Starting phenix.real_space_refine on Sun May 3 05:32:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9lga_63059/05_2026/9lga_63059_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9lga_63059/05_2026/9lga_63059.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.36 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9lga_63059/05_2026/9lga_63059.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9lga_63059/05_2026/9lga_63059.map" model { file = "/net/cci-nas-00/data/ceres_data/9lga_63059/05_2026/9lga_63059_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9lga_63059/05_2026/9lga_63059_neut.cif" } resolution = 3.36 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= 0.067 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 6926 2.51 5 N 1761 2.21 5 O 1894 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10638 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 10585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1333, 10585 Classifications: {'peptide': 1333} Link IDs: {'PTRANS': 49, 'TRANS': 1283} Chain breaks: 8 Chain: "A" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 53 Unusual residues: {'4YH': 1, 'GSH': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 2.63, per 1000 atoms: 0.25 Number of scatterers: 10638 At special positions: 0 Unit cell: (81, 114, 151, 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 1894 8.00 N 1761 7.00 C 6926 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: 0.85 Conformation dependent library (CDL) restraints added in 595.1 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: 53 helices and 5 sheets defined 72.3% alpha, 5.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.41 Creating SS restraints... Processing helix chain 'A' and resid 17 through 22 removed outlier: 3.676A 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 136 through 160 removed outlier: 4.643A pdb=" N TRP A 142 " --> pdb=" O MET A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 191 removed outlier: 3.543A pdb=" N PHE A 175 " --> pdb=" O ARG A 171 " (cutoff:3.500A) removed outlier: 4.033A 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 221 through 223 No H-bonds generated for 'chain 'A' and resid 221 through 223' 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 340 Proline residue: A 323 - end of helix removed outlier: 3.882A pdb=" N PHE A 340 " --> pdb=" O ASP A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 355 Processing helix chain 'A' and resid 359 through 408 removed outlier: 3.938A pdb=" N GLY A 363 " --> pdb=" O PRO A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 418 removed outlier: 3.544A pdb=" N SER A 418 " --> pdb=" O ALA A 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 419 through 441 removed outlier: 3.883A pdb=" N ASP A 430 " --> pdb=" O LEU A 426 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ALA A 431 " --> pdb=" O MET A 427 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N THR A 439 " --> pdb=" O MET A 435 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N TYR A 440 " --> pdb=" O ASP A 436 " (cutoff:3.500A) Processing helix chain 'A' and resid 442 through 462 Proline residue: A 448 - end of helix Processing helix chain 'A' and resid 465 through 510 removed outlier: 3.750A pdb=" N GLY A 469 " --> pdb=" O SER A 465 " (cutoff:3.500A) Proline residue: A 478 - end of helix removed outlier: 3.861A pdb=" N ARG A 501 " --> pdb=" O SER A 497 " (cutoff:3.500A) Processing helix chain 'A' and resid 511 through 519 Processing helix chain 'A' and resid 520 through 555 removed outlier: 3.610A pdb=" N VAL A 538 " --> pdb=" O GLU A 534 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N TYR A 544 " --> pdb=" O LYS A 540 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEU A 545 " --> pdb=" O LYS A 541 " (cutoff:3.500A) Processing helix chain 'A' and resid 555 through 572 removed outlier: 3.559A pdb=" N SER A 563 " --> pdb=" O LEU A 559 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N ASP A 572 " --> pdb=" O TYR A 568 " (cutoff:3.500A) Processing helix chain 'A' and resid 578 through 621 removed outlier: 3.740A pdb=" N VAL A 584 " --> pdb=" O GLN A 580 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N SER A 585 " --> pdb=" O LYS A 581 " (cutoff:3.500A) removed outlier: 4.260A 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 removed outlier: 3.508A pdb=" N SER A 612 " --> pdb=" O GLN A 608 " (cutoff:3.500A) Processing helix chain 'A' and resid 626 through 630 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: 3.659A 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: 3.658A pdb=" N ARG A 758 " --> pdb=" O SER A 755 " (cutoff:3.500A) removed outlier: 3.710A 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 969 removed outlier: 3.831A 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 1010 through 1058 removed outlier: 3.753A pdb=" N ARG A1014 " --> pdb=" O HIS A1010 " (cutoff:3.500A) Processing helix chain 'A' and resid 1059 through 1066 removed outlier: 3.578A pdb=" N PHE A1063 " --> pdb=" O PRO A1059 " (cutoff:3.500A) Processing helix chain 'A' and resid 1067 through 1084 removed outlier: 3.616A pdb=" N LEU A1071 " --> pdb=" O PRO A1067 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N GLU A1078 " --> pdb=" O ARG A1074 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N LEU A1079 " --> pdb=" O PHE A1075 " (cutoff:3.500A) Processing helix chain 'A' and resid 1084 through 1111 removed outlier: 4.086A pdb=" N GLN A1088 " --> pdb=" O SER A1084 " (cutoff:3.500A) Processing helix chain 'A' and resid 1112 through 1116 Processing helix chain 'A' and resid 1117 through 1160 removed outlier: 3.798A pdb=" N SER A1135 " --> pdb=" O PHE A1131 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ARG A1137 " --> pdb=" O VAL A1133 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N GLN A1138 " --> pdb=" O ALA A1134 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N SER A1144 " --> pdb=" O LYS A1140 " (cutoff:3.500A) removed outlier: 4.053A 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 1225 through 1264 removed outlier: 3.534A pdb=" N THR A1240 " --> pdb=" O SER A1236 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N THR A1241 " --> pdb=" O LEU A1237 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ASN A1244 " --> pdb=" O THR A1240 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N TRP A1245 " --> pdb=" O THR A1241 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N VAL A1258 " --> pdb=" O GLU A1254 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N ALA A1259 " --> pdb=" O THR A1255 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N VAL A1260 " --> pdb=" O ASN A1256 " (cutoff:3.500A) Processing helix chain 'A' and resid 1331 through 1340 removed outlier: 3.668A 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: 3.864A 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: 3.976A pdb=" N GLN A1474 " --> pdb=" O THR A1470 " (cutoff:3.500A) Processing helix chain 'A' and resid 1486 through 1493 removed outlier: 3.879A 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: 4.053A 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: 5.593A pdb=" N ILE A 664 " --> pdb=" O ASN A 648 " (cutoff:3.500A) removed outlier: 6.896A 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: 7.074A 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: 6.508A 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: 6.256A 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: 6.329A pdb=" N VAL A 674 " --> pdb=" O LEU A 824 " (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: 6.075A pdb=" N ALA A 675 " --> pdb=" O ILE A 839 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1003 through 1004 Processing sheet with id=AA4, first strand: chain 'A' and resid 1309 through 1316 removed outlier: 5.577A pdb=" N LYS A1310 " --> pdb=" O LEU A1299 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N LEU A1299 " --> pdb=" O LYS A1310 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N VAL A1314 " --> pdb=" O ARG A1295 " (cutoff:3.500A) removed outlier: 4.967A 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=AA5, 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: 8.028A 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: 6.681A pdb=" N VAL A1325 " --> pdb=" O LEU A1499 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N VAL A1496 " --> pdb=" O TRP A1507 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N TRP A1507 " --> pdb=" O VAL A1496 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N VAL A1498 " --> pdb=" O GLN A1505 " (cutoff:3.500A) 693 hydrogen bonds defined for protein. 2040 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.24 Time building geometry restraints manager: 1.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.27: 1676 1.27 - 1.41: 2726 1.41 - 1.54: 6354 1.54 - 1.68: 26 1.68 - 1.81: 92 Bond restraints: 10874 Sorted by residual: bond pdb=" N VAL A1289 " pdb=" CA VAL A1289 " ideal model delta sigma weight residual 1.460 1.492 -0.032 8.60e-03 1.35e+04 1.35e+01 bond pdb=" N PHE A 594 " pdb=" CA PHE A 594 " ideal model delta sigma weight residual 1.462 1.489 -0.027 7.70e-03 1.69e+04 1.22e+01 bond pdb=" C3 GSH A1602 " pdb=" O32 GSH A1602 " ideal model delta sigma weight residual 1.308 1.239 0.069 2.00e-02 2.50e+03 1.19e+01 bond pdb=" C1 GSH A1602 " pdb=" O12 GSH A1602 " ideal model delta sigma weight residual 1.307 1.242 0.065 1.90e-02 2.77e+03 1.18e+01 bond pdb=" N TRP A1286 " pdb=" CA TRP A1286 " ideal model delta sigma weight residual 1.462 1.487 -0.025 7.70e-03 1.69e+04 1.05e+01 ... (remaining 10869 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.87: 14013 1.87 - 3.73: 663 3.73 - 5.60: 63 5.60 - 7.47: 14 7.47 - 9.33: 7 Bond angle restraints: 14760 Sorted by residual: angle pdb=" N VAL A1289 " pdb=" CA VAL A1289 " pdb=" C VAL A1289 " ideal model delta sigma weight residual 113.71 107.66 6.05 9.50e-01 1.11e+00 4.06e+01 angle pdb=" N PRO A 627 " pdb=" CA PRO A 627 " pdb=" C PRO A 627 " ideal model delta sigma weight residual 113.65 106.74 6.91 1.35e+00 5.49e-01 2.62e+01 angle pdb=" N TRP A 553 " pdb=" CA TRP A 553 " pdb=" C TRP A 553 " ideal model delta sigma weight residual 114.12 107.55 6.57 1.39e+00 5.18e-01 2.23e+01 angle pdb=" N ASN A1207 " pdb=" CA ASN A1207 " pdb=" C ASN A1207 " ideal model delta sigma weight residual 111.36 106.98 4.38 1.09e+00 8.42e-01 1.61e+01 angle pdb=" N LEU A 139 " pdb=" CA LEU A 139 " pdb=" C LEU A 139 " ideal model delta sigma weight residual 112.12 106.97 5.15 1.34e+00 5.57e-01 1.48e+01 ... (remaining 14755 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.57: 6089 28.57 - 57.14: 338 57.14 - 85.71: 47 85.71 - 114.28: 2 114.28 - 142.85: 4 Dihedral angle restraints: 6480 sinusoidal: 2589 harmonic: 3891 Sorted by residual: dihedral pdb=" C22 4YH A1601 " pdb=" C1 4YH A1601 " pdb=" C15 4YH A1601 " pdb=" C28 4YH A1601 " ideal model delta sinusoidal sigma weight residual -91.13 51.72 -142.85 1 3.00e+01 1.11e-03 1.92e+01 dihedral pdb=" C28 4YH A1601 " pdb=" C1 4YH A1601 " pdb=" C15 4YH A1601 " pdb=" C3 4YH A1601 " ideal model delta sinusoidal sigma weight residual 205.29 65.92 139.37 1 3.00e+01 1.11e-03 1.88e+01 dihedral pdb=" C22 4YH A1601 " pdb=" C1 4YH A1601 " pdb=" C15 4YH A1601 " pdb=" C29 4YH A1601 " ideal model delta sinusoidal sigma weight residual 36.95 174.48 -137.53 1 3.00e+01 1.11e-03 1.85e+01 ... (remaining 6477 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 1424 0.065 - 0.130: 235 0.130 - 0.195: 53 0.195 - 0.260: 2 0.260 - 0.326: 1 Chirality restraints: 1715 Sorted by residual: chirality pdb=" C1 4YH A1601 " pdb=" C15 4YH A1601 " pdb=" C2 4YH A1601 " pdb=" C22 4YH A1601 " both_signs ideal model delta sigma weight residual False 2.35 2.68 -0.33 2.00e-01 2.50e+01 2.65e+00 chirality pdb=" CA CYS A 43 " pdb=" N CYS A 43 " pdb=" C CYS A 43 " pdb=" CB CYS A 43 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.07e+00 chirality pdb=" CA ILE A1342 " pdb=" N ILE A1342 " pdb=" C ILE A1342 " pdb=" CB ILE A1342 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.21 2.00e-01 2.50e+01 1.06e+00 ... (remaining 1712 not shown) Planarity restraints: 1824 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 GSH A1602 " -0.084 2.00e-02 2.50e+03 1.84e-01 4.24e+02 pdb=" CA2 GSH A1602 " 0.168 2.00e-02 2.50e+03 pdb=" CA3 GSH A1602 " 0.227 2.00e-02 2.50e+03 pdb=" N3 GSH A1602 " -0.287 2.00e-02 2.50e+03 pdb=" O2 GSH A1602 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG1 GSH A1602 " 0.141 2.00e-02 2.50e+03 1.58e-01 3.11e+02 pdb=" CD1 GSH A1602 " -0.057 2.00e-02 2.50e+03 pdb=" OE1 GSH A1602 " -0.022 2.00e-02 2.50e+03 pdb=" CA2 GSH A1602 " 0.192 2.00e-02 2.50e+03 pdb=" N2 GSH A1602 " -0.253 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS A1264 " 0.016 2.00e-02 2.50e+03 3.11e-02 9.65e+00 pdb=" C LYS A1264 " -0.054 2.00e-02 2.50e+03 pdb=" O LYS A1264 " 0.019 2.00e-02 2.50e+03 pdb=" N GLU A1265 " 0.019 2.00e-02 2.50e+03 ... (remaining 1821 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 3098 2.82 - 3.34: 11069 3.34 - 3.86: 18362 3.86 - 4.38: 20852 4.38 - 4.90: 35815 Nonbonded interactions: 89196 Sorted by model distance: nonbonded pdb=" O ALA A 484 " pdb=" OG1 THR A 487 " model vdw 2.298 3.040 nonbonded pdb=" NH1 ARG A1341 " pdb=" O ILE A1357 " model vdw 2.344 3.120 nonbonded pdb=" OH TYR A1132 " pdb=" OD1 ASN A1195 " model vdw 2.353 3.040 nonbonded pdb=" O THR A1111 " pdb=" OG1 THR A1111 " model vdw 2.366 3.040 nonbonded pdb=" NZ LYS A 396 " pdb=" OD1 ASN A1184 " model vdw 2.375 3.120 ... (remaining 89191 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: 2.170 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: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 11.990 Find NCS groups from input model: 0.050 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:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7345 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 : 0.006 0.069 10874 Z= 0.396 Angle : 0.828 9.334 14760 Z= 0.546 Chirality : 0.052 0.326 1715 Planarity : 0.011 0.184 1824 Dihedral : 17.328 142.848 3958 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 0.00 % Allowed : 19.81 % 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: 0.18 (0.22), residues: 1315 helix: 0.68 (0.17), residues: 872 sheet: -0.52 (0.56), residues: 76 loop : -0.89 (0.31), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 735 TYR 0.016 0.001 TYR A 783 PHE 0.028 0.002 PHE A 865 TRP 0.021 0.001 TRP A 553 HIS 0.006 0.001 HIS A 985 Details of bonding type rmsd covalent geometry : bond 0.00585 (10874) covalent geometry : angle 0.82768 (14760) hydrogen bonds : bond 0.15321 ( 693) hydrogen bonds : angle 6.56840 ( 2040) *********************** 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 233 residues out of total 1171 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 233 time to evaluate : 0.403 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 ASN cc_start: 0.7389 (t0) cc_final: 0.7079 (t0) REVERT: A 475 LEU cc_start: 0.8800 (mm) cc_final: 0.8482 (mp) REVERT: A 476 MET cc_start: 0.7717 (tpp) cc_final: 0.7503 (mmp) REVERT: A 761 ILE cc_start: 0.8183 (pt) cc_final: 0.7927 (mt) REVERT: A 1034 MET cc_start: 0.8232 (mmm) cc_final: 0.7553 (tpp) outliers start: 0 outliers final: 0 residues processed: 233 average time/residue: 0.1258 time to fit residues: 40.0062 Evaluate side-chains 125 residues out of total 1171 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 125 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 20.0000 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 10.0000 chunk 91 optimal weight: 1.9990 chunk 55 optimal weight: 5.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 71 ASN ** A 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 362 GLN A 719 ASN ** A 809 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 992 ASN A1207 ASN A1256 ASN A1363 HIS A1392 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.159198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.110451 restraints weight = 13978.361| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 2.33 r_work: 0.3209 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3055 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.2373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 10874 Z= 0.222 Angle : 0.623 8.027 14760 Z= 0.320 Chirality : 0.043 0.236 1715 Planarity : 0.004 0.051 1824 Dihedral : 10.996 124.760 1483 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 3.67 % Allowed : 21.01 % Favored : 75.32 % 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: 1.27 (0.23), residues: 1315 helix: 1.63 (0.17), residues: 885 sheet: -0.18 (0.55), residues: 77 loop : -0.89 (0.32), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A1300 TYR 0.023 0.002 TYR A 710 PHE 0.029 0.002 PHE A 558 TRP 0.018 0.002 TRP A 142 HIS 0.006 0.001 HIS A 382 Details of bonding type rmsd covalent geometry : bond 0.00521 (10874) covalent geometry : angle 0.62329 (14760) hydrogen bonds : bond 0.04919 ( 693) hydrogen bonds : angle 4.53588 ( 2040) *********************** 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 180 residues out of total 1171 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 137 time to evaluate : 0.403 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 40 TRP cc_start: 0.6981 (m-10) cc_final: 0.6605 (m-10) REVERT: A 47 TRP cc_start: 0.7625 (m100) cc_final: 0.6939 (m100) REVERT: A 117 MET cc_start: 0.5924 (mmm) cc_final: 0.5316 (mmm) REVERT: A 387 ILE cc_start: 0.8843 (OUTLIER) cc_final: 0.8628 (mp) REVERT: A 443 MET cc_start: 0.8440 (mmm) cc_final: 0.7941 (mmt) REVERT: A 475 LEU cc_start: 0.8888 (mm) cc_final: 0.8670 (mp) REVERT: A 476 MET cc_start: 0.7844 (tpp) cc_final: 0.7295 (mtt) REVERT: A 518 TYR cc_start: 0.8380 (m-80) cc_final: 0.8073 (m-80) REVERT: A 686 SER cc_start: 0.8084 (m) cc_final: 0.7714 (t) REVERT: A 707 SER cc_start: 0.7468 (OUTLIER) cc_final: 0.7181 (p) REVERT: A 731 GLN cc_start: 0.8411 (tp-100) cc_final: 0.8001 (pm20) REVERT: A 1121 LEU cc_start: 0.8679 (OUTLIER) cc_final: 0.8145 (mp) REVERT: A 1309 LEU cc_start: 0.7778 (mt) cc_final: 0.7519 (mt) REVERT: A 1501 LYS cc_start: 0.8703 (tptp) cc_final: 0.8428 (tptp) outliers start: 43 outliers final: 18 residues processed: 170 average time/residue: 0.0964 time to fit residues: 24.3221 Evaluate side-chains 144 residues out of total 1171 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 123 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 ARG Chi-restraints excluded: chain A residue 135 SER Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 657 ASP Chi-restraints excluded: chain A residue 707 SER Chi-restraints excluded: chain A residue 719 ASN Chi-restraints excluded: chain A residue 809 ASN Chi-restraints excluded: chain A residue 823 LEU Chi-restraints excluded: chain A residue 1003 ILE Chi-restraints excluded: chain A residue 1010 HIS Chi-restraints excluded: chain A residue 1109 LEU Chi-restraints excluded: chain A residue 1121 LEU Chi-restraints excluded: chain A residue 1204 CYS Chi-restraints excluded: chain A residue 1240 THR Chi-restraints excluded: chain A residue 1255 THR Chi-restraints excluded: chain A residue 1258 VAL Chi-restraints excluded: chain A residue 1336 THR Chi-restraints excluded: chain A residue 1357 ILE Chi-restraints excluded: chain A residue 1363 HIS Chi-restraints excluded: chain A residue 1371 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 74 optimal weight: 3.9990 chunk 86 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 93 optimal weight: 0.5980 chunk 31 optimal weight: 0.5980 chunk 96 optimal weight: 1.9990 chunk 90 optimal weight: 0.6980 chunk 127 optimal weight: 7.9990 chunk 122 optimal weight: 5.9990 chunk 39 optimal weight: 0.0070 chunk 40 optimal weight: 1.9990 overall best weight: 0.7800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 230 GLN ** A 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 719 ASN ** A 809 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.162302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.120232 restraints weight = 14172.221| |-----------------------------------------------------------------------------| r_work (start): 0.3541 rms_B_bonded: 2.38 r_work: 0.3263 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3120 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.2822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 10874 Z= 0.156 Angle : 0.556 10.262 14760 Z= 0.282 Chirality : 0.040 0.134 1715 Planarity : 0.004 0.050 1824 Dihedral : 10.600 118.709 1483 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 3.25 % Allowed : 21.09 % Favored : 75.66 % 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: 1.49 (0.23), residues: 1315 helix: 1.81 (0.17), residues: 876 sheet: -0.16 (0.55), residues: 77 loop : -0.76 (0.32), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 723 TYR 0.016 0.001 TYR A1242 PHE 0.024 0.001 PHE A 558 TRP 0.017 0.001 TRP A 94 HIS 0.012 0.001 HIS A1363 Details of bonding type rmsd covalent geometry : bond 0.00356 (10874) covalent geometry : angle 0.55573 (14760) hydrogen bonds : bond 0.04379 ( 693) hydrogen bonds : angle 4.29222 ( 2040) *********************** 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 164 residues out of total 1171 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 126 time to evaluate : 0.443 Fit side-chains REVERT: A 40 TRP cc_start: 0.6897 (m-10) cc_final: 0.6581 (m-10) REVERT: A 47 TRP cc_start: 0.7589 (m100) cc_final: 0.7048 (m100) REVERT: A 117 MET cc_start: 0.6155 (mmm) cc_final: 0.5174 (mmm) REVERT: A 228 MET cc_start: 0.8684 (mmp) cc_final: 0.8463 (mmt) REVERT: A 387 ILE cc_start: 0.8791 (OUTLIER) cc_final: 0.8564 (mp) REVERT: A 443 MET cc_start: 0.8322 (mmm) cc_final: 0.7937 (mmt) REVERT: A 518 TYR cc_start: 0.8148 (m-80) cc_final: 0.7941 (m-80) REVERT: A 686 SER cc_start: 0.7979 (m) cc_final: 0.7549 (t) REVERT: A 731 GLN cc_start: 0.8420 (tp-100) cc_final: 0.8099 (pm20) REVERT: A 1079 LEU cc_start: 0.8517 (OUTLIER) cc_final: 0.8289 (mm) REVERT: A 1121 LEU cc_start: 0.8680 (OUTLIER) cc_final: 0.8288 (mp) REVERT: A 1491 MET cc_start: 0.8209 (tpp) cc_final: 0.7937 (mtm) outliers start: 38 outliers final: 17 residues processed: 153 average time/residue: 0.0830 time to fit residues: 19.6893 Evaluate side-chains 136 residues out of total 1171 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 116 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 ARG Chi-restraints excluded: chain A residue 135 SER Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain A residue 657 ASP Chi-restraints excluded: chain A residue 824 LEU Chi-restraints excluded: chain A residue 1003 ILE Chi-restraints excluded: chain A residue 1010 HIS Chi-restraints excluded: chain A residue 1011 THR Chi-restraints excluded: chain A residue 1055 VAL Chi-restraints excluded: chain A residue 1079 LEU Chi-restraints excluded: chain A residue 1121 LEU Chi-restraints excluded: chain A residue 1156 GLU Chi-restraints excluded: chain A residue 1171 GLU Chi-restraints excluded: chain A residue 1204 CYS Chi-restraints excluded: chain A residue 1258 VAL Chi-restraints excluded: chain A residue 1336 THR Chi-restraints excluded: chain A residue 1357 ILE Chi-restraints excluded: chain A residue 1439 LEU Chi-restraints excluded: chain A residue 1475 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 0 optimal weight: 4.9990 chunk 91 optimal weight: 2.9990 chunk 72 optimal weight: 0.5980 chunk 52 optimal weight: 1.9990 chunk 41 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 47 optimal weight: 0.8980 chunk 77 optimal weight: 10.0000 chunk 67 optimal weight: 9.9990 chunk 40 optimal weight: 0.8980 chunk 106 optimal weight: 1.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 GLN A 71 ASN ** A 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 809 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1256 ASN A1363 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.160269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.116422 restraints weight = 14374.843| |-----------------------------------------------------------------------------| r_work (start): 0.3488 rms_B_bonded: 2.25 r_work: 0.3214 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3071 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.3193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 10874 Z= 0.204 Angle : 0.583 12.660 14760 Z= 0.294 Chirality : 0.042 0.285 1715 Planarity : 0.004 0.048 1824 Dihedral : 10.357 114.542 1483 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 4.36 % Allowed : 20.84 % Favored : 74.81 % 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: 1.34 (0.23), residues: 1315 helix: 1.66 (0.17), residues: 879 sheet: -0.02 (0.57), residues: 77 loop : -0.78 (0.32), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1366 TYR 0.017 0.002 TYR A1242 PHE 0.028 0.002 PHE A 558 TRP 0.013 0.001 TRP A1245 HIS 0.006 0.001 HIS A 382 Details of bonding type rmsd covalent geometry : bond 0.00478 (10874) covalent geometry : angle 0.58289 (14760) hydrogen bonds : bond 0.04420 ( 693) hydrogen bonds : angle 4.29699 ( 2040) *********************** 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 176 residues out of total 1171 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 125 time to evaluate : 0.439 Fit side-chains REVERT: A 40 TRP cc_start: 0.6924 (m-10) cc_final: 0.6661 (m-10) REVERT: A 47 TRP cc_start: 0.7759 (m100) cc_final: 0.7296 (m100) REVERT: A 117 MET cc_start: 0.6164 (mmm) cc_final: 0.5083 (mmm) REVERT: A 387 ILE cc_start: 0.8799 (OUTLIER) cc_final: 0.8584 (mp) REVERT: A 686 SER cc_start: 0.8094 (m) cc_final: 0.7672 (t) REVERT: A 719 ASN cc_start: 0.8350 (OUTLIER) cc_final: 0.8144 (t0) REVERT: A 731 GLN cc_start: 0.8520 (tp-100) cc_final: 0.8202 (pm20) REVERT: A 1079 LEU cc_start: 0.8635 (OUTLIER) cc_final: 0.8433 (mm) REVERT: A 1085 MET cc_start: 0.8069 (ptp) cc_final: 0.7460 (tpp) REVERT: A 1121 LEU cc_start: 0.8785 (OUTLIER) cc_final: 0.8445 (mp) REVERT: A 1175 ARG cc_start: 0.7892 (ttm-80) cc_final: 0.7580 (tmm160) REVERT: A 1295 ARG cc_start: 0.8024 (ttp-170) cc_final: 0.7416 (mtm-85) REVERT: A 1321 LYS cc_start: 0.6575 (OUTLIER) cc_final: 0.6018 (mmtt) outliers start: 51 outliers final: 30 residues processed: 161 average time/residue: 0.0989 time to fit residues: 23.6415 Evaluate side-chains 152 residues out of total 1171 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 117 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 PHE Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 128 ARG Chi-restraints excluded: chain A residue 135 SER Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain A residue 477 VAL Chi-restraints excluded: chain A residue 556 THR Chi-restraints excluded: chain A residue 719 ASN Chi-restraints excluded: chain A residue 824 LEU Chi-restraints excluded: chain A residue 1003 ILE Chi-restraints excluded: chain A residue 1010 HIS Chi-restraints excluded: chain A residue 1011 THR Chi-restraints excluded: chain A residue 1041 ILE Chi-restraints excluded: chain A residue 1055 VAL Chi-restraints excluded: chain A residue 1079 LEU Chi-restraints excluded: chain A residue 1109 LEU Chi-restraints excluded: chain A residue 1121 LEU Chi-restraints excluded: chain A residue 1156 GLU Chi-restraints excluded: chain A residue 1171 GLU Chi-restraints excluded: chain A residue 1204 CYS Chi-restraints excluded: chain A residue 1255 THR Chi-restraints excluded: chain A residue 1258 VAL Chi-restraints excluded: chain A residue 1321 LYS Chi-restraints excluded: chain A residue 1336 THR Chi-restraints excluded: chain A residue 1357 ILE Chi-restraints excluded: chain A residue 1363 HIS Chi-restraints excluded: chain A residue 1364 ASP Chi-restraints excluded: chain A residue 1371 ILE Chi-restraints excluded: chain A residue 1387 LEU Chi-restraints excluded: chain A residue 1431 VAL Chi-restraints excluded: chain A residue 1439 LEU Chi-restraints excluded: chain A residue 1475 PHE Chi-restraints excluded: chain A residue 1489 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 56 optimal weight: 0.6980 chunk 87 optimal weight: 0.8980 chunk 91 optimal weight: 0.8980 chunk 41 optimal weight: 0.7980 chunk 88 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 90 optimal weight: 0.7980 chunk 14 optimal weight: 4.9990 chunk 61 optimal weight: 0.9990 chunk 106 optimal weight: 0.5980 chunk 9 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 GLN A 71 ASN ** A 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 809 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.161013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.117067 restraints weight = 14150.081| |-----------------------------------------------------------------------------| r_work (start): 0.3504 rms_B_bonded: 2.10 r_work: 0.3258 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3119 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.3348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10874 Z= 0.150 Angle : 0.545 11.688 14760 Z= 0.273 Chirality : 0.040 0.268 1715 Planarity : 0.004 0.047 1824 Dihedral : 10.017 118.086 1483 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 3.59 % Allowed : 21.78 % Favored : 74.64 % 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: 1.74 (0.17), residues: 885 sheet: -0.04 (0.58), residues: 77 loop : -0.75 (0.32), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 723 TYR 0.014 0.001 TYR A 518 PHE 0.024 0.001 PHE A 865 TRP 0.014 0.001 TRP A 94 HIS 0.008 0.001 HIS A1363 Details of bonding type rmsd covalent geometry : bond 0.00342 (10874) covalent geometry : angle 0.54533 (14760) hydrogen bonds : bond 0.04160 ( 693) hydrogen bonds : angle 4.19915 ( 2040) *********************** 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 169 residues out of total 1171 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 127 time to evaluate : 0.426 Fit side-chains REVERT: A 40 TRP cc_start: 0.6895 (m-10) cc_final: 0.6686 (m-10) REVERT: A 47 TRP cc_start: 0.7796 (m100) cc_final: 0.7355 (m100) REVERT: A 117 MET cc_start: 0.6141 (mmm) cc_final: 0.5012 (mmm) REVERT: A 387 ILE cc_start: 0.8788 (OUTLIER) cc_final: 0.8577 (mp) REVERT: A 443 MET cc_start: 0.8423 (mmt) cc_final: 0.7768 (mmt) REVERT: A 503 LYS cc_start: 0.7429 (ttpp) cc_final: 0.7072 (pttt) REVERT: A 686 SER cc_start: 0.8049 (m) cc_final: 0.7622 (t) REVERT: A 731 GLN cc_start: 0.8527 (tp-100) cc_final: 0.8160 (pm20) REVERT: A 1034 MET cc_start: 0.8553 (tpp) cc_final: 0.8168 (tpp) REVERT: A 1079 LEU cc_start: 0.8567 (OUTLIER) cc_final: 0.8352 (mm) REVERT: A 1085 MET cc_start: 0.7942 (ptp) cc_final: 0.7397 (tpp) REVERT: A 1121 LEU cc_start: 0.8765 (OUTLIER) cc_final: 0.8479 (mp) REVERT: A 1175 ARG cc_start: 0.7834 (ttm-80) cc_final: 0.7556 (tmm160) REVERT: A 1280 MET cc_start: 0.7311 (ppp) cc_final: 0.6836 (ppp) REVERT: A 1295 ARG cc_start: 0.7993 (ttp-170) cc_final: 0.7472 (mtm-85) REVERT: A 1491 MET cc_start: 0.8105 (tpp) cc_final: 0.7904 (mtm) outliers start: 42 outliers final: 25 residues processed: 158 average time/residue: 0.0844 time to fit residues: 20.2718 Evaluate side-chains 140 residues out of total 1171 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 112 time to evaluate : 0.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 PHE Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 128 ARG Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain A residue 556 THR Chi-restraints excluded: chain A residue 824 LEU Chi-restraints excluded: chain A residue 1003 ILE Chi-restraints excluded: chain A residue 1010 HIS Chi-restraints excluded: chain A residue 1011 THR Chi-restraints excluded: chain A residue 1041 ILE Chi-restraints excluded: chain A residue 1055 VAL Chi-restraints excluded: chain A residue 1079 LEU Chi-restraints excluded: chain A residue 1086 ILE Chi-restraints excluded: chain A residue 1113 MET Chi-restraints excluded: chain A residue 1121 LEU Chi-restraints excluded: chain A residue 1156 GLU Chi-restraints excluded: chain A residue 1171 GLU Chi-restraints excluded: chain A residue 1204 CYS Chi-restraints excluded: chain A residue 1239 VAL Chi-restraints excluded: chain A residue 1255 THR Chi-restraints excluded: chain A residue 1258 VAL Chi-restraints excluded: chain A residue 1336 THR Chi-restraints excluded: chain A residue 1357 ILE Chi-restraints excluded: chain A residue 1371 ILE Chi-restraints excluded: chain A residue 1431 VAL Chi-restraints excluded: chain A residue 1439 LEU Chi-restraints excluded: chain A residue 1475 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 103 optimal weight: 0.9990 chunk 81 optimal weight: 0.5980 chunk 10 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 72 optimal weight: 0.9990 chunk 102 optimal weight: 0.6980 chunk 119 optimal weight: 0.9990 chunk 15 optimal weight: 4.9990 chunk 117 optimal weight: 0.0970 chunk 91 optimal weight: 2.9990 chunk 125 optimal weight: 10.0000 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 GLN A 71 ASN ** A 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 719 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.161739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.118050 restraints weight = 14379.637| |-----------------------------------------------------------------------------| r_work (start): 0.3520 rms_B_bonded: 2.20 r_work: 0.3270 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3132 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.3508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10874 Z= 0.141 Angle : 0.539 12.540 14760 Z= 0.268 Chirality : 0.040 0.256 1715 Planarity : 0.004 0.046 1824 Dihedral : 9.561 119.151 1483 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 3.76 % Allowed : 20.92 % Favored : 75.32 % 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: 1.59 (0.23), residues: 1315 helix: 1.88 (0.17), residues: 879 sheet: -0.41 (0.55), residues: 87 loop : -0.62 (0.33), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 723 TYR 0.021 0.001 TYR A 518 PHE 0.023 0.001 PHE A 558 TRP 0.013 0.001 TRP A1245 HIS 0.007 0.001 HIS A1363 Details of bonding type rmsd covalent geometry : bond 0.00320 (10874) covalent geometry : angle 0.53854 (14760) hydrogen bonds : bond 0.04025 ( 693) hydrogen bonds : angle 4.10518 ( 2040) *********************** 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 167 residues out of total 1171 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 123 time to evaluate : 0.431 Fit side-chains REVERT: A 47 TRP cc_start: 0.7822 (m100) cc_final: 0.7403 (m100) REVERT: A 117 MET cc_start: 0.6353 (mmm) cc_final: 0.5057 (mmm) REVERT: A 128 ARG cc_start: 0.7617 (OUTLIER) cc_final: 0.7012 (ttm-80) REVERT: A 387 ILE cc_start: 0.8758 (OUTLIER) cc_final: 0.8549 (mp) REVERT: A 503 LYS cc_start: 0.7385 (ttpp) cc_final: 0.7022 (pttt) REVERT: A 518 TYR cc_start: 0.8162 (m-80) cc_final: 0.7948 (m-80) REVERT: A 686 SER cc_start: 0.8051 (m) cc_final: 0.7631 (t) REVERT: A 1079 LEU cc_start: 0.8528 (OUTLIER) cc_final: 0.8317 (mm) REVERT: A 1085 MET cc_start: 0.7861 (ptp) cc_final: 0.7397 (tpp) REVERT: A 1121 LEU cc_start: 0.8727 (OUTLIER) cc_final: 0.8417 (mp) REVERT: A 1175 ARG cc_start: 0.7839 (ttm-80) cc_final: 0.7561 (tmm160) REVERT: A 1242 TYR cc_start: 0.8480 (m-10) cc_final: 0.8204 (m-10) REVERT: A 1280 MET cc_start: 0.7369 (ppp) cc_final: 0.7072 (ppp) REVERT: A 1295 ARG cc_start: 0.7967 (ttp-170) cc_final: 0.7558 (mtm-85) outliers start: 44 outliers final: 28 residues processed: 155 average time/residue: 0.0834 time to fit residues: 19.4419 Evaluate side-chains 148 residues out of total 1171 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 116 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 PHE Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 128 ARG Chi-restraints excluded: chain A residue 135 SER Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain A residue 556 THR Chi-restraints excluded: chain A residue 657 ASP Chi-restraints excluded: chain A residue 662 HIS Chi-restraints excluded: chain A residue 817 LEU Chi-restraints excluded: chain A residue 824 LEU Chi-restraints excluded: chain A residue 1003 ILE Chi-restraints excluded: chain A residue 1010 HIS Chi-restraints excluded: chain A residue 1011 THR Chi-restraints excluded: chain A residue 1041 ILE Chi-restraints excluded: chain A residue 1055 VAL Chi-restraints excluded: chain A residue 1079 LEU Chi-restraints excluded: chain A residue 1086 ILE Chi-restraints excluded: chain A residue 1113 MET Chi-restraints excluded: chain A residue 1121 LEU Chi-restraints excluded: chain A residue 1156 GLU Chi-restraints excluded: chain A residue 1171 GLU Chi-restraints excluded: chain A residue 1204 CYS Chi-restraints excluded: chain A residue 1231 LEU Chi-restraints excluded: chain A residue 1239 VAL Chi-restraints excluded: chain A residue 1255 THR Chi-restraints excluded: chain A residue 1258 VAL Chi-restraints excluded: chain A residue 1336 THR Chi-restraints excluded: chain A residue 1357 ILE Chi-restraints excluded: chain A residue 1371 ILE Chi-restraints excluded: chain A residue 1431 VAL Chi-restraints excluded: chain A residue 1439 LEU Chi-restraints excluded: chain A residue 1475 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 77 optimal weight: 0.8980 chunk 96 optimal weight: 2.9990 chunk 95 optimal weight: 0.5980 chunk 8 optimal weight: 7.9990 chunk 6 optimal weight: 2.9990 chunk 114 optimal weight: 9.9990 chunk 59 optimal weight: 0.9990 chunk 47 optimal weight: 0.2980 chunk 78 optimal weight: 3.9990 chunk 102 optimal weight: 0.9990 chunk 104 optimal weight: 0.6980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 GLN A 71 ASN ** A 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.162198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.118100 restraints weight = 14358.768| |-----------------------------------------------------------------------------| r_work (start): 0.3528 rms_B_bonded: 2.18 r_work: 0.3276 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3138 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.3650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10874 Z= 0.141 Angle : 0.538 10.620 14760 Z= 0.268 Chirality : 0.040 0.235 1715 Planarity : 0.004 0.046 1824 Dihedral : 9.019 122.368 1483 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 3.42 % Allowed : 21.35 % Favored : 75.23 % 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: 1.62 (0.23), residues: 1315 helix: 1.89 (0.17), residues: 879 sheet: -0.37 (0.56), residues: 87 loop : -0.61 (0.33), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1384 TYR 0.011 0.001 TYR A 710 PHE 0.023 0.001 PHE A 558 TRP 0.032 0.001 TRP A 40 HIS 0.006 0.001 HIS A 985 Details of bonding type rmsd covalent geometry : bond 0.00321 (10874) covalent geometry : angle 0.53811 (14760) hydrogen bonds : bond 0.03970 ( 693) hydrogen bonds : angle 4.08497 ( 2040) *********************** 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 162 residues out of total 1171 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 122 time to evaluate : 0.270 Fit side-chains revert: symmetry clash REVERT: A 47 TRP cc_start: 0.7846 (m100) cc_final: 0.7491 (m100) REVERT: A 66 GLN cc_start: 0.8426 (OUTLIER) cc_final: 0.8199 (pp30) REVERT: A 387 ILE cc_start: 0.8745 (OUTLIER) cc_final: 0.8537 (mp) REVERT: A 503 LYS cc_start: 0.7348 (ttpp) cc_final: 0.6934 (pttt) REVERT: A 518 TYR cc_start: 0.8129 (m-80) cc_final: 0.7905 (m-80) REVERT: A 686 SER cc_start: 0.8048 (m) cc_final: 0.7610 (t) REVERT: A 1079 LEU cc_start: 0.8487 (OUTLIER) cc_final: 0.7980 (mm) REVERT: A 1085 MET cc_start: 0.7841 (ptp) cc_final: 0.7359 (tpp) REVERT: A 1121 LEU cc_start: 0.8696 (OUTLIER) cc_final: 0.8408 (mp) REVERT: A 1175 ARG cc_start: 0.7804 (ttm-80) cc_final: 0.7492 (tmm160) REVERT: A 1242 TYR cc_start: 0.8465 (m-10) cc_final: 0.8169 (m-10) REVERT: A 1280 MET cc_start: 0.7339 (ppp) cc_final: 0.6974 (ppp) REVERT: A 1295 ARG cc_start: 0.7992 (ttp-170) cc_final: 0.7432 (mtt90) REVERT: A 1321 LYS cc_start: 0.6918 (OUTLIER) cc_final: 0.6209 (mmtt) REVERT: A 1491 MET cc_start: 0.8103 (tpp) cc_final: 0.7798 (mtm) outliers start: 40 outliers final: 30 residues processed: 151 average time/residue: 0.0855 time to fit residues: 19.3869 Evaluate side-chains 152 residues out of total 1171 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 117 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 PHE Chi-restraints excluded: chain A residue 66 GLN Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 135 SER Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain A residue 556 THR Chi-restraints excluded: chain A residue 657 ASP Chi-restraints excluded: chain A residue 662 HIS Chi-restraints excluded: chain A residue 817 LEU Chi-restraints excluded: chain A residue 823 LEU Chi-restraints excluded: chain A residue 1003 ILE Chi-restraints excluded: chain A residue 1010 HIS Chi-restraints excluded: chain A residue 1011 THR Chi-restraints excluded: chain A residue 1016 SER Chi-restraints excluded: chain A residue 1041 ILE Chi-restraints excluded: chain A residue 1055 VAL Chi-restraints excluded: chain A residue 1079 LEU Chi-restraints excluded: chain A residue 1086 ILE Chi-restraints excluded: chain A residue 1113 MET Chi-restraints excluded: chain A residue 1121 LEU Chi-restraints excluded: chain A residue 1156 GLU Chi-restraints excluded: chain A residue 1171 GLU Chi-restraints excluded: chain A residue 1204 CYS Chi-restraints excluded: chain A residue 1231 LEU Chi-restraints excluded: chain A residue 1239 VAL Chi-restraints excluded: chain A residue 1255 THR Chi-restraints excluded: chain A residue 1258 VAL Chi-restraints excluded: chain A residue 1321 LYS Chi-restraints excluded: chain A residue 1336 THR Chi-restraints excluded: chain A residue 1357 ILE Chi-restraints excluded: chain A residue 1371 ILE Chi-restraints excluded: chain A residue 1431 VAL Chi-restraints excluded: chain A residue 1439 LEU Chi-restraints excluded: chain A residue 1475 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 75 optimal weight: 1.9990 chunk 48 optimal weight: 0.9980 chunk 76 optimal weight: 2.9990 chunk 100 optimal weight: 0.7980 chunk 58 optimal weight: 0.9980 chunk 46 optimal weight: 0.9980 chunk 127 optimal weight: 5.9990 chunk 16 optimal weight: 4.9990 chunk 34 optimal weight: 0.9990 chunk 20 optimal weight: 0.9980 chunk 66 optimal weight: 4.9990 overall best weight: 0.9580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 GLN A 71 ASN ** A 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1099 ASN A1238 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.161703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.117667 restraints weight = 14421.661| |-----------------------------------------------------------------------------| r_work (start): 0.3520 rms_B_bonded: 2.32 r_work: 0.3257 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3115 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.3677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 10874 Z= 0.165 Angle : 0.578 14.479 14760 Z= 0.281 Chirality : 0.041 0.216 1715 Planarity : 0.004 0.045 1824 Dihedral : 8.741 122.948 1483 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 3.59 % Allowed : 21.26 % Favored : 75.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.58 (0.23), residues: 1315 helix: 1.85 (0.17), residues: 879 sheet: -0.35 (0.56), residues: 87 loop : -0.61 (0.33), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 194 TYR 0.012 0.001 TYR A1242 PHE 0.024 0.001 PHE A 558 TRP 0.014 0.001 TRP A 40 HIS 0.006 0.001 HIS A1363 Details of bonding type rmsd covalent geometry : bond 0.00384 (10874) covalent geometry : angle 0.57834 (14760) hydrogen bonds : bond 0.04018 ( 693) hydrogen bonds : angle 4.11763 ( 2040) *********************** 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 160 residues out of total 1171 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 118 time to evaluate : 0.420 Fit side-chains revert: symmetry clash REVERT: A 47 TRP cc_start: 0.7872 (m100) cc_final: 0.7509 (m100) REVERT: A 66 GLN cc_start: 0.8579 (OUTLIER) cc_final: 0.8247 (pp30) REVERT: A 387 ILE cc_start: 0.8759 (OUTLIER) cc_final: 0.8556 (mp) REVERT: A 503 LYS cc_start: 0.7424 (ttpp) cc_final: 0.7025 (pttt) REVERT: A 686 SER cc_start: 0.8094 (m) cc_final: 0.7670 (t) REVERT: A 1085 MET cc_start: 0.7966 (ptp) cc_final: 0.7494 (tpp) REVERT: A 1121 LEU cc_start: 0.8729 (OUTLIER) cc_final: 0.8463 (mp) REVERT: A 1175 ARG cc_start: 0.7875 (ttm-80) cc_final: 0.7563 (tmm160) REVERT: A 1280 MET cc_start: 0.7351 (ppp) cc_final: 0.6941 (ppp) REVERT: A 1295 ARG cc_start: 0.7987 (ttp-170) cc_final: 0.7423 (mtt90) REVERT: A 1321 LYS cc_start: 0.6939 (OUTLIER) cc_final: 0.6241 (mmtt) REVERT: A 1475 PHE cc_start: 0.7105 (OUTLIER) cc_final: 0.6094 (t80) REVERT: A 1491 MET cc_start: 0.8091 (tpp) cc_final: 0.7760 (mtm) outliers start: 42 outliers final: 33 residues processed: 150 average time/residue: 0.0913 time to fit residues: 20.4599 Evaluate side-chains 152 residues out of total 1171 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 114 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 PHE Chi-restraints excluded: chain A residue 66 GLN Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 135 SER Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain A residue 556 THR Chi-restraints excluded: chain A residue 657 ASP Chi-restraints excluded: chain A residue 662 HIS Chi-restraints excluded: chain A residue 707 SER Chi-restraints excluded: chain A residue 816 LEU Chi-restraints excluded: chain A residue 817 LEU Chi-restraints excluded: chain A residue 823 LEU Chi-restraints excluded: chain A residue 1003 ILE Chi-restraints excluded: chain A residue 1010 HIS Chi-restraints excluded: chain A residue 1011 THR Chi-restraints excluded: chain A residue 1016 SER Chi-restraints excluded: chain A residue 1041 ILE Chi-restraints excluded: chain A residue 1055 VAL Chi-restraints excluded: chain A residue 1086 ILE Chi-restraints excluded: chain A residue 1099 ASN Chi-restraints excluded: chain A residue 1113 MET Chi-restraints excluded: chain A residue 1121 LEU Chi-restraints excluded: chain A residue 1156 GLU Chi-restraints excluded: chain A residue 1171 GLU Chi-restraints excluded: chain A residue 1204 CYS Chi-restraints excluded: chain A residue 1231 LEU Chi-restraints excluded: chain A residue 1239 VAL Chi-restraints excluded: chain A residue 1255 THR Chi-restraints excluded: chain A residue 1258 VAL Chi-restraints excluded: chain A residue 1321 LYS Chi-restraints excluded: chain A residue 1336 THR Chi-restraints excluded: chain A residue 1357 ILE Chi-restraints excluded: chain A residue 1371 ILE Chi-restraints excluded: chain A residue 1387 LEU Chi-restraints excluded: chain A residue 1431 VAL Chi-restraints excluded: chain A residue 1439 LEU Chi-restraints excluded: chain A residue 1475 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 9 optimal weight: 4.9990 chunk 74 optimal weight: 5.9990 chunk 111 optimal weight: 8.9990 chunk 129 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 101 optimal weight: 0.5980 chunk 109 optimal weight: 1.9990 chunk 39 optimal weight: 0.0570 chunk 24 optimal weight: 0.6980 chunk 21 optimal weight: 0.5980 chunk 132 optimal weight: 4.9990 overall best weight: 0.7900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 GLN A 71 ASN ** A 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1099 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.161922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.118399 restraints weight = 14309.836| |-----------------------------------------------------------------------------| r_work (start): 0.3532 rms_B_bonded: 2.23 r_work: 0.3269 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3131 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.3755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10874 Z= 0.151 Angle : 0.579 13.423 14760 Z= 0.282 Chirality : 0.040 0.188 1715 Planarity : 0.004 0.045 1824 Dihedral : 8.462 124.358 1483 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 3.42 % Allowed : 21.52 % Favored : 75.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.55 (0.23), residues: 1315 helix: 1.82 (0.17), residues: 883 sheet: -0.34 (0.56), residues: 87 loop : -0.61 (0.33), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1445 TYR 0.018 0.001 TYR A 518 PHE 0.023 0.001 PHE A 558 TRP 0.014 0.001 TRP A1245 HIS 0.006 0.001 HIS A1363 Details of bonding type rmsd covalent geometry : bond 0.00347 (10874) covalent geometry : angle 0.57877 (14760) hydrogen bonds : bond 0.04027 ( 693) hydrogen bonds : angle 4.11474 ( 2040) *********************** 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 160 residues out of total 1171 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 120 time to evaluate : 0.401 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 40 TRP cc_start: 0.6949 (m-10) cc_final: 0.6736 (m-10) REVERT: A 47 TRP cc_start: 0.7875 (m100) cc_final: 0.7520 (m100) REVERT: A 128 ARG cc_start: 0.7656 (OUTLIER) cc_final: 0.7120 (ttm-80) REVERT: A 387 ILE cc_start: 0.8752 (OUTLIER) cc_final: 0.8532 (mp) REVERT: A 503 LYS cc_start: 0.7359 (ttpp) cc_final: 0.6952 (pttt) REVERT: A 518 TYR cc_start: 0.8190 (m-80) cc_final: 0.7937 (m-80) REVERT: A 686 SER cc_start: 0.8056 (m) cc_final: 0.7624 (t) REVERT: A 1085 MET cc_start: 0.7848 (ptp) cc_final: 0.7381 (tpp) REVERT: A 1121 LEU cc_start: 0.8687 (OUTLIER) cc_final: 0.8405 (mp) REVERT: A 1175 ARG cc_start: 0.7808 (ttm-80) cc_final: 0.7489 (tmm160) REVERT: A 1280 MET cc_start: 0.7418 (ppp) cc_final: 0.7019 (ppp) REVERT: A 1295 ARG cc_start: 0.8089 (ttp-170) cc_final: 0.7569 (mtt90) REVERT: A 1321 LYS cc_start: 0.6899 (OUTLIER) cc_final: 0.6178 (mmtt) REVERT: A 1475 PHE cc_start: 0.7107 (OUTLIER) cc_final: 0.6076 (t80) REVERT: A 1491 MET cc_start: 0.8105 (tpp) cc_final: 0.7879 (mtm) outliers start: 40 outliers final: 30 residues processed: 151 average time/residue: 0.0888 time to fit residues: 19.7491 Evaluate side-chains 156 residues out of total 1171 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 121 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 PHE Chi-restraints excluded: chain A residue 128 ARG Chi-restraints excluded: chain A residue 135 SER Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain A residue 477 VAL Chi-restraints excluded: chain A residue 556 THR Chi-restraints excluded: chain A residue 662 HIS Chi-restraints excluded: chain A residue 816 LEU Chi-restraints excluded: chain A residue 817 LEU Chi-restraints excluded: chain A residue 823 LEU Chi-restraints excluded: chain A residue 1003 ILE Chi-restraints excluded: chain A residue 1010 HIS Chi-restraints excluded: chain A residue 1011 THR Chi-restraints excluded: chain A residue 1016 SER Chi-restraints excluded: chain A residue 1041 ILE Chi-restraints excluded: chain A residue 1055 VAL Chi-restraints excluded: chain A residue 1086 ILE Chi-restraints excluded: chain A residue 1113 MET Chi-restraints excluded: chain A residue 1121 LEU Chi-restraints excluded: chain A residue 1156 GLU Chi-restraints excluded: chain A residue 1171 GLU Chi-restraints excluded: chain A residue 1204 CYS Chi-restraints excluded: chain A residue 1231 LEU Chi-restraints excluded: chain A residue 1239 VAL Chi-restraints excluded: chain A residue 1255 THR Chi-restraints excluded: chain A residue 1258 VAL Chi-restraints excluded: chain A residue 1321 LYS Chi-restraints excluded: chain A residue 1336 THR Chi-restraints excluded: chain A residue 1371 ILE Chi-restraints excluded: chain A residue 1387 LEU Chi-restraints excluded: chain A residue 1407 LEU Chi-restraints excluded: chain A residue 1431 VAL Chi-restraints excluded: chain A residue 1439 LEU Chi-restraints excluded: chain A residue 1475 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 111 optimal weight: 8.9990 chunk 101 optimal weight: 0.7980 chunk 7 optimal weight: 2.9990 chunk 1 optimal weight: 0.8980 chunk 27 optimal weight: 0.7980 chunk 86 optimal weight: 1.9990 chunk 117 optimal weight: 4.9990 chunk 98 optimal weight: 2.9990 chunk 9 optimal weight: 4.9990 chunk 127 optimal weight: 0.9990 chunk 65 optimal weight: 0.9980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 71 ASN ** A 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.161423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.117392 restraints weight = 14245.807| |-----------------------------------------------------------------------------| r_work (start): 0.3520 rms_B_bonded: 2.30 r_work: 0.3250 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3105 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.3778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 10874 Z= 0.161 Angle : 0.579 13.330 14760 Z= 0.284 Chirality : 0.040 0.172 1715 Planarity : 0.004 0.045 1824 Dihedral : 8.245 124.897 1483 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 3.25 % Allowed : 21.61 % Favored : 75.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.53 (0.23), residues: 1315 helix: 1.80 (0.17), residues: 883 sheet: -0.36 (0.56), residues: 87 loop : -0.61 (0.33), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 632 TYR 0.016 0.001 TYR A 518 PHE 0.023 0.001 PHE A 558 TRP 0.019 0.001 TRP A 94 HIS 0.006 0.001 HIS A1363 Details of bonding type rmsd covalent geometry : bond 0.00374 (10874) covalent geometry : angle 0.57904 (14760) hydrogen bonds : bond 0.04047 ( 693) hydrogen bonds : angle 4.13779 ( 2040) ********************** 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 158 residues out of total 1171 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 120 time to evaluate : 0.421 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 47 TRP cc_start: 0.7871 (m100) cc_final: 0.7534 (m100) REVERT: A 128 ARG cc_start: 0.7634 (OUTLIER) cc_final: 0.7050 (ttm-80) REVERT: A 387 ILE cc_start: 0.8766 (OUTLIER) cc_final: 0.8548 (mp) REVERT: A 427 MET cc_start: 0.8452 (ttm) cc_final: 0.8210 (ttm) REVERT: A 503 LYS cc_start: 0.7442 (ttpp) cc_final: 0.7034 (pttt) REVERT: A 513 LYS cc_start: 0.8962 (OUTLIER) cc_final: 0.8752 (tptp) REVERT: A 518 TYR cc_start: 0.8255 (m-80) cc_final: 0.7975 (m-80) REVERT: A 686 SER cc_start: 0.8135 (m) cc_final: 0.7720 (t) REVERT: A 1085 MET cc_start: 0.7932 (ptp) cc_final: 0.7480 (tpp) REVERT: A 1121 LEU cc_start: 0.8729 (OUTLIER) cc_final: 0.8466 (mp) REVERT: A 1175 ARG cc_start: 0.7896 (ttm-80) cc_final: 0.7581 (tmm160) REVERT: A 1280 MET cc_start: 0.7459 (ppp) cc_final: 0.7049 (ppp) REVERT: A 1295 ARG cc_start: 0.8097 (ttp-170) cc_final: 0.7585 (mtt90) REVERT: A 1321 LYS cc_start: 0.6935 (OUTLIER) cc_final: 0.6217 (mmtt) REVERT: A 1453 ASP cc_start: 0.8031 (m-30) cc_final: 0.7022 (t0) REVERT: A 1475 PHE cc_start: 0.7112 (OUTLIER) cc_final: 0.6069 (t80) REVERT: A 1491 MET cc_start: 0.8068 (tpp) cc_final: 0.7849 (mtm) outliers start: 38 outliers final: 31 residues processed: 151 average time/residue: 0.1010 time to fit residues: 22.3096 Evaluate side-chains 154 residues out of total 1171 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 117 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 PHE Chi-restraints excluded: chain A residue 128 ARG Chi-restraints excluded: chain A residue 135 SER Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain A residue 477 VAL Chi-restraints excluded: chain A residue 513 LYS Chi-restraints excluded: chain A residue 556 THR Chi-restraints excluded: chain A residue 662 HIS Chi-restraints excluded: chain A residue 707 SER Chi-restraints excluded: chain A residue 816 LEU Chi-restraints excluded: chain A residue 817 LEU Chi-restraints excluded: chain A residue 823 LEU Chi-restraints excluded: chain A residue 1003 ILE Chi-restraints excluded: chain A residue 1010 HIS Chi-restraints excluded: chain A residue 1011 THR Chi-restraints excluded: chain A residue 1016 SER Chi-restraints excluded: chain A residue 1041 ILE Chi-restraints excluded: chain A residue 1055 VAL Chi-restraints excluded: chain A residue 1086 ILE Chi-restraints excluded: chain A residue 1113 MET Chi-restraints excluded: chain A residue 1121 LEU Chi-restraints excluded: chain A residue 1156 GLU Chi-restraints excluded: chain A residue 1171 GLU Chi-restraints excluded: chain A residue 1204 CYS Chi-restraints excluded: chain A residue 1231 LEU Chi-restraints excluded: chain A residue 1239 VAL Chi-restraints excluded: chain A residue 1255 THR Chi-restraints excluded: chain A residue 1258 VAL Chi-restraints excluded: chain A residue 1321 LYS Chi-restraints excluded: chain A residue 1336 THR Chi-restraints excluded: chain A residue 1371 ILE Chi-restraints excluded: chain A residue 1387 LEU Chi-restraints excluded: chain A residue 1407 LEU Chi-restraints excluded: chain A residue 1431 VAL Chi-restraints excluded: chain A residue 1439 LEU Chi-restraints excluded: chain A residue 1475 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 90 optimal weight: 0.7980 chunk 111 optimal weight: 10.0000 chunk 35 optimal weight: 1.9990 chunk 63 optimal weight: 0.7980 chunk 71 optimal weight: 7.9990 chunk 117 optimal weight: 3.9990 chunk 18 optimal weight: 0.9990 chunk 105 optimal weight: 2.9990 chunk 101 optimal weight: 0.9980 chunk 118 optimal weight: 0.9980 chunk 28 optimal weight: 0.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 71 ASN ** A 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.161002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.117891 restraints weight = 14362.472| |-----------------------------------------------------------------------------| r_work (start): 0.3516 rms_B_bonded: 2.27 r_work: 0.3249 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3105 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.3802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 10874 Z= 0.161 Angle : 0.579 13.330 14760 Z= 0.284 Chirality : 0.040 0.172 1715 Planarity : 0.004 0.045 1824 Dihedral : 8.245 124.897 1483 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 3.25 % Allowed : 21.86 % Favored : 74.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.53 (0.23), residues: 1315 helix: 1.80 (0.17), residues: 883 sheet: -0.36 (0.56), residues: 87 loop : -0.61 (0.33), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 632 TYR 0.016 0.001 TYR A 518 PHE 0.023 0.001 PHE A 558 TRP 0.019 0.001 TRP A 94 HIS 0.006 0.001 HIS A1363 Details of bonding type rmsd covalent geometry : bond 0.00374 (10874) covalent geometry : angle 0.57905 (14760) hydrogen bonds : bond 0.04047 ( 693) hydrogen bonds : angle 4.13779 ( 2040) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3033.29 seconds wall clock time: 52 minutes 40.54 seconds (3160.54 seconds total)