cc_start: 0.7854 (mm-30) cc_final: 0.7653 (mm-30) REVERT: A 1175 ARG cc_start: 0.7681 (ttp-170) cc_final: 0.7358 (mtm-85) outliers start: 2 outliers final: 1 residues processed: 196 average time/residue: 0.4963 time to fit residues: 104.9909 Evaluate side-chains 128 residues out of total 1171 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 127 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1355 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 98 optimal weight: 0.9990 chunk 107 optimal weight: 0.5980 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 0.5980 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 0.5980 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 0.6980 chunk 55 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 60 HIS A 125 GLN A 260 ASN A 590 ASN A 714 GLN A 805 HIS A1207 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.173563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.119769 restraints weight = 11972.929| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 1.84 r_work: 0.3179 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3034 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 moved from start: 0.1703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 10975 Z= 0.165 Angle : 0.613 7.132 14930 Z= 0.308 Chirality : 0.043 0.235 1733 Planarity : 0.004 0.050 1832 Dihedral : 8.971 95.378 1702 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 5.04 % Allowed : 20.75 % Favored : 74.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.28 (0.23), residues: 1315 helix: 1.59 (0.17), residues: 895 sheet: -0.64 (0.55), residues: 70 loop : -0.67 (0.33), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 233 TYR 0.028 0.001 TYR A 318 PHE 0.023 0.002 PHE A 594 TRP 0.019 0.001 TRP A1197 HIS 0.006 0.001 HIS A 382 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.16 (10975) covalent geometry : angle 0.61286 / 0.31 (14930) hydrogen bonds : bond 0.04988 / 3.12 ( 706) hydrogen bonds : angle 4.48176 / 3.22 ( 2082) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2630 Ramachandran restraints generated. 1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2630 Ramachandran restraints generated. 1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1171 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 139 time to evaluate : 0.398 Fit side-chains REVERT: A 28 ASP cc_start: 0.6820 (t0) cc_final: 0.6488 (t0) REVERT: A 129 ARG cc_start: 0.6375 (OUTLIER) cc_final: 0.5874 (mmt180) REVERT: A 227 MET cc_start: 0.8315 (OUTLIER) cc_final: 0.7940 (ttm) REVERT: A 240 ASP cc_start: 0.8308 (m-30) cc_final: 0.7926 (m-30) REVERT: A 250 SER cc_start: 0.7840 (OUTLIER) cc_final: 0.7356 (m) REVERT: A 259 LYS cc_start: 0.7674 (mtpm) cc_final: 0.7073 (ttpp) REVERT: A 357 LYS cc_start: 0.7341 (pptt) cc_final: 0.6845 (ptmm) REVERT: A 476 MET cc_start: 0.7987 (tpp) cc_final: 0.7729 (mmt) REVERT: A 590 ASN cc_start: 0.8016 (m-40) cc_final: 0.7708 (m-40) REVERT: A 694 GLU cc_start: 0.7986 (mm-30) cc_final: 0.7624 (mm-30) REVERT: A 723 ARG cc_start: 0.7475 (ttt-90) cc_final: 0.7271 (ttt180) REVERT: A 735 ARG cc_start: 0.7688 (ptt90) cc_final: 0.7287 (ptp-110) REVERT: A 787 ASP cc_start: 0.7173 (t0) cc_final: 0.6861 (m-30) REVERT: A 792 ASP cc_start: 0.7838 (t0) cc_final: 0.7337 (t0) REVERT: A 1073 ASN cc_start: 0.7492 (m-40) cc_final: 0.6332 (t0) REVERT: A 1147 ARG cc_start: 0.8397 (ttm170) cc_final: 0.8193 (ttm110) REVERT: A 1175 ARG cc_start: 0.7636 (ttp-170) cc_final: 0.7295 (mtm-85) REVERT: A 1211 LEU cc_start: 0.8128 (OUTLIER) cc_final: 0.7787 (tp) REVERT: A 1276 GLN cc_start: 0.8145 (mm-40) cc_final: 0.7123 (mp10) REVERT: A 1278 GLN cc_start: 0.6907 (OUTLIER) cc_final: 0.6597 (mp10) REVERT: A 1300 ARG cc_start: 0.6858 (tmt170) cc_final: 0.6142 (tmm-80) REVERT: A 1320 GLU cc_start: 0.6486 (OUTLIER) cc_final: 0.5641 (tm-30) outliers start: 59 outliers final: 17 residues processed: 182 average time/residue: 0.4124 time to fit residues: 82.2427 Evaluate side-chains 149 residues out of total 1171 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 126 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 SER Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 129 ARG Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 227 MET Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 626 ASP Chi-restraints excluded: chain A residue 650 THR Chi-restraints excluded: chain A residue 698 VAL Chi-restraints excluded: chain A residue 801 HIS Chi-restraints excluded: chain A residue 805 HIS Chi-restraints excluded: chain A residue 819 ASN Chi-restraints excluded: chain A residue 831 TYR Chi-restraints excluded: chain A residue 1211 LEU Chi-restraints excluded: chain A residue 1240 THR Chi-restraints excluded: chain A residue 1253 MET Chi-restraints excluded: chain A residue 1278 GLN Chi-restraints excluded: chain A residue 1320 GLU Chi-restraints excluded: chain A residue 1322 VAL Chi-restraints excluded: chain A residue 1450 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 16 optimal weight: 6.9990 chunk 92 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 55 optimal weight: 0.0970 chunk 120 optimal weight: 2.9990 chunk 18 optimal weight: 0.5980 chunk 51 optimal weight: 0.8980 chunk 79 optimal weight: 0.9990 chunk 78 optimal weight: 4.9990 chunk 7 optimal weight: 8.9990 chunk 56 optimal weight: 3.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 714 GLN A 805 HIS A1485 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.170822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.116293 restraints weight = 11994.433| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 1.82 r_work: 0.3102 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2961 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.2087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 10975 Z= 0.180 Angle : 0.581 7.235 14930 Z= 0.296 Chirality : 0.042 0.205 1733 Planarity : 0.004 0.052 1832 Dihedral : 8.269 83.778 1700 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 5.04 % Allowed : 21.09 % Favored : 73.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.38 (0.23), residues: 1315 helix: 1.66 (0.17), residues: 896 sheet: -0.67 (0.54), residues: 70 loop : -0.62 (0.33), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 171 TYR 0.020 0.002 TYR A 318 PHE 0.021 0.002 PHE A 865 TRP 0.018 0.001 TRP A1197 HIS 0.019 0.002 HIS A 801 Details of bonding type rmsd/Z covalent geometry : bond 0.00419 / 0.18 (10975) covalent geometry : angle 0.58115 / 0.30 (14930) hydrogen bonds : bond 0.04932 / 3.08 ( 706) hydrogen bonds : angle 4.40193 / 3.16 ( 2082) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2630 Ramachandran restraints generated. 1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2630 Ramachandran restraints generated. 1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1171 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 130 time to evaluate : 0.291 Fit side-chains REVERT: A 67 MET cc_start: 0.5538 (mmm) cc_final: 0.5098 (tpp) REVERT: A 106 PHE cc_start: 0.6127 (m-80) cc_final: 0.5647 (m-80) REVERT: A 129 ARG cc_start: 0.6303 (OUTLIER) cc_final: 0.5818 (mmt180) REVERT: A 130 ARG cc_start: 0.6499 (OUTLIER) cc_final: 0.6235 (mmm-85) REVERT: A 240 ASP cc_start: 0.8219 (m-30) cc_final: 0.7855 (m-30) REVERT: A 250 SER cc_start: 0.7806 (OUTLIER) cc_final: 0.7233 (m) REVERT: A 259 LYS cc_start: 0.7769 (mtpm) cc_final: 0.7119 (ttpp) REVERT: A 476 MET cc_start: 0.8007 (tpp) cc_final: 0.7709 (mmt) REVERT: A 539 LEU cc_start: 0.7647 (OUTLIER) cc_final: 0.7408 (mp) REVERT: A 590 ASN cc_start: 0.8029 (m-40) cc_final: 0.7697 (m-40) REVERT: A 696 ASP cc_start: 0.8093 (t70) cc_final: 0.7754 (t0) REVERT: A 723 ARG cc_start: 0.7477 (ttt-90) cc_final: 0.7249 (ttt180) REVERT: A 735 ARG cc_start: 0.7705 (ptt90) cc_final: 0.7291 (ptp-110) REVERT: A 787 ASP cc_start: 0.7268 (t0) cc_final: 0.6798 (m-30) REVERT: A 792 ASP cc_start: 0.7901 (t0) cc_final: 0.7323 (t0) REVERT: A 1175 ARG cc_start: 0.7698 (ttp-110) cc_final: 0.7344 (mtm-85) REVERT: A 1211 LEU cc_start: 0.8232 (OUTLIER) cc_final: 0.7818 (tp) REVERT: A 1278 GLN cc_start: 0.6899 (OUTLIER) cc_final: 0.6580 (mp10) REVERT: A 1280 MET cc_start: 0.7776 (OUTLIER) cc_final: 0.7165 (pmm) REVERT: A 1300 ARG cc_start: 0.6787 (tmt170) cc_final: 0.6579 (tmt90) REVERT: A 1320 GLU cc_start: 0.6487 (OUTLIER) cc_final: 0.5638 (tm-30) REVERT: A 1385 MET cc_start: 0.7285 (mmp) cc_final: 0.5864 (tmm) outliers start: 59 outliers final: 23 residues processed: 172 average time/residue: 0.4474 time to fit residues: 84.2612 Evaluate side-chains 150 residues out of total 1171 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 119 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 54 PHE Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 129 ARG Chi-restraints excluded: chain A residue 130 ARG Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 391 SER Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 626 ASP Chi-restraints excluded: chain A residue 650 THR Chi-restraints excluded: chain A residue 698 VAL Chi-restraints excluded: chain A residue 707 SER Chi-restraints excluded: chain A residue 801 HIS Chi-restraints excluded: chain A residue 802 VAL Chi-restraints excluded: chain A residue 805 HIS Chi-restraints excluded: chain A residue 819 ASN Chi-restraints excluded: chain A residue 831 TYR Chi-restraints excluded: chain A residue 1011 THR Chi-restraints excluded: chain A residue 1032 TYR Chi-restraints excluded: chain A residue 1211 LEU Chi-restraints excluded: chain A residue 1224 LEU Chi-restraints excluded: chain A residue 1240 THR Chi-restraints excluded: chain A residue 1253 MET Chi-restraints excluded: chain A residue 1278 GLN Chi-restraints excluded: chain A residue 1280 MET Chi-restraints excluded: chain A residue 1320 GLU Chi-restraints excluded: chain A residue 1339 LEU Chi-restraints excluded: chain A residue 1365 LEU Chi-restraints excluded: chain A residue 1450 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 33 optimal weight: 0.8980 chunk 90 optimal weight: 0.9980 chunk 111 optimal weight: 0.2980 chunk 112 optimal weight: 3.9990 chunk 72 optimal weight: 3.9990 chunk 92 optimal weight: 0.9990 chunk 3 optimal weight: 6.9990 chunk 6 optimal weight: 0.8980 chunk 8 optimal weight: 1.9990 chunk 11 optimal weight: 4.9990 chunk 18 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 71 ASN A 125 GLN A 580 GLN ** A 805 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 984 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.171343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.117104 restraints weight = 12059.626| |-----------------------------------------------------------------------------| r_work (start): 0.3235 rms_B_bonded: 1.82 r_work: 0.3107 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2967 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.2360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 10975 Z= 0.160 Angle : 0.556 7.251 14930 Z= 0.282 Chirality : 0.042 0.219 1733 Planarity : 0.004 0.050 1832 Dihedral : 7.400 79.021 1700 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 4.70 % Allowed : 21.52 % Favored : 73.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.46 (0.23), residues: 1315 helix: 1.75 (0.17), residues: 891 sheet: -0.65 (0.55), residues: 70 loop : -0.63 (0.32), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1201 TYR 0.018 0.001 TYR A 852 PHE 0.023 0.002 PHE A 329 TRP 0.017 0.001 TRP A1197 HIS 0.010 0.001 HIS A 805 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.16 (10975) covalent geometry : angle 0.55572 / 0.28 (14930) hydrogen bonds : bond 0.04658 / 2.91 ( 706) hydrogen bonds : angle 4.28855 / 3.08 ( 2082) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2630 Ramachandran restraints generated. 1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2630 Ramachandran restraints generated. 1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1171 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 132 time to evaluate : 0.482 Fit side-chains REVERT: A 28 ASP cc_start: 0.6395 (t0) cc_final: 0.6187 (t0) REVERT: A 67 MET cc_start: 0.5475 (mmm) cc_final: 0.5150 (tpp) REVERT: A 128 ARG cc_start: 0.5625 (ttp80) cc_final: 0.5376 (ttt-90) REVERT: A 129 ARG cc_start: 0.6395 (OUTLIER) cc_final: 0.5906 (mmt180) REVERT: A 130 ARG cc_start: 0.6546 (OUTLIER) cc_final: 0.6299 (mmm-85) REVERT: A 240 ASP cc_start: 0.8249 (m-30) cc_final: 0.7870 (m-30) REVERT: A 250 SER cc_start: 0.7797 (OUTLIER) cc_final: 0.7226 (m) REVERT: A 259 LYS cc_start: 0.7737 (mtpm) cc_final: 0.7095 (ttpp) REVERT: A 357 LYS cc_start: 0.7232 (pptt) cc_final: 0.6513 (mmmt) REVERT: A 476 MET cc_start: 0.7974 (tpp) cc_final: 0.7725 (mmt) REVERT: A 539 LEU cc_start: 0.7665 (OUTLIER) cc_final: 0.7425 (mp) REVERT: A 590 ASN cc_start: 0.8056 (m-40) cc_final: 0.7703 (m-40) REVERT: A 696 ASP cc_start: 0.8110 (t70) cc_final: 0.7774 (t0) REVERT: A 723 ARG cc_start: 0.7450 (ttt-90) cc_final: 0.7077 (ttt180) REVERT: A 735 ARG cc_start: 0.7764 (ptt90) cc_final: 0.7303 (ptp-110) REVERT: A 787 ASP cc_start: 0.7314 (t0) cc_final: 0.6889 (m-30) REVERT: A 792 ASP cc_start: 0.7946 (t0) cc_final: 0.7356 (t0) REVERT: A 1211 LEU cc_start: 0.8249 (OUTLIER) cc_final: 0.7811 (tp) REVERT: A 1278 GLN cc_start: 0.6923 (OUTLIER) cc_final: 0.6599 (mp10) REVERT: A 1280 MET cc_start: 0.7799 (OUTLIER) cc_final: 0.7260 (pmm) REVERT: A 1300 ARG cc_start: 0.6649 (tmt170) cc_final: 0.6421 (tmt90) REVERT: A 1320 GLU cc_start: 0.6517 (OUTLIER) cc_final: 0.5661 (tm-30) REVERT: A 1385 MET cc_start: 0.7258 (mmp) cc_final: 0.5879 (tmm) outliers start: 55 outliers final: 23 residues processed: 168 average time/residue: 0.4795 time to fit residues: 88.2618 Evaluate side-chains 153 residues out of total 1171 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 122 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 54 PHE Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 129 ARG Chi-restraints excluded: chain A residue 130 ARG Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 391 SER Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 650 THR Chi-restraints excluded: chain A residue 698 VAL Chi-restraints excluded: chain A residue 707 SER Chi-restraints excluded: chain A residue 801 HIS Chi-restraints excluded: chain A residue 831 TYR Chi-restraints excluded: chain A residue 1011 THR Chi-restraints excluded: chain A residue 1032 TYR Chi-restraints excluded: chain A residue 1136 SER Chi-restraints excluded: chain A residue 1211 LEU Chi-restraints excluded: chain A residue 1224 LEU Chi-restraints excluded: chain A residue 1249 MET Chi-restraints excluded: chain A residue 1278 GLN Chi-restraints excluded: chain A residue 1280 MET Chi-restraints excluded: chain A residue 1320 GLU Chi-restraints excluded: chain A residue 1339 LEU Chi-restraints excluded: chain A residue 1355 ILE Chi-restraints excluded: chain A residue 1365 LEU Chi-restraints excluded: chain A residue 1450 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 119 optimal weight: 3.9990 chunk 28 optimal weight: 0.9980 chunk 124 optimal weight: 9.9990 chunk 97 optimal weight: 0.6980 chunk 23 optimal weight: 0.9990 chunk 110 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 7 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 122 optimal weight: 2.9990 chunk 113 optimal weight: 6.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 580 GLN A 805 HIS A 809 ASN A1184 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.168201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.113260 restraints weight = 12043.916| |-----------------------------------------------------------------------------| r_work (start): 0.3193 rms_B_bonded: 1.84 r_work: 0.3064 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2922 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.2648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 10975 Z= 0.228 Angle : 0.601 7.398 14930 Z= 0.307 Chirality : 0.044 0.211 1733 Planarity : 0.004 0.054 1832 Dihedral : 7.137 89.006 1700 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 5.38 % Allowed : 21.61 % Favored : 73.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.22 (0.23), residues: 1315 helix: 1.56 (0.17), residues: 885 sheet: -0.52 (0.58), residues: 70 loop : -0.72 (0.32), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A1291 TYR 0.021 0.002 TYR A1242 PHE 0.025 0.002 PHE A 558 TRP 0.018 0.001 TRP A1197 HIS 0.005 0.001 HIS A 985 Details of bonding type rmsd/Z covalent geometry : bond 0.00544 / 0.23 (10975) covalent geometry : angle 0.60109 / 0.31 (14930) hydrogen bonds : bond 0.05154 / 3.21 ( 706) hydrogen bonds : angle 4.41974 / 3.17 ( 2082) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2630 Ramachandran restraints generated. 1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2630 Ramachandran restraints generated. 1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1171 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 133 time to evaluate : 0.434 Fit side-chains REVERT: A 67 MET cc_start: 0.5666 (mmm) cc_final: 0.5365 (tpp) REVERT: A 128 ARG cc_start: 0.5658 (ttp80) cc_final: 0.5337 (ttt-90) REVERT: A 129 ARG cc_start: 0.6256 (OUTLIER) cc_final: 0.5757 (mmt180) REVERT: A 240 ASP cc_start: 0.8194 (m-30) cc_final: 0.7798 (m-30) REVERT: A 259 LYS cc_start: 0.7696 (mtpm) cc_final: 0.7058 (ttpp) REVERT: A 357 LYS cc_start: 0.7073 (pptt) cc_final: 0.6662 (mmmt) REVERT: A 435 MET cc_start: 0.8197 (OUTLIER) cc_final: 0.7982 (ttp) REVERT: A 476 MET cc_start: 0.7952 (tpp) cc_final: 0.7650 (mmt) REVERT: A 539 LEU cc_start: 0.7667 (OUTLIER) cc_final: 0.7444 (mp) REVERT: A 545 LEU cc_start: 0.8054 (OUTLIER) cc_final: 0.7821 (mt) REVERT: A 590 ASN cc_start: 0.8007 (m-40) cc_final: 0.7592 (m-40) REVERT: A 628 ASP cc_start: 0.7353 (p0) cc_final: 0.6646 (t70) REVERT: A 655 ARG cc_start: 0.6726 (mmp-170) cc_final: 0.6524 (mmp-170) REVERT: A 735 ARG cc_start: 0.7816 (ptt90) cc_final: 0.7410 (ptp-110) REVERT: A 787 ASP cc_start: 0.7322 (t0) cc_final: 0.6866 (m-30) REVERT: A 792 ASP cc_start: 0.7972 (t0) cc_final: 0.7351 (t0) REVERT: A 1211 LEU cc_start: 0.8148 (OUTLIER) cc_final: 0.7647 (tp) REVERT: A 1278 GLN cc_start: 0.6849 (OUTLIER) cc_final: 0.6549 (mp10) REVERT: A 1280 MET cc_start: 0.7832 (OUTLIER) cc_final: 0.7183 (pmm) REVERT: A 1300 ARG cc_start: 0.6708 (tmt170) cc_final: 0.6402 (tmt90) REVERT: A 1320 GLU cc_start: 0.6525 (OUTLIER) cc_final: 0.5694 (tm-30) REVERT: A 1384 ARG cc_start: 0.7182 (OUTLIER) cc_final: 0.6953 (tpt170) REVERT: A 1385 MET cc_start: 0.7312 (mmp) cc_final: 0.6000 (tmm) outliers start: 63 outliers final: 29 residues processed: 176 average time/residue: 0.4750 time to fit residues: 91.7997 Evaluate side-chains 158 residues out of total 1171 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 120 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 54 PHE Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 129 ARG Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 391 SER Chi-restraints excluded: chain A residue 435 MET Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 626 ASP Chi-restraints excluded: chain A residue 650 THR Chi-restraints excluded: chain A residue 698 VAL Chi-restraints excluded: chain A residue 707 SER Chi-restraints excluded: chain A residue 801 HIS Chi-restraints excluded: chain A residue 805 HIS Chi-restraints excluded: chain A residue 831 TYR Chi-restraints excluded: chain A residue 834 GLN Chi-restraints excluded: chain A residue 1011 THR Chi-restraints excluded: chain A residue 1032 TYR Chi-restraints excluded: chain A residue 1136 SER Chi-restraints excluded: chain A residue 1211 LEU Chi-restraints excluded: chain A residue 1224 LEU Chi-restraints excluded: chain A residue 1240 THR Chi-restraints excluded: chain A residue 1278 GLN Chi-restraints excluded: chain A residue 1280 MET Chi-restraints excluded: chain A residue 1309 LEU Chi-restraints excluded: chain A residue 1320 GLU Chi-restraints excluded: chain A residue 1339 LEU Chi-restraints excluded: chain A residue 1363 HIS Chi-restraints excluded: chain A residue 1365 LEU Chi-restraints excluded: chain A residue 1384 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 25 optimal weight: 0.9980 chunk 58 optimal weight: 5.9990 chunk 131 optimal weight: 4.9990 chunk 49 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 108 optimal weight: 0.8980 chunk 50 optimal weight: 0.5980 chunk 125 optimal weight: 7.9990 chunk 41 optimal weight: 0.8980 chunk 24 optimal weight: 0.8980 chunk 101 optimal weight: 0.5980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 580 GLN A 805 HIS A 827 HIS A1184 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.169738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.115406 restraints weight = 12023.128| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 1.82 r_work: 0.3129 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2988 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.2746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 10975 Z= 0.162 Angle : 0.557 9.496 14930 Z= 0.282 Chirality : 0.042 0.204 1733 Planarity : 0.004 0.052 1832 Dihedral : 6.567 84.310 1700 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 4.87 % Allowed : 22.54 % Favored : 72.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.36 (0.23), residues: 1315 helix: 1.65 (0.17), residues: 889 sheet: -0.53 (0.58), residues: 70 loop : -0.63 (0.32), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 130 TYR 0.016 0.001 TYR A 318 PHE 0.027 0.002 PHE A 558 TRP 0.017 0.001 TRP A1197 HIS 0.007 0.001 HIS A 805 Details of bonding type rmsd/Z covalent geometry : bond 0.00374 / 0.16 (10975) covalent geometry : angle 0.55729 / 0.28 (14930) hydrogen bonds : bond 0.04693 / 2.93 ( 706) hydrogen bonds : angle 4.28214 / 3.07 ( 2082) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2630 Ramachandran restraints generated. 1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2630 Ramachandran restraints generated. 1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1171 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 132 time to evaluate : 0.439 Fit side-chains REVERT: A 128 ARG cc_start: 0.5820 (ttp80) cc_final: 0.5530 (ttt-90) REVERT: A 129 ARG cc_start: 0.6305 (OUTLIER) cc_final: 0.5791 (mmt180) REVERT: A 240 ASP cc_start: 0.8218 (m-30) cc_final: 0.7836 (m-30) REVERT: A 259 LYS cc_start: 0.7720 (mtpm) cc_final: 0.7085 (ttpp) REVERT: A 357 LYS cc_start: 0.7214 (pptt) cc_final: 0.6755 (mmmt) REVERT: A 476 MET cc_start: 0.7967 (tpp) cc_final: 0.7685 (mmt) REVERT: A 590 ASN cc_start: 0.8045 (m-40) cc_final: 0.7671 (m-40) REVERT: A 628 ASP cc_start: 0.7442 (p0) cc_final: 0.6820 (t70) REVERT: A 696 ASP cc_start: 0.8124 (t70) cc_final: 0.7777 (OUTLIER) REVERT: A 735 ARG cc_start: 0.7805 (ptt90) cc_final: 0.7417 (ptp-110) REVERT: A 787 ASP cc_start: 0.7355 (t0) cc_final: 0.7012 (m-30) REVERT: A 792 ASP cc_start: 0.7964 (t0) cc_final: 0.7399 (t0) REVERT: A 1211 LEU cc_start: 0.8244 (OUTLIER) cc_final: 0.7798 (tp) REVERT: A 1278 GLN cc_start: 0.6812 (OUTLIER) cc_final: 0.6509 (mp10) REVERT: A 1280 MET cc_start: 0.7791 (OUTLIER) cc_final: 0.7207 (pmm) REVERT: A 1300 ARG cc_start: 0.6692 (tmt170) cc_final: 0.6390 (tmt90) REVERT: A 1320 GLU cc_start: 0.6548 (OUTLIER) cc_final: 0.5692 (tm-30) REVERT: A 1385 MET cc_start: 0.7377 (mmp) cc_final: 0.5953 (tmm) outliers start: 57 outliers final: 28 residues processed: 168 average time/residue: 0.4472 time to fit residues: 83.0232 Evaluate side-chains 157 residues out of total 1171 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 125 time to evaluate : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 54 PHE Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 129 ARG Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 391 SER Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 650 THR Chi-restraints excluded: chain A residue 698 VAL Chi-restraints excluded: chain A residue 805 HIS Chi-restraints excluded: chain A residue 827 HIS Chi-restraints excluded: chain A residue 831 TYR Chi-restraints excluded: chain A residue 1011 THR Chi-restraints excluded: chain A residue 1032 TYR Chi-restraints excluded: chain A residue 1136 SER Chi-restraints excluded: chain A residue 1211 LEU Chi-restraints excluded: chain A residue 1240 THR Chi-restraints excluded: chain A residue 1249 MET Chi-restraints excluded: chain A residue 1278 GLN Chi-restraints excluded: chain A residue 1280 MET Chi-restraints excluded: chain A residue 1309 LEU Chi-restraints excluded: chain A residue 1320 GLU Chi-restraints excluded: chain A residue 1339 LEU Chi-restraints excluded: chain A residue 1355 ILE Chi-restraints excluded: chain A residue 1365 LEU Chi-restraints excluded: chain A residue 1371 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 94 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 108 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 43 optimal weight: 0.5980 chunk 75 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 88 optimal weight: 0.7980 chunk 20 optimal weight: 0.3980 chunk 31 optimal weight: 0.9980 chunk 131 optimal weight: 3.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 580 GLN ** A 805 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 827 HIS A1184 ASN A1406 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.169914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.115557 restraints weight = 11963.544| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 1.83 r_work: 0.3146 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3001 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.2853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 10975 Z= 0.160 Angle : 0.559 8.778 14930 Z= 0.282 Chirality : 0.042 0.201 1733 Planarity : 0.004 0.051 1832 Dihedral : 6.295 81.496 1700 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 4.70 % Allowed : 23.57 % Favored : 71.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.40 (0.23), residues: 1315 helix: 1.69 (0.17), residues: 889 sheet: -0.54 (0.58), residues: 70 loop : -0.65 (0.32), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1291 TYR 0.020 0.001 TYR A1242 PHE 0.027 0.002 PHE A 558 TRP 0.017 0.001 TRP A1197 HIS 0.011 0.001 HIS A 805 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.16 (10975) covalent geometry : angle 0.55876 / 0.28 (14930) hydrogen bonds : bond 0.04624 / 2.88 ( 706) hydrogen bonds : angle 4.24726 / 3.05 ( 2082) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2630 Ramachandran restraints generated. 1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2630 Ramachandran restraints generated. 1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1171 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 130 time to evaluate : 0.390 Fit side-chains REVERT: A 129 ARG cc_start: 0.6325 (OUTLIER) cc_final: 0.5774 (mmt-90) REVERT: A 240 ASP cc_start: 0.8158 (m-30) cc_final: 0.7749 (m-30) REVERT: A 259 LYS cc_start: 0.7724 (mtpm) cc_final: 0.7093 (ttpp) REVERT: A 357 LYS cc_start: 0.7233 (pptt) cc_final: 0.6789 (mmmt) REVERT: A 476 MET cc_start: 0.7994 (tpp) cc_final: 0.7684 (mmt) REVERT: A 590 ASN cc_start: 0.8044 (m-40) cc_final: 0.7712 (m-40) REVERT: A 628 ASP cc_start: 0.7448 (p0) cc_final: 0.6873 (t70) REVERT: A 696 ASP cc_start: 0.8089 (t70) cc_final: 0.7832 (OUTLIER) REVERT: A 735 ARG cc_start: 0.7860 (ptt90) cc_final: 0.7428 (ptp-110) REVERT: A 787 ASP cc_start: 0.7387 (t0) cc_final: 0.7028 (m-30) REVERT: A 792 ASP cc_start: 0.7974 (t0) cc_final: 0.7473 (t0) REVERT: A 841 MET cc_start: 0.7373 (ptp) cc_final: 0.6774 (ptm) REVERT: A 1211 LEU cc_start: 0.8302 (OUTLIER) cc_final: 0.7857 (tp) REVERT: A 1278 GLN cc_start: 0.6839 (OUTLIER) cc_final: 0.6537 (mp10) REVERT: A 1280 MET cc_start: 0.7864 (OUTLIER) cc_final: 0.7269 (pmm) REVERT: A 1300 ARG cc_start: 0.6710 (tmt170) cc_final: 0.6382 (tmt90) REVERT: A 1320 GLU cc_start: 0.6439 (OUTLIER) cc_final: 0.5725 (tm-30) REVERT: A 1359 LYS cc_start: 0.8399 (mmtm) cc_final: 0.8097 (mmtp) REVERT: A 1385 MET cc_start: 0.7402 (mmp) cc_final: 0.6043 (tmm) outliers start: 55 outliers final: 32 residues processed: 165 average time/residue: 0.4618 time to fit residues: 83.7591 Evaluate side-chains 158 residues out of total 1171 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 122 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 54 PHE Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 129 ARG Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 246 LYS Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 391 SER Chi-restraints excluded: chain A residue 465 SER Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 650 THR Chi-restraints excluded: chain A residue 698 VAL Chi-restraints excluded: chain A residue 802 VAL Chi-restraints excluded: chain A residue 827 HIS Chi-restraints excluded: chain A residue 831 TYR Chi-restraints excluded: chain A residue 1011 THR Chi-restraints excluded: chain A residue 1032 TYR Chi-restraints excluded: chain A residue 1211 LEU Chi-restraints excluded: chain A residue 1224 LEU Chi-restraints excluded: chain A residue 1240 THR Chi-restraints excluded: chain A residue 1249 MET Chi-restraints excluded: chain A residue 1278 GLN Chi-restraints excluded: chain A residue 1280 MET Chi-restraints excluded: chain A residue 1309 LEU Chi-restraints excluded: chain A residue 1320 GLU Chi-restraints excluded: chain A residue 1322 VAL Chi-restraints excluded: chain A residue 1355 ILE Chi-restraints excluded: chain A residue 1363 HIS Chi-restraints excluded: chain A residue 1365 LEU Chi-restraints excluded: chain A residue 1371 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 25 optimal weight: 1.9990 chunk 2 optimal weight: 0.7980 chunk 46 optimal weight: 0.5980 chunk 5 optimal weight: 2.9990 chunk 7 optimal weight: 9.9990 chunk 96 optimal weight: 0.5980 chunk 113 optimal weight: 5.9990 chunk 11 optimal weight: 0.8980 chunk 8 optimal weight: 5.9990 chunk 48 optimal weight: 1.9990 chunk 60 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 125 GLN A 580 GLN A 805 HIS A 827 HIS A1184 ASN A1406 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.170325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.125275 restraints weight = 11953.687| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 2.17 r_work: 0.3119 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2974 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.2917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 10975 Z= 0.154 Angle : 0.560 9.709 14930 Z= 0.282 Chirality : 0.041 0.199 1733 Planarity : 0.004 0.051 1832 Dihedral : 6.160 80.268 1700 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 4.27 % Allowed : 23.91 % Favored : 71.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.46 (0.23), residues: 1315 helix: 1.75 (0.17), residues: 892 sheet: -0.57 (0.59), residues: 68 loop : -0.67 (0.32), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A1065 TYR 0.022 0.001 TYR A1242 PHE 0.027 0.002 PHE A 558 TRP 0.017 0.001 TRP A1245 HIS 0.008 0.001 HIS A 827 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.15 (10975) covalent geometry : angle 0.56043 / 0.28 (14930) hydrogen bonds : bond 0.04553 / 2.84 ( 706) hydrogen bonds : angle 4.20134 / 3.01 ( 2082) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2630 Ramachandran restraints generated. 1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2630 Ramachandran restraints generated. 1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1171 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 128 time to evaluate : 0.419 Fit side-chains REVERT: A 129 ARG cc_start: 0.6268 (OUTLIER) cc_final: 0.5792 (mmt-90) REVERT: A 240 ASP cc_start: 0.8163 (m-30) cc_final: 0.7750 (m-30) REVERT: A 259 LYS cc_start: 0.7731 (mtpm) cc_final: 0.7105 (ttpp) REVERT: A 357 LYS cc_start: 0.7171 (pptt) cc_final: 0.6814 (mmmt) REVERT: A 476 MET cc_start: 0.7993 (tpp) cc_final: 0.7695 (mmt) REVERT: A 590 ASN cc_start: 0.8085 (m-40) cc_final: 0.7745 (m-40) REVERT: A 628 ASP cc_start: 0.7495 (p0) cc_final: 0.6994 (t70) REVERT: A 696 ASP cc_start: 0.8128 (t70) cc_final: 0.7907 (OUTLIER) REVERT: A 735 ARG cc_start: 0.7879 (ptt90) cc_final: 0.7453 (ptp-110) REVERT: A 787 ASP cc_start: 0.7438 (t0) cc_final: 0.7075 (m-30) REVERT: A 792 ASP cc_start: 0.7846 (t0) cc_final: 0.7362 (t70) REVERT: A 841 MET cc_start: 0.7420 (ptp) cc_final: 0.6831 (ptm) REVERT: A 1211 LEU cc_start: 0.8324 (OUTLIER) cc_final: 0.7907 (tp) REVERT: A 1278 GLN cc_start: 0.6843 (OUTLIER) cc_final: 0.6543 (mp10) REVERT: A 1280 MET cc_start: 0.7936 (OUTLIER) cc_final: 0.7307 (pmm) REVERT: A 1300 ARG cc_start: 0.6677 (tmt170) cc_final: 0.6319 (tmt90) REVERT: A 1359 LYS cc_start: 0.8390 (mmtm) cc_final: 0.8092 (mmtp) REVERT: A 1385 MET cc_start: 0.7372 (mmp) cc_final: 0.6024 (tmm) REVERT: A 1495 ARG cc_start: 0.6564 (mmt180) cc_final: 0.6156 (ttt90) outliers start: 50 outliers final: 31 residues processed: 158 average time/residue: 0.4754 time to fit residues: 82.3944 Evaluate side-chains 157 residues out of total 1171 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 123 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 54 PHE Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 129 ARG Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 391 SER Chi-restraints excluded: chain A residue 465 SER Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 650 THR Chi-restraints excluded: chain A residue 698 VAL Chi-restraints excluded: chain A residue 805 HIS Chi-restraints excluded: chain A residue 819 ASN Chi-restraints excluded: chain A residue 827 HIS Chi-restraints excluded: chain A residue 831 TYR Chi-restraints excluded: chain A residue 834 GLN Chi-restraints excluded: chain A residue 1011 THR Chi-restraints excluded: chain A residue 1032 TYR Chi-restraints excluded: chain A residue 1136 SER Chi-restraints excluded: chain A residue 1211 LEU Chi-restraints excluded: chain A residue 1240 THR Chi-restraints excluded: chain A residue 1249 MET Chi-restraints excluded: chain A residue 1278 GLN Chi-restraints excluded: chain A residue 1280 MET Chi-restraints excluded: chain A residue 1322 VAL Chi-restraints excluded: chain A residue 1355 ILE Chi-restraints excluded: chain A residue 1363 HIS Chi-restraints excluded: chain A residue 1365 LEU Chi-restraints excluded: chain A residue 1371 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 37 optimal weight: 0.8980 chunk 90 optimal weight: 0.5980 chunk 61 optimal weight: 0.0040 chunk 22 optimal weight: 0.6980 chunk 110 optimal weight: 2.9990 chunk 70 optimal weight: 0.7980 chunk 20 optimal weight: 1.9990 chunk 74 optimal weight: 3.9990 chunk 11 optimal weight: 4.9990 chunk 127 optimal weight: 0.8980 chunk 52 optimal weight: 1.9990 overall best weight: 0.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 580 GLN A 805 HIS A 809 ASN A 827 HIS A1406 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.173159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.131905 restraints weight = 11945.292| |-----------------------------------------------------------------------------| r_work (start): 0.3423 rms_B_bonded: 1.89 r_work: 0.3165 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3035 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.2987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10975 Z= 0.146 Angle : 0.563 10.366 14930 Z= 0.282 Chirality : 0.041 0.197 1733 Planarity : 0.004 0.050 1832 Dihedral : 6.093 80.006 1700 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 3.50 % Allowed : 24.51 % Favored : 71.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.50 (0.23), residues: 1315 helix: 1.79 (0.17), residues: 892 sheet: -0.62 (0.59), residues: 68 loop : -0.67 (0.32), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A1065 TYR 0.021 0.001 TYR A1242 PHE 0.028 0.002 PHE A 558 TRP 0.018 0.001 TRP A1245 HIS 0.013 0.001 HIS A 805 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.15 (10975) covalent geometry : angle 0.56345 / 0.28 (14930) hydrogen bonds : bond 0.04476 / 2.79 ( 706) hydrogen bonds : angle 4.17153 / 2.99 ( 2082) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2630 Ramachandran restraints generated. 1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2630 Ramachandran restraints generated. 1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1171 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 131 time to evaluate : 0.342 Fit side-chains REVERT: A 30 THR cc_start: 0.7082 (OUTLIER) cc_final: 0.6788 (t) REVERT: A 129 ARG cc_start: 0.6595 (OUTLIER) cc_final: 0.6154 (mmt180) REVERT: A 240 ASP cc_start: 0.8438 (m-30) cc_final: 0.8122 (m-30) REVERT: A 250 SER cc_start: 0.8191 (OUTLIER) cc_final: 0.7738 (m) REVERT: A 259 LYS cc_start: 0.8133 (mtpm) cc_final: 0.7601 (ttpp) REVERT: A 357 LYS cc_start: 0.7256 (pptt) cc_final: 0.7012 (mmmt) REVERT: A 476 MET cc_start: 0.8330 (tpp) cc_final: 0.8023 (mmt) REVERT: A 628 ASP cc_start: 0.7452 (p0) cc_final: 0.7136 (t70) REVERT: A 696 ASP cc_start: 0.8255 (t70) cc_final: 0.7696 (m-30) REVERT: A 735 ARG cc_start: 0.7781 (ptt90) cc_final: 0.7493 (ptp-110) REVERT: A 787 ASP cc_start: 0.7544 (t0) cc_final: 0.7342 (m-30) REVERT: A 792 ASP cc_start: 0.7909 (t0) cc_final: 0.7572 (t0) REVERT: A 841 MET cc_start: 0.7794 (ptp) cc_final: 0.7139 (ptm) REVERT: A 1211 LEU cc_start: 0.8843 (OUTLIER) cc_final: 0.8384 (tp) REVERT: A 1280 MET cc_start: 0.7839 (OUTLIER) cc_final: 0.7374 (pmm) REVERT: A 1300 ARG cc_start: 0.6863 (tmt170) cc_final: 0.6568 (tmt90) REVERT: A 1359 LYS cc_start: 0.8633 (mmtm) cc_final: 0.8347 (mmtp) REVERT: A 1385 MET cc_start: 0.7715 (mmp) cc_final: 0.6374 (tmm) REVERT: A 1495 ARG cc_start: 0.6771 (mmt180) cc_final: 0.5518 (mpp-170) outliers start: 41 outliers final: 23 residues processed: 157 average time/residue: 0.4940 time to fit residues: 85.0353 Evaluate side-chains 149 residues out of total 1171 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 121 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 54 PHE Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 129 ARG Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 465 SER Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 650 THR Chi-restraints excluded: chain A residue 698 VAL Chi-restraints excluded: chain A residue 805 HIS Chi-restraints excluded: chain A residue 831 TYR Chi-restraints excluded: chain A residue 834 GLN Chi-restraints excluded: chain A residue 1011 THR Chi-restraints excluded: chain A residue 1032 TYR Chi-restraints excluded: chain A residue 1136 SER Chi-restraints excluded: chain A residue 1211 LEU Chi-restraints excluded: chain A residue 1240 THR Chi-restraints excluded: chain A residue 1249 MET Chi-restraints excluded: chain A residue 1280 MET Chi-restraints excluded: chain A residue 1322 VAL Chi-restraints excluded: chain A residue 1363 HIS Chi-restraints excluded: chain A residue 1365 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 101 optimal weight: 0.9990 chunk 88 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 129 optimal weight: 9.9990 chunk 77 optimal weight: 0.9990 chunk 1 optimal weight: 0.6980 chunk 31 optimal weight: 0.5980 chunk 98 optimal weight: 0.6980 chunk 48 optimal weight: 0.8980 chunk 13 optimal weight: 2.9990 chunk 127 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 805 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 809 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 827 HIS A1406 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.172677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.131233 restraints weight = 11888.312| |-----------------------------------------------------------------------------| r_work (start): 0.3481 rms_B_bonded: 1.91 r_work: 0.3229 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3098 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.3050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 10975 Z= 0.160 Angle : 0.576 10.878 14930 Z= 0.288 Chirality : 0.042 0.197 1733 Planarity : 0.004 0.051 1832 Dihedral : 6.068 79.933 1700 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 2.90 % Allowed : 25.28 % Favored : 71.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.47 (0.23), residues: 1315 helix: 1.76 (0.17), residues: 893 sheet: -0.57 (0.59), residues: 68 loop : -0.67 (0.32), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A1065 TYR 0.022 0.001 TYR A1242 PHE 0.027 0.002 PHE A 558 TRP 0.017 0.001 TRP A1245 HIS 0.022 0.001 HIS A 805 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.16 (10975) covalent geometry : angle 0.57613 / 0.29 (14930) hydrogen bonds : bond 0.04535 / 2.83 ( 706) hydrogen bonds : angle 4.19852 / 3.01 ( 2082) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2630 Ramachandran restraints generated. 1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2630 Ramachandran restraints generated. 1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1171 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 126 time to evaluate : 0.424 Fit side-chains REVERT: A 129 ARG cc_start: 0.6652 (OUTLIER) cc_final: 0.6207 (mmt180) REVERT: A 240 ASP cc_start: 0.8480 (m-30) cc_final: 0.8183 (m-30) REVERT: A 259 LYS cc_start: 0.8182 (mtpm) cc_final: 0.7675 (ttpp) REVERT: A 476 MET cc_start: 0.8356 (tpp) cc_final: 0.8045 (mmt) REVERT: A 628 ASP cc_start: 0.7529 (p0) cc_final: 0.7221 (t70) REVERT: A 735 ARG cc_start: 0.7762 (ptt90) cc_final: 0.7511 (ptp-110) REVERT: A 841 MET cc_start: 0.7843 (ptp) cc_final: 0.7166 (ptm) REVERT: A 1211 LEU cc_start: 0.8907 (OUTLIER) cc_final: 0.8456 (tp) REVERT: A 1280 MET cc_start: 0.7880 (OUTLIER) cc_final: 0.7455 (pmm) REVERT: A 1300 ARG cc_start: 0.6922 (tmt170) cc_final: 0.6608 (tmt90) REVERT: A 1359 LYS cc_start: 0.8703 (mmtm) cc_final: 0.8423 (mmtp) REVERT: A 1385 MET cc_start: 0.7831 (mmp) cc_final: 0.6424 (tmm) REVERT: A 1495 ARG cc_start: 0.6853 (mmt180) cc_final: 0.5552 (mpp-170) outliers start: 34 outliers final: 24 residues processed: 146 average time/residue: 0.4872 time to fit residues: 78.1886 Evaluate side-chains 148 residues out of total 1171 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 121 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 54 PHE Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 129 ARG Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 465 SER Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 650 THR Chi-restraints excluded: chain A residue 698 VAL Chi-restraints excluded: chain A residue 831 TYR Chi-restraints excluded: chain A residue 1011 THR Chi-restraints excluded: chain A residue 1032 TYR Chi-restraints excluded: chain A residue 1136 SER Chi-restraints excluded: chain A residue 1211 LEU Chi-restraints excluded: chain A residue 1240 THR Chi-restraints excluded: chain A residue 1249 MET Chi-restraints excluded: chain A residue 1280 MET Chi-restraints excluded: chain A residue 1307 LEU Chi-restraints excluded: chain A residue 1355 ILE Chi-restraints excluded: chain A residue 1363 HIS Chi-restraints excluded: chain A residue 1365 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 110 optimal weight: 2.9990 chunk 56 optimal weight: 4.9990 chunk 127 optimal weight: 0.7980 chunk 59 optimal weight: 2.9990 chunk 35 optimal weight: 0.1980 chunk 11 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 89 optimal weight: 0.6980 chunk 38 optimal weight: 0.0570 chunk 105 optimal weight: 2.9990 overall best weight: 0.7500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 805 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 809 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 827 HIS A1406 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.172743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.131498 restraints weight = 11980.665| |-----------------------------------------------------------------------------| r_work (start): 0.3485 rms_B_bonded: 2.07 r_work: 0.3206 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3074 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.3105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 10975 Z= 0.158 Angle : 0.580 11.764 14930 Z= 0.289 Chirality : 0.042 0.197 1733 Planarity : 0.004 0.051 1832 Dihedral : 5.994 80.120 1700 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 2.99 % Allowed : 25.45 % Favored : 71.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.50 (0.23), residues: 1315 helix: 1.77 (0.17), residues: 894 sheet: -0.45 (0.60), residues: 68 loop : -0.66 (0.32), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A1065 TYR 0.022 0.001 TYR A1242 PHE 0.028 0.002 PHE A 558 TRP 0.018 0.001 TRP A1245 HIS 0.007 0.001 HIS A 382 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.16 (10975) covalent geometry : angle 0.57973 / 0.29 (14930) hydrogen bonds : bond 0.04528 / 2.82 ( 706) hydrogen bonds : angle 4.19129 / 3.00 ( 2082) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3731.09 seconds wall clock time: 64 minutes 30.64 seconds (3870.64 seconds total)