Starting phenix.real_space_refine on Wed Feb 4 13:47:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9lg7_63056/02_2026/9lg7_63056_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9lg7_63056/02_2026/9lg7_63056.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.64 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9lg7_63056/02_2026/9lg7_63056_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9lg7_63056/02_2026/9lg7_63056_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9lg7_63056/02_2026/9lg7_63056.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9lg7_63056/02_2026/9lg7_63056.map" } resolution = 3.64 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= 0.062 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 58 5.16 5 C 6945 2.51 5 N 1771 2.21 5 O 1903 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 32 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10679 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 10635 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1338, 10635 Classifications: {'peptide': 1338} Link IDs: {'PTRANS': 50, 'TRANS': 1287} Chain breaks: 8 Chain: "A" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'GJF': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.62, per 1000 atoms: 0.25 Number of scatterers: 10679 At special positions: 0 Unit cell: (92.56, 127.92, 153.92, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 58 16.00 P 2 15.00 O 1903 8.00 N 1771 7.00 C 6945 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: 0.95 Conformation dependent library (CDL) restraints added in 548.5 milliseconds 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2534 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 7 sheets defined 72.1% alpha, 7.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.42 Creating SS restraints... Processing helix chain 'A' and resid 17 through 22 removed outlier: 3.526A pdb=" N THR A 21 " --> pdb=" O GLU A 17 " (cutoff:3.500A) Processing helix chain 'A' and resid 30 through 60 removed outlier: 3.959A 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: 3.865A 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: 3.551A 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: 4.177A pdb=" N TRP A 142 " --> pdb=" O MET A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 191 removed outlier: 4.034A pdb=" N PHE A 191 " --> pdb=" O VAL A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 212 Processing helix chain 'A' and resid 214 through 221 Processing helix chain 'A' and resid 224 through 234 Processing helix chain 'A' and resid 245 through 248 Processing helix chain 'A' and resid 249 through 268 Proline residue: A 255 - end of helix Processing helix chain 'A' and resid 312 through 321 removed outlier: 3.755A pdb=" N VAL A 316 " --> pdb=" O SER A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 326 Processing helix chain 'A' and resid 326 through 355 removed outlier: 4.164A pdb=" N LEU A 330 " --> pdb=" O LEU A 326 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N PHE A 331 " --> pdb=" O MET A 327 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLY A 342 " --> pdb=" O MET A 338 " (cutoff:3.500A) Proline residue: A 343 - end of helix Processing helix chain 'A' and resid 359 through 410 removed outlier: 3.877A pdb=" N GLY A 363 " --> pdb=" O PRO A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 418 removed outlier: 3.828A pdb=" N SER A 417 " --> pdb=" O ALA A 413 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N SER A 418 " --> pdb=" O ALA A 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 419 through 429 Processing helix chain 'A' and resid 429 through 438 removed outlier: 3.775A pdb=" N PHE A 434 " --> pdb=" O ASP A 430 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N MET A 435 " --> pdb=" O ALA A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 441 No H-bonds generated for 'chain 'A' and resid 439 through 441' Processing helix chain 'A' and resid 442 through 462 Proline residue: A 448 - end of helix Processing helix chain 'A' and resid 464 through 471 removed outlier: 4.006A pdb=" N ALA A 468 " --> pdb=" O PRO A 464 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 510 Proline residue: A 478 - end of helix Processing helix chain 'A' and resid 511 through 519 removed outlier: 3.560A pdb=" N LEU A 515 " --> pdb=" O GLY A 511 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 572 removed outlier: 3.815A pdb=" N VAL A 538 " --> pdb=" O GLU A 534 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N VAL A 548 " --> pdb=" O TYR A 544 " (cutoff:3.500A) Proline residue: A 557 - end of helix removed outlier: 4.013A pdb=" N ASP A 572 " --> pdb=" O TYR A 568 " (cutoff:3.500A) Processing helix chain 'A' and resid 579 through 598 removed outlier: 3.566A pdb=" N VAL A 584 " --> pdb=" O GLN A 580 " (cutoff:3.500A) removed outlier: 5.152A pdb=" N SER A 585 " --> pdb=" O LYS A 581 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N PHE A 594 " --> pdb=" O ASN A 590 " (cutoff:3.500A) Proline residue: A 595 - end of helix Processing helix chain 'A' and resid 598 through 621 Processing helix chain 'A' and resid 626 through 630 Processing helix chain 'A' and resid 683 through 692 removed outlier: 3.686A 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: 4.369A pdb=" N GLU A 742 " --> pdb=" O LYS A 738 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ALA A 743 " --> pdb=" O ALA A 739 " (cutoff:3.500A) Processing helix chain 'A' and resid 746 through 753 Processing helix chain 'A' and resid 755 through 759 removed outlier: 3.659A pdb=" N ARG A 758 " --> pdb=" O SER A 755 " (cutoff:3.500A) removed outlier: 3.710A 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 784 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: 3.863A pdb=" N TYR A 869 " --> pdb=" O PHE A 865 " (cutoff:3.500A) Processing helix chain 'A' and resid 959 through 970 removed outlier: 3.746A pdb=" N TRP A 963 " --> pdb=" O LEU A 959 " (cutoff:3.500A) Processing helix chain 'A' and resid 970 through 1000 removed outlier: 3.549A pdb=" N ASP A1000 " --> pdb=" O SER A 996 " (cutoff:3.500A) Processing helix chain 'A' and resid 1011 through 1058 removed outlier: 3.813A pdb=" N LEU A1015 " --> pdb=" O THR A1011 " (cutoff:3.500A) Processing helix chain 'A' and resid 1059 through 1066 removed outlier: 3.832A pdb=" N PHE A1063 " --> pdb=" O PRO A1059 " (cutoff:3.500A) Processing helix chain 'A' and resid 1069 through 1084 removed outlier: 3.748A pdb=" N ASN A1073 " --> pdb=" O GLY A1069 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ARG A1074 " --> pdb=" O ASN A1070 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLU A1078 " --> pdb=" O ARG A1074 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N LEU A1079 " --> pdb=" O PHE A1075 " (cutoff:3.500A) Processing helix chain 'A' and resid 1084 through 1111 removed outlier: 3.821A pdb=" N GLN A1088 " --> pdb=" O SER A1084 " (cutoff:3.500A) Processing helix chain 'A' and resid 1117 through 1167 removed outlier: 4.087A pdb=" N GLN A1138 " --> pdb=" O ALA A1134 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LEU A1139 " --> pdb=" O SER A1135 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ARG A1141 " --> pdb=" O ARG A1137 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N SER A1148 " --> pdb=" O SER A1144 " (cutoff:3.500A) Proline residue: A1149 - end of helix removed outlier: 5.806A pdb=" N SER A1162 " --> pdb=" O LEU A1158 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N VAL A1163 " --> pdb=" O LEU A1159 " (cutoff:3.500A) Processing helix chain 'A' and resid 1169 through 1219 Proline residue: A1190 - end of helix Processing helix chain 'A' and resid 1225 through 1264 removed outlier: 4.542A pdb=" N THR A1240 " --> pdb=" O SER A1236 " (cutoff:3.500A) removed outlier: 5.256A pdb=" N THR A1241 " --> pdb=" O LEU A1237 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N TYR A1242 " --> pdb=" O GLN A1238 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N VAL A1258 " --> pdb=" O GLU A1254 " (cutoff:3.500A) removed outlier: 5.318A pdb=" N ALA A1259 " --> pdb=" O THR A1255 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N VAL A1260 " --> pdb=" O ASN A1256 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLU A1261 " --> pdb=" O ILE A1257 " (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: 3.863A pdb=" N HIS A1420 " --> pdb=" O LYS A1417 " (cutoff:3.500A) Processing helix chain 'A' and resid 1430 through 1446 removed outlier: 3.638A pdb=" N LYS A1446 " --> pdb=" O ALA A1442 " (cutoff:3.500A) Processing helix chain 'A' and resid 1463 through 1474 removed outlier: 3.975A pdb=" N GLN A1474 " --> pdb=" O THR A1470 " (cutoff:3.500A) Processing helix chain 'A' and resid 1486 through 1493 removed outlier: 3.878A pdb=" N ILE A1490 " --> pdb=" O ARG A1486 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N ASP A1492 " --> pdb=" O ASN A1488 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N TYR A1493 " --> pdb=" O THR A1489 " (cutoff:3.500A) Processing helix chain 'A' and resid 1509 through 1514 Processing sheet with id=AA1, first strand: chain 'A' and resid 661 through 668 removed outlier: 6.969A pdb=" N HIS A 662 " --> pdb=" O THR A 650 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N THR A 650 " --> pdb=" O HIS A 662 " (cutoff:3.500A) removed outlier: 5.985A pdb=" N ILE A 664 " --> pdb=" O ASN A 648 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N VAL A 646 " --> pdb=" O VAL A 702 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N VAL A 702 " --> pdb=" O VAL A 646 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N ASN A 648 " --> pdb=" O GLY A 700 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLY A 700 " --> pdb=" O ASN A 648 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N THR A 650 " --> pdb=" O VAL A 698 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 673 through 676 removed outlier: 6.222A pdb=" N VAL A 674 " --> pdb=" O LEU A 824 " (cutoff:3.500A) removed outlier: 6.300A 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) Processing sheet with id=AA3, first strand: chain 'A' and resid 838 through 841 removed outlier: 3.928A pdb=" N GLY A 850 " --> pdb=" O ILE A 838 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N GLU A 848 " --> pdb=" O VAL A 840 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1003 through 1004 Processing sheet with id=AA5, first strand: chain 'A' and resid 1309 through 1316 removed outlier: 5.875A pdb=" N LYS A1310 " --> pdb=" O LEU A1299 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N LEU A1299 " --> pdb=" O LYS A1310 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N VAL A1314 " --> pdb=" O ARG A1295 " (cutoff:3.500A) removed outlier: 4.966A pdb=" N ARG A1295 " --> pdb=" O VAL A1314 " (cutoff:3.500A) removed outlier: 7.244A 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=AA6, first strand: chain 'A' and resid 1309 through 1316 removed outlier: 5.875A pdb=" N LYS A1310 " --> pdb=" O LEU A1299 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N LEU A1299 " --> pdb=" O LYS A1310 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N VAL A1314 " --> pdb=" O ARG A1295 " (cutoff:3.500A) removed outlier: 4.966A pdb=" N ARG A1295 " --> pdb=" O VAL A1314 " (cutoff:3.500A) removed outlier: 7.244A 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=AA7, first strand: chain 'A' and resid 1369 through 1372 removed outlier: 6.390A pdb=" N LEU A1450 " --> pdb=" O LEU A1481 " (cutoff:3.500A) removed outlier: 8.029A pdb=" N ILE A1483 " --> pdb=" O LEU A1450 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N LEU A1452 " --> pdb=" O ILE A1483 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N GLY A1323 " --> pdb=" O ILE A1497 " (cutoff:3.500A) removed outlier: 7.676A pdb=" N LEU A1499 " --> pdb=" O GLY A1323 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N VAL A1325 " --> pdb=" O LEU A1499 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N VAL A1496 " --> pdb=" O TRP A1507 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N TRP A1507 " --> pdb=" O VAL A1496 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N VAL A1498 " --> pdb=" O GLN A1505 " (cutoff:3.500A) 688 hydrogen bonds defined for protein. 2019 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: 2.03 Time building geometry restraints manager: 1.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.34: 3083 1.34 - 1.47: 2662 1.47 - 1.61: 5082 1.61 - 1.75: 4 1.75 - 1.89: 93 Bond restraints: 10924 Sorted by residual: bond pdb=" P2 GJF A1601 " pdb=" S2 GJF A1601 " ideal model delta sigma weight residual 2.082 1.885 0.197 2.00e-02 2.50e+03 9.67e+01 bond pdb=" P1 GJF A1601 " pdb=" S1 GJF A1601 " ideal model delta sigma weight residual 2.070 1.882 0.188 2.00e-02 2.50e+03 8.81e+01 bond pdb=" C14 GJF A1601 " pdb=" N7 GJF A1601 " ideal model delta sigma weight residual 1.336 1.446 -0.110 2.00e-02 2.50e+03 3.00e+01 bond pdb=" C3 GJF A1601 " pdb=" N8 GJF A1601 " ideal model delta sigma weight residual 1.342 1.451 -0.109 2.00e-02 2.50e+03 2.95e+01 bond pdb=" C5 GJF A1601 " pdb=" C6 GJF A1601 " ideal model delta sigma weight residual 1.522 1.433 0.089 2.00e-02 2.50e+03 1.97e+01 ... (remaining 10919 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.67: 14701 3.67 - 7.34: 122 7.34 - 11.01: 15 11.01 - 14.68: 1 14.68 - 18.35: 2 Bond angle restraints: 14841 Sorted by residual: angle pdb=" O6 GJF A1601 " pdb=" P2 GJF A1601 " pdb=" O9 GJF A1601 " ideal model delta sigma weight residual 104.39 122.74 -18.35 3.00e+00 1.11e-01 3.74e+01 angle pdb=" O3 GJF A1601 " pdb=" P1 GJF A1601 " pdb=" O7 GJF A1601 " ideal model delta sigma weight residual 102.52 120.56 -18.04 3.00e+00 1.11e-01 3.62e+01 angle pdb=" C LYS A 486 " pdb=" N THR A 487 " pdb=" CA THR A 487 " ideal model delta sigma weight residual 120.60 113.07 7.53 1.60e+00 3.91e-01 2.21e+01 angle pdb=" N LEU A 592 " pdb=" CA LEU A 592 " pdb=" C LEU A 592 " ideal model delta sigma weight residual 113.41 108.09 5.32 1.22e+00 6.72e-01 1.90e+01 angle pdb=" N LYS A1264 " pdb=" CA LYS A1264 " pdb=" C LYS A1264 " ideal model delta sigma weight residual 113.15 108.21 4.94 1.19e+00 7.06e-01 1.72e+01 ... (remaining 14836 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.03: 5731 19.03 - 38.06: 595 38.06 - 57.09: 124 57.09 - 76.11: 51 76.11 - 95.14: 19 Dihedral angle restraints: 6520 sinusoidal: 2612 harmonic: 3908 Sorted by residual: dihedral pdb=" CG ARG A1472 " pdb=" CD ARG A1472 " pdb=" NE ARG A1472 " pdb=" CZ ARG A1472 " ideal model delta sinusoidal sigma weight residual -90.00 -40.21 -49.79 2 1.50e+01 4.44e-03 1.24e+01 dihedral pdb=" C16 GJF A1601 " pdb=" C17 GJF A1601 " pdb=" C18 GJF A1601 " pdb=" C19 GJF A1601 " ideal model delta sinusoidal sigma weight residual 39.74 -55.40 95.14 1 3.00e+01 1.11e-03 1.16e+01 dihedral pdb=" C19 GJF A1601 " pdb=" C17 GJF A1601 " pdb=" C18 GJF A1601 " pdb=" O9 GJF A1601 " ideal model delta sinusoidal sigma weight residual -157.87 -63.04 -94.83 1 3.00e+01 1.11e-03 1.16e+01 ... (remaining 6517 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 1186 0.051 - 0.102: 341 0.102 - 0.152: 142 0.152 - 0.203: 54 0.203 - 0.254: 6 Chirality restraints: 1729 Sorted by residual: chirality pdb=" C16 GJF A1601 " pdb=" C15 GJF A1601 " pdb=" C17 GJF A1601 " pdb=" O8 GJF A1601 " both_signs ideal model delta sigma weight residual False 2.40 2.65 -0.25 2.00e-01 2.50e+01 1.61e+00 chirality pdb=" CA VAL A 677 " pdb=" N VAL A 677 " pdb=" C VAL A 677 " pdb=" CB VAL A 677 " both_signs ideal model delta sigma weight residual False 2.44 2.67 -0.23 2.00e-01 2.50e+01 1.36e+00 chirality pdb=" CA ILE A 630 " pdb=" N ILE A 630 " pdb=" C ILE A 630 " pdb=" CB ILE A 630 " both_signs ideal model delta sigma weight residual False 2.43 2.66 -0.23 2.00e-01 2.50e+01 1.32e+00 ... (remaining 1726 not shown) Planarity restraints: 1830 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 775 " 0.284 9.50e-02 1.11e+02 1.27e-01 9.92e+00 pdb=" NE ARG A 775 " -0.017 2.00e-02 2.50e+03 pdb=" CZ ARG A 775 " -0.001 2.00e-02 2.50e+03 pdb=" NH1 ARG A 775 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG A 775 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 501 " 0.278 9.50e-02 1.11e+02 1.25e-01 9.52e+00 pdb=" NE ARG A 501 " -0.017 2.00e-02 2.50e+03 pdb=" CZ ARG A 501 " -0.002 2.00e-02 2.50e+03 pdb=" NH1 ARG A 501 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG A 501 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 422 " 0.014 2.00e-02 2.50e+03 2.88e-02 8.31e+00 pdb=" C GLU A 422 " -0.050 2.00e-02 2.50e+03 pdb=" O GLU A 422 " 0.019 2.00e-02 2.50e+03 pdb=" N ILE A 423 " 0.017 2.00e-02 2.50e+03 ... (remaining 1827 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1096 2.75 - 3.29: 11328 3.29 - 3.82: 17924 3.82 - 4.36: 20921 4.36 - 4.90: 35499 Nonbonded interactions: 86768 Sorted by model distance: nonbonded pdb=" OD1 ASN A 992 " pdb=" OH TYR A1235 " model vdw 2.209 3.040 nonbonded pdb=" O LYS A 486 " pdb=" OG1 THR A 489 " model vdw 2.226 3.040 nonbonded pdb=" O VAL A 571 " pdb=" OD1 ASP A 572 " model vdw 2.235 3.040 nonbonded pdb=" NH1 ARG A1341 " pdb=" O ILE A1357 " model vdw 2.345 3.120 nonbonded pdb=" O VAL A 316 " pdb=" OG1 THR A 320 " model vdw 2.354 3.040 ... (remaining 86763 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 group one per residue 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: 2.450 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.110 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 11.540 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:1.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6606 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 : 0.008 0.197 10924 Z= 0.551 Angle : 1.031 18.349 14841 Z= 0.692 Chirality : 0.062 0.254 1729 Planarity : 0.009 0.127 1830 Dihedral : 17.280 95.142 3986 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 0.00 % Allowed : 20.31 % Favored : 79.69 % 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: -0.27 (0.23), residues: 1320 helix: 0.47 (0.18), residues: 861 sheet: -0.77 (0.60), residues: 63 loop : -1.37 (0.30), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 735 TYR 0.019 0.002 TYR A 318 PHE 0.030 0.002 PHE A 981 TRP 0.025 0.002 TRP A 459 HIS 0.004 0.001 HIS A 805 Details of bonding type rmsd covalent geometry : bond 0.00818 (10924) covalent geometry : angle 1.03069 (14841) hydrogen bonds : bond 0.17257 ( 686) hydrogen bonds : angle 6.61831 ( 2019) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 265 time to evaluate : 0.407 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 217 SER cc_start: 0.8262 (m) cc_final: 0.7883 (p) REVERT: A 223 TRP cc_start: 0.8412 (p-90) cc_final: 0.6961 (p-90) REVERT: A 264 GLU cc_start: 0.7982 (tp30) cc_final: 0.7691 (mm-30) REVERT: A 339 MET cc_start: 0.7742 (ttm) cc_final: 0.7442 (ttm) REVERT: A 443 MET cc_start: 0.7711 (mmm) cc_final: 0.7233 (mmt) REVERT: A 472 VAL cc_start: 0.8524 (p) cc_final: 0.8243 (t) REVERT: A 475 LEU cc_start: 0.7799 (tp) cc_final: 0.6868 (tt) REVERT: A 556 THR cc_start: 0.8672 (m) cc_final: 0.8471 (m) REVERT: A 963 TRP cc_start: 0.7595 (t-100) cc_final: 0.7270 (t60) REVERT: A 1085 MET cc_start: 0.6781 (mmm) cc_final: 0.6486 (tpp) REVERT: A 1124 ILE cc_start: 0.7755 (mm) cc_final: 0.7517 (mt) outliers start: 0 outliers final: 0 residues processed: 265 average time/residue: 0.1341 time to fit residues: 46.9317 Evaluate side-chains 143 residues out of total 1177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 143 time to evaluate : 0.429 ------------------------------------------------------------------------------- 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: 0.5980 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 0.3980 chunk 103 optimal weight: 0.7980 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 0.7980 chunk 55 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 HIS A 206 ASN ** A 382 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 575 ASN A 774 GLN A1054 ASN A1207 ASN A1222 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.171930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.127062 restraints weight = 14527.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.122573 restraints weight = 12039.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.124498 restraints weight = 11860.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.125290 restraints weight = 8053.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.125743 restraints weight = 7215.912| |-----------------------------------------------------------------------------| r_work (final): 0.3612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7262 moved from start: 0.2461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 10924 Z= 0.162 Angle : 0.622 10.665 14841 Z= 0.319 Chirality : 0.042 0.250 1729 Planarity : 0.004 0.042 1830 Dihedral : 9.629 85.453 1497 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.63 % Allowed : 20.31 % Favored : 77.06 % 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: 0.88 (0.23), residues: 1320 helix: 1.46 (0.18), residues: 877 sheet: -0.86 (0.58), residues: 63 loop : -1.21 (0.30), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.024 0.001 ARG A1057 TYR 0.018 0.002 TYR A 318 PHE 0.025 0.002 PHE A 524 TRP 0.026 0.001 TRP A1275 HIS 0.006 0.001 HIS A 60 Details of bonding type rmsd covalent geometry : bond 0.00358 (10924) covalent geometry : angle 0.62228 (14841) hydrogen bonds : bond 0.05502 ( 686) hydrogen bonds : angle 4.48579 ( 2019) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 161 time to evaluate : 0.339 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 378 THR cc_start: 0.8104 (OUTLIER) cc_final: 0.7578 (t) REVERT: A 472 VAL cc_start: 0.8678 (p) cc_final: 0.8434 (t) REVERT: A 473 MET cc_start: 0.7716 (mtt) cc_final: 0.7442 (mtp) REVERT: A 475 LEU cc_start: 0.8237 (tp) cc_final: 0.7174 (tt) REVERT: A 505 MET cc_start: 0.8137 (mmm) cc_final: 0.7834 (tpp) REVERT: A 562 LEU cc_start: 0.8338 (tp) cc_final: 0.8086 (tt) REVERT: A 731 GLN cc_start: 0.7474 (mp10) cc_final: 0.7269 (mm-40) REVERT: A 793 ASP cc_start: 0.7803 (t0) cc_final: 0.7521 (t0) REVERT: A 849 MET cc_start: 0.7251 (tmm) cc_final: 0.6924 (tpt) REVERT: A 963 TRP cc_start: 0.7943 (t-100) cc_final: 0.7250 (t60) REVERT: A 1079 LEU cc_start: 0.7674 (tt) cc_final: 0.7410 (tp) REVERT: A 1085 MET cc_start: 0.7514 (mmm) cc_final: 0.7099 (tpp) REVERT: A 1113 MET cc_start: 0.6668 (tmm) cc_final: 0.6281 (tmm) REVERT: A 1368 LYS cc_start: 0.7974 (mmtt) cc_final: 0.7612 (mtpt) outliers start: 31 outliers final: 15 residues processed: 189 average time/residue: 0.1037 time to fit residues: 28.0509 Evaluate side-chains 140 residues out of total 1177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 124 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 PHE Chi-restraints excluded: chain A residue 59 HIS Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain A residue 378 THR Chi-restraints excluded: chain A residue 540 LYS Chi-restraints excluded: chain A residue 840 VAL 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 1105 ILE Chi-restraints excluded: chain A residue 1109 LEU Chi-restraints excluded: chain A residue 1158 LEU Chi-restraints excluded: chain A residue 1252 GLU Chi-restraints excluded: chain A residue 1263 LEU Chi-restraints excluded: chain A residue 1414 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 90 optimal weight: 0.0030 chunk 85 optimal weight: 4.9990 chunk 51 optimal weight: 0.9990 chunk 123 optimal weight: 20.0000 chunk 29 optimal weight: 0.9990 chunk 127 optimal weight: 10.0000 chunk 64 optimal weight: 0.9990 chunk 100 optimal weight: 0.9990 chunk 104 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 111 optimal weight: 0.5980 overall best weight: 0.7196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 382 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.168458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.124046 restraints weight = 14754.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.123017 restraints weight = 12418.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.123786 restraints weight = 12762.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.124950 restraints weight = 7196.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.126354 restraints weight = 5944.476| |-----------------------------------------------------------------------------| r_work (final): 0.3603 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7249 moved from start: 0.3259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10924 Z= 0.150 Angle : 0.591 14.017 14841 Z= 0.296 Chirality : 0.041 0.211 1729 Planarity : 0.004 0.043 1830 Dihedral : 9.323 82.968 1497 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.80 % Allowed : 21.84 % Favored : 75.36 % 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: 1.09 (0.23), residues: 1320 helix: 1.66 (0.18), residues: 869 sheet: -0.92 (0.57), residues: 63 loop : -1.13 (0.29), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A1057 TYR 0.017 0.001 TYR A 318 PHE 0.026 0.002 PHE A1062 TRP 0.040 0.001 TRP A1275 HIS 0.005 0.001 HIS A 382 Details of bonding type rmsd covalent geometry : bond 0.00331 (10924) covalent geometry : angle 0.59125 (14841) hydrogen bonds : bond 0.04853 ( 686) hydrogen bonds : angle 4.20649 ( 2019) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 134 time to evaluate : 0.446 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 473 MET cc_start: 0.7736 (mtt) cc_final: 0.7375 (mtp) REVERT: A 475 LEU cc_start: 0.8314 (tp) cc_final: 0.7239 (tt) REVERT: A 793 ASP cc_start: 0.7903 (t0) cc_final: 0.7516 (t0) REVERT: A 963 TRP cc_start: 0.7982 (t-100) cc_final: 0.7254 (t60) REVERT: A 1077 LYS cc_start: 0.8153 (ptpt) cc_final: 0.7763 (ptmt) REVERT: A 1085 MET cc_start: 0.7645 (mmm) cc_final: 0.7176 (tpp) REVERT: A 1113 MET cc_start: 0.6676 (OUTLIER) cc_final: 0.6161 (tmm) REVERT: A 1368 LYS cc_start: 0.7980 (mmtt) cc_final: 0.7684 (mtpt) outliers start: 33 outliers final: 15 residues processed: 161 average time/residue: 0.1051 time to fit residues: 24.6652 Evaluate side-chains 134 residues out of total 1177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 118 time to evaluate : 0.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 SER Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 339 MET Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 508 ILE Chi-restraints excluded: chain A residue 650 THR Chi-restraints excluded: chain A residue 811 ILE Chi-restraints excluded: chain A residue 840 VAL Chi-restraints excluded: chain A residue 1011 THR Chi-restraints excluded: chain A residue 1041 ILE Chi-restraints excluded: chain A residue 1105 ILE Chi-restraints excluded: chain A residue 1109 LEU Chi-restraints excluded: chain A residue 1113 MET Chi-restraints excluded: chain A residue 1158 LEU Chi-restraints excluded: chain A residue 1263 LEU Chi-restraints excluded: chain A residue 1414 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 99 optimal weight: 0.6980 chunk 102 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 26 optimal weight: 0.5980 chunk 47 optimal weight: 3.9990 chunk 84 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 42 optimal weight: 0.9990 chunk 18 optimal weight: 0.7980 chunk 2 optimal weight: 0.4980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 382 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1238 GLN ** A1363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1485 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.166842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.122187 restraints weight = 14719.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.122290 restraints weight = 12213.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.122645 restraints weight = 12467.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.123676 restraints weight = 6891.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.125135 restraints weight = 5689.319| |-----------------------------------------------------------------------------| r_work (final): 0.3594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7270 moved from start: 0.3715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 10924 Z= 0.146 Angle : 0.569 12.762 14841 Z= 0.284 Chirality : 0.040 0.220 1729 Planarity : 0.004 0.043 1830 Dihedral : 9.252 83.639 1497 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 2.72 % Allowed : 22.51 % Favored : 74.77 % 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: 1.29 (0.23), residues: 1320 helix: 1.79 (0.18), residues: 872 sheet: -0.94 (0.56), residues: 63 loop : -1.01 (0.29), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 501 TYR 0.017 0.001 TYR A 318 PHE 0.018 0.001 PHE A 50 TRP 0.011 0.001 TRP A1275 HIS 0.007 0.001 HIS A 985 Details of bonding type rmsd covalent geometry : bond 0.00330 (10924) covalent geometry : angle 0.56934 (14841) hydrogen bonds : bond 0.04635 ( 686) hydrogen bonds : angle 4.00432 ( 2019) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 129 time to evaluate : 0.422 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 443 MET cc_start: 0.8612 (mmp) cc_final: 0.8226 (mmm) REVERT: A 473 MET cc_start: 0.7605 (mtt) cc_final: 0.7157 (mtp) REVERT: A 475 LEU cc_start: 0.8295 (tp) cc_final: 0.7196 (tt) REVERT: A 476 MET cc_start: 0.6270 (mmt) cc_final: 0.5863 (mmt) REVERT: A 793 ASP cc_start: 0.7917 (t0) cc_final: 0.7482 (t0) REVERT: A 849 MET cc_start: 0.7276 (tmm) cc_final: 0.6734 (tpt) REVERT: A 963 TRP cc_start: 0.8016 (t-100) cc_final: 0.7263 (t60) REVERT: A 981 PHE cc_start: 0.8559 (t80) cc_final: 0.8203 (t80) REVERT: A 1077 LYS cc_start: 0.8191 (ptpt) cc_final: 0.7753 (ptmt) REVERT: A 1085 MET cc_start: 0.7677 (mmm) cc_final: 0.7209 (tpp) REVERT: A 1113 MET cc_start: 0.6671 (OUTLIER) cc_final: 0.6243 (tpp) REVERT: A 1368 LYS cc_start: 0.7929 (mmtt) cc_final: 0.7546 (mtpt) outliers start: 32 outliers final: 20 residues processed: 156 average time/residue: 0.1019 time to fit residues: 23.0652 Evaluate side-chains 139 residues out of total 1177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 118 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 212 SER Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 375 CYS Chi-restraints excluded: chain A residue 385 PHE Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 650 THR Chi-restraints excluded: chain A residue 811 ILE Chi-restraints excluded: chain A residue 831 TYR Chi-restraints excluded: chain A residue 840 VAL Chi-restraints excluded: chain A residue 855 LEU Chi-restraints excluded: chain A residue 1011 THR Chi-restraints excluded: chain A residue 1109 LEU Chi-restraints excluded: chain A residue 1113 MET Chi-restraints excluded: chain A residue 1136 SER Chi-restraints excluded: chain A residue 1158 LEU Chi-restraints excluded: chain A residue 1263 LEU Chi-restraints excluded: chain A residue 1408 LYS Chi-restraints excluded: chain A residue 1414 LEU Chi-restraints excluded: chain A residue 1431 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 103 optimal weight: 0.8980 chunk 83 optimal weight: 4.9990 chunk 26 optimal weight: 0.5980 chunk 43 optimal weight: 6.9990 chunk 70 optimal weight: 0.0980 chunk 59 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 107 optimal weight: 0.8980 chunk 77 optimal weight: 8.9990 chunk 98 optimal weight: 1.9990 chunk 49 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 382 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 432 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.166091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.120699 restraints weight = 14677.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.118817 restraints weight = 12797.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.119722 restraints weight = 13859.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.120975 restraints weight = 8243.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.121626 restraints weight = 6861.535| |-----------------------------------------------------------------------------| r_work (final): 0.3560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7328 moved from start: 0.4062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10924 Z= 0.135 Angle : 0.557 9.632 14841 Z= 0.277 Chirality : 0.040 0.203 1729 Planarity : 0.003 0.043 1830 Dihedral : 9.122 84.578 1497 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.80 % Allowed : 22.85 % Favored : 74.34 % 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: 1.41 (0.23), residues: 1320 helix: 1.88 (0.18), residues: 872 sheet: -0.78 (0.60), residues: 63 loop : -0.96 (0.30), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 128 TYR 0.016 0.001 TYR A 318 PHE 0.024 0.001 PHE A 50 TRP 0.012 0.001 TRP A1275 HIS 0.007 0.001 HIS A 985 Details of bonding type rmsd covalent geometry : bond 0.00304 (10924) covalent geometry : angle 0.55709 (14841) hydrogen bonds : bond 0.04451 ( 686) hydrogen bonds : angle 3.93450 ( 2019) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 126 time to evaluate : 0.326 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 TYR cc_start: 0.7244 (t80) cc_final: 0.7018 (t80) REVERT: A 444 ILE cc_start: 0.9314 (tt) cc_final: 0.9069 (tt) REVERT: A 473 MET cc_start: 0.7594 (mtt) cc_final: 0.7215 (mtp) REVERT: A 476 MET cc_start: 0.6337 (mmt) cc_final: 0.6061 (mmt) REVERT: A 695 MET cc_start: 0.8838 (mmm) cc_final: 0.8616 (mmm) REVERT: A 793 ASP cc_start: 0.8025 (t0) cc_final: 0.7561 (t0) REVERT: A 849 MET cc_start: 0.7168 (tmm) cc_final: 0.6659 (tpt) REVERT: A 963 TRP cc_start: 0.8085 (t-100) cc_final: 0.7291 (t60) REVERT: A 981 PHE cc_start: 0.8581 (t80) cc_final: 0.8326 (t80) REVERT: A 1077 LYS cc_start: 0.8203 (ptpt) cc_final: 0.7793 (ptmt) REVERT: A 1085 MET cc_start: 0.7718 (mmm) cc_final: 0.7246 (tpp) REVERT: A 1113 MET cc_start: 0.6807 (OUTLIER) cc_final: 0.6362 (tpp) outliers start: 33 outliers final: 20 residues processed: 156 average time/residue: 0.1012 time to fit residues: 23.0326 Evaluate side-chains 136 residues out of total 1177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 115 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 212 SER Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 375 CYS Chi-restraints excluded: chain A residue 385 PHE Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 611 VAL Chi-restraints excluded: chain A residue 811 ILE Chi-restraints excluded: chain A residue 831 TYR Chi-restraints excluded: chain A residue 840 VAL Chi-restraints excluded: chain A residue 1011 THR Chi-restraints excluded: chain A residue 1032 TYR Chi-restraints excluded: chain A residue 1109 LEU Chi-restraints excluded: chain A residue 1113 MET Chi-restraints excluded: chain A residue 1136 SER Chi-restraints excluded: chain A residue 1158 LEU Chi-restraints excluded: chain A residue 1258 VAL Chi-restraints excluded: chain A residue 1371 ILE Chi-restraints excluded: chain A residue 1414 LEU Chi-restraints excluded: chain A residue 1431 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 103 optimal weight: 0.7980 chunk 34 optimal weight: 5.9990 chunk 92 optimal weight: 0.7980 chunk 102 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 17 optimal weight: 0.0070 chunk 123 optimal weight: 5.9990 chunk 46 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 96 optimal weight: 0.6980 chunk 10 optimal weight: 2.9990 overall best weight: 0.8600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.164475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.119087 restraints weight = 14652.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.116257 restraints weight = 11979.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.117102 restraints weight = 13714.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.118350 restraints weight = 8159.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.120127 restraints weight = 6725.857| |-----------------------------------------------------------------------------| r_work (final): 0.3535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7351 moved from start: 0.4298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10924 Z= 0.149 Angle : 0.564 8.938 14841 Z= 0.282 Chirality : 0.040 0.206 1729 Planarity : 0.004 0.044 1830 Dihedral : 9.132 86.205 1497 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 3.06 % Allowed : 22.51 % Favored : 74.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.48 (0.23), residues: 1320 helix: 1.87 (0.18), residues: 879 sheet: -0.74 (0.61), residues: 63 loop : -0.81 (0.30), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 128 TYR 0.016 0.001 TYR A 318 PHE 0.020 0.001 PHE A 50 TRP 0.013 0.001 TRP A1275 HIS 0.010 0.001 HIS A1363 Details of bonding type rmsd covalent geometry : bond 0.00341 (10924) covalent geometry : angle 0.56371 (14841) hydrogen bonds : bond 0.04491 ( 686) hydrogen bonds : angle 3.90787 ( 2019) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 123 time to evaluate : 0.435 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 TYR cc_start: 0.7246 (t80) cc_final: 0.6947 (t80) REVERT: A 444 ILE cc_start: 0.9356 (tt) cc_final: 0.9127 (tt) REVERT: A 473 MET cc_start: 0.7592 (mtt) cc_final: 0.7275 (mtp) REVERT: A 476 MET cc_start: 0.6457 (mmt) cc_final: 0.6231 (mmt) REVERT: A 793 ASP cc_start: 0.8065 (t0) cc_final: 0.7599 (t0) REVERT: A 849 MET cc_start: 0.7165 (tmm) cc_final: 0.6661 (tpt) REVERT: A 963 TRP cc_start: 0.8129 (t-100) cc_final: 0.7298 (t60) REVERT: A 981 PHE cc_start: 0.8552 (t80) cc_final: 0.8334 (t80) REVERT: A 1077 LYS cc_start: 0.8120 (ptpt) cc_final: 0.7759 (ptmt) REVERT: A 1085 MET cc_start: 0.7687 (mmm) cc_final: 0.7256 (tpp) REVERT: A 1113 MET cc_start: 0.6839 (OUTLIER) cc_final: 0.6415 (tpp) REVERT: A 1126 PHE cc_start: 0.7835 (t80) cc_final: 0.7537 (t80) outliers start: 36 outliers final: 25 residues processed: 156 average time/residue: 0.0911 time to fit residues: 20.8128 Evaluate side-chains 143 residues out of total 1177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 117 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 212 SER Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 375 CYS Chi-restraints excluded: chain A residue 385 PHE Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 611 VAL Chi-restraints excluded: chain A residue 650 THR Chi-restraints excluded: chain A residue 811 ILE Chi-restraints excluded: chain A residue 821 THR Chi-restraints excluded: chain A residue 831 TYR Chi-restraints excluded: chain A residue 840 VAL Chi-restraints excluded: chain A residue 1011 THR Chi-restraints excluded: chain A residue 1032 TYR Chi-restraints excluded: chain A residue 1041 ILE Chi-restraints excluded: chain A residue 1109 LEU Chi-restraints excluded: chain A residue 1113 MET Chi-restraints excluded: chain A residue 1158 LEU Chi-restraints excluded: chain A residue 1239 VAL Chi-restraints excluded: chain A residue 1258 VAL Chi-restraints excluded: chain A residue 1371 ILE Chi-restraints excluded: chain A residue 1408 LYS Chi-restraints excluded: chain A residue 1414 LEU Chi-restraints excluded: chain A residue 1431 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 13 optimal weight: 1.9990 chunk 37 optimal weight: 0.6980 chunk 106 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 2 optimal weight: 0.2980 chunk 121 optimal weight: 0.0770 chunk 120 optimal weight: 9.9990 chunk 85 optimal weight: 0.6980 chunk 99 optimal weight: 0.2980 chunk 57 optimal weight: 0.8980 chunk 38 optimal weight: 0.9980 overall best weight: 0.4138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.166882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.122776 restraints weight = 14646.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.119045 restraints weight = 12699.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.120592 restraints weight = 13947.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.121579 restraints weight = 7825.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.123155 restraints weight = 6644.381| |-----------------------------------------------------------------------------| r_work (final): 0.3560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7338 moved from start: 0.4479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10924 Z= 0.119 Angle : 0.548 8.661 14841 Z= 0.269 Chirality : 0.039 0.199 1729 Planarity : 0.003 0.042 1830 Dihedral : 9.017 85.362 1497 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 2.63 % Allowed : 22.68 % Favored : 74.68 % 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: 1.60 (0.23), residues: 1320 helix: 1.99 (0.18), residues: 873 sheet: -0.65 (0.63), residues: 63 loop : -0.82 (0.30), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 128 TYR 0.013 0.001 TYR A 869 PHE 0.020 0.001 PHE A 50 TRP 0.018 0.001 TRP A1275 HIS 0.008 0.001 HIS A 985 Details of bonding type rmsd covalent geometry : bond 0.00256 (10924) covalent geometry : angle 0.54796 (14841) hydrogen bonds : bond 0.04196 ( 686) hydrogen bonds : angle 3.84060 ( 2019) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 124 time to evaluate : 0.268 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 473 MET cc_start: 0.7521 (mtt) cc_final: 0.7277 (mtp) REVERT: A 476 MET cc_start: 0.6509 (mmt) cc_final: 0.6293 (mmt) REVERT: A 526 ASP cc_start: 0.8268 (t0) cc_final: 0.7989 (m-30) REVERT: A 793 ASP cc_start: 0.8036 (t0) cc_final: 0.7553 (t0) REVERT: A 849 MET cc_start: 0.7188 (tmm) cc_final: 0.6643 (tpt) REVERT: A 963 TRP cc_start: 0.8058 (t-100) cc_final: 0.7266 (t60) REVERT: A 1077 LYS cc_start: 0.8139 (ptpt) cc_final: 0.7774 (ptmt) REVERT: A 1085 MET cc_start: 0.7633 (mmm) cc_final: 0.6675 (tpp) REVERT: A 1113 MET cc_start: 0.6726 (OUTLIER) cc_final: 0.6389 (tpp) REVERT: A 1126 PHE cc_start: 0.7772 (t80) cc_final: 0.7507 (t80) REVERT: A 1253 MET cc_start: 0.7680 (tpp) cc_final: 0.7211 (tpp) outliers start: 31 outliers final: 26 residues processed: 153 average time/residue: 0.0832 time to fit residues: 18.6647 Evaluate side-chains 145 residues out of total 1177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 118 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 212 SER Chi-restraints excluded: chain A residue 259 LYS Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 385 PHE Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 611 VAL Chi-restraints excluded: chain A residue 618 VAL Chi-restraints excluded: chain A residue 650 THR Chi-restraints excluded: chain A residue 811 ILE Chi-restraints excluded: chain A residue 821 THR Chi-restraints excluded: chain A residue 831 TYR Chi-restraints excluded: chain A residue 840 VAL Chi-restraints excluded: chain A residue 1011 THR Chi-restraints excluded: chain A residue 1032 TYR Chi-restraints excluded: chain A residue 1072 VAL Chi-restraints excluded: chain A residue 1109 LEU Chi-restraints excluded: chain A residue 1113 MET Chi-restraints excluded: chain A residue 1239 VAL Chi-restraints excluded: chain A residue 1371 ILE Chi-restraints excluded: chain A residue 1408 LYS Chi-restraints excluded: chain A residue 1414 LEU Chi-restraints excluded: chain A residue 1431 VAL Chi-restraints excluded: chain A residue 1514 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 128 optimal weight: 8.9990 chunk 89 optimal weight: 6.9990 chunk 132 optimal weight: 9.9990 chunk 45 optimal weight: 0.8980 chunk 58 optimal weight: 0.6980 chunk 27 optimal weight: 0.6980 chunk 100 optimal weight: 0.7980 chunk 110 optimal weight: 3.9990 chunk 15 optimal weight: 0.9990 chunk 82 optimal weight: 0.6980 chunk 125 optimal weight: 30.0000 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 382 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 510 ASN ** A1363 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 = 0.4068 r_free = 0.4068 target = 0.165494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.120738 restraints weight = 14705.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.117351 restraints weight = 13497.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.118977 restraints weight = 12855.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.119990 restraints weight = 7934.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.120549 restraints weight = 7006.518| |-----------------------------------------------------------------------------| r_work (final): 0.3542 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7374 moved from start: 0.4643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 10924 Z= 0.143 Angle : 0.579 8.935 14841 Z= 0.284 Chirality : 0.040 0.201 1729 Planarity : 0.004 0.043 1830 Dihedral : 9.087 86.729 1497 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 2.46 % Allowed : 23.11 % Favored : 74.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.60 (0.23), residues: 1320 helix: 1.96 (0.18), residues: 874 sheet: -0.67 (0.63), residues: 63 loop : -0.73 (0.30), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 128 TYR 0.012 0.001 TYR A 318 PHE 0.021 0.001 PHE A1062 TRP 0.013 0.001 TRP A 47 HIS 0.009 0.001 HIS A 985 Details of bonding type rmsd covalent geometry : bond 0.00327 (10924) covalent geometry : angle 0.57870 (14841) hydrogen bonds : bond 0.04368 ( 686) hydrogen bonds : angle 3.88427 ( 2019) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 124 time to evaluate : 0.244 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 LEU cc_start: 0.7122 (tt) cc_final: 0.5835 (mt) REVERT: A 473 MET cc_start: 0.7554 (mtt) cc_final: 0.7297 (mtp) REVERT: A 476 MET cc_start: 0.6503 (mmt) cc_final: 0.6290 (mmt) REVERT: A 534 GLU cc_start: 0.8460 (mm-30) cc_final: 0.7604 (mt-10) REVERT: A 793 ASP cc_start: 0.8060 (t0) cc_final: 0.7601 (t0) REVERT: A 849 MET cc_start: 0.7202 (tmm) cc_final: 0.6664 (tpt) REVERT: A 963 TRP cc_start: 0.8073 (t-100) cc_final: 0.7278 (t60) REVERT: A 1077 LYS cc_start: 0.8099 (ptpt) cc_final: 0.7697 (ptmt) REVERT: A 1085 MET cc_start: 0.7630 (mmm) cc_final: 0.7145 (tpt) REVERT: A 1113 MET cc_start: 0.6827 (OUTLIER) cc_final: 0.6374 (tpp) REVERT: A 1126 PHE cc_start: 0.7753 (t80) cc_final: 0.7500 (t80) outliers start: 29 outliers final: 27 residues processed: 150 average time/residue: 0.0868 time to fit residues: 19.1812 Evaluate side-chains 145 residues out of total 1177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 117 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 212 SER Chi-restraints excluded: chain A residue 259 LYS Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 338 MET Chi-restraints excluded: chain A residue 375 CYS Chi-restraints excluded: chain A residue 385 PHE Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 611 VAL Chi-restraints excluded: chain A residue 618 VAL Chi-restraints excluded: chain A residue 650 THR Chi-restraints excluded: chain A residue 811 ILE Chi-restraints excluded: chain A residue 821 THR Chi-restraints excluded: chain A residue 831 TYR Chi-restraints excluded: chain A residue 840 VAL Chi-restraints excluded: chain A residue 1032 TYR Chi-restraints excluded: chain A residue 1072 VAL Chi-restraints excluded: chain A residue 1109 LEU Chi-restraints excluded: chain A residue 1113 MET Chi-restraints excluded: chain A residue 1239 VAL Chi-restraints excluded: chain A residue 1371 ILE Chi-restraints excluded: chain A residue 1408 LYS Chi-restraints excluded: chain A residue 1414 LEU Chi-restraints excluded: chain A residue 1431 VAL Chi-restraints excluded: chain A residue 1514 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 118 optimal weight: 6.9990 chunk 28 optimal weight: 0.7980 chunk 64 optimal weight: 1.9990 chunk 45 optimal weight: 0.8980 chunk 111 optimal weight: 0.6980 chunk 43 optimal weight: 0.7980 chunk 123 optimal weight: 6.9990 chunk 48 optimal weight: 2.9990 chunk 2 optimal weight: 0.9980 chunk 32 optimal weight: 0.8980 chunk 44 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.164820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.119454 restraints weight = 14733.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.117560 restraints weight = 13091.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.118190 restraints weight = 15004.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.119899 restraints weight = 8418.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.120549 restraints weight = 6693.355| |-----------------------------------------------------------------------------| r_work (final): 0.3539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7380 moved from start: 0.4788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 10924 Z= 0.146 Angle : 0.590 11.668 14841 Z= 0.289 Chirality : 0.041 0.203 1729 Planarity : 0.004 0.044 1830 Dihedral : 9.166 86.829 1497 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 2.72 % Allowed : 23.02 % Favored : 74.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.57 (0.23), residues: 1320 helix: 1.92 (0.18), residues: 874 sheet: -0.52 (0.57), residues: 72 loop : -0.75 (0.31), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 128 TYR 0.012 0.001 TYR A 318 PHE 0.019 0.001 PHE A 50 TRP 0.017 0.001 TRP A 47 HIS 0.006 0.001 HIS A 985 Details of bonding type rmsd covalent geometry : bond 0.00336 (10924) covalent geometry : angle 0.59022 (14841) hydrogen bonds : bond 0.04357 ( 686) hydrogen bonds : angle 3.90517 ( 2019) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 126 time to evaluate : 0.434 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 TRP cc_start: 0.7181 (t-100) cc_final: 0.6947 (t-100) REVERT: A 80 LEU cc_start: 0.7189 (tt) cc_final: 0.5924 (mt) REVERT: A 473 MET cc_start: 0.7593 (mtt) cc_final: 0.7321 (mtp) REVERT: A 534 GLU cc_start: 0.8445 (mm-30) cc_final: 0.7629 (mt-10) REVERT: A 793 ASP cc_start: 0.8053 (t0) cc_final: 0.7603 (t0) REVERT: A 835 MET cc_start: 0.7430 (mmm) cc_final: 0.7162 (mmp) REVERT: A 849 MET cc_start: 0.7206 (tmm) cc_final: 0.6670 (tpt) REVERT: A 963 TRP cc_start: 0.8108 (t-100) cc_final: 0.7328 (t60) REVERT: A 1077 LYS cc_start: 0.8150 (ptpt) cc_final: 0.7718 (ptmt) REVERT: A 1085 MET cc_start: 0.7581 (mmm) cc_final: 0.6910 (tpt) REVERT: A 1113 MET cc_start: 0.6786 (OUTLIER) cc_final: 0.6367 (tpp) REVERT: A 1126 PHE cc_start: 0.7777 (t80) cc_final: 0.7496 (t80) REVERT: A 1359 LYS cc_start: 0.9060 (mmtm) cc_final: 0.8499 (ptpt) outliers start: 32 outliers final: 29 residues processed: 155 average time/residue: 0.0930 time to fit residues: 21.2209 Evaluate side-chains 149 residues out of total 1177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 119 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 212 SER Chi-restraints excluded: chain A residue 312 SER Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 338 MET Chi-restraints excluded: chain A residue 375 CYS Chi-restraints excluded: chain A residue 385 PHE Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 611 VAL Chi-restraints excluded: chain A residue 618 VAL Chi-restraints excluded: chain A residue 650 THR Chi-restraints excluded: chain A residue 761 ILE Chi-restraints excluded: chain A residue 811 ILE Chi-restraints excluded: chain A residue 821 THR Chi-restraints excluded: chain A residue 831 TYR Chi-restraints excluded: chain A residue 840 VAL Chi-restraints excluded: chain A residue 1032 TYR Chi-restraints excluded: chain A residue 1072 VAL Chi-restraints excluded: chain A residue 1109 LEU Chi-restraints excluded: chain A residue 1113 MET Chi-restraints excluded: chain A residue 1239 VAL Chi-restraints excluded: chain A residue 1263 LEU Chi-restraints excluded: chain A residue 1408 LYS Chi-restraints excluded: chain A residue 1414 LEU Chi-restraints excluded: chain A residue 1431 VAL Chi-restraints excluded: chain A residue 1514 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 35 optimal weight: 2.9990 chunk 112 optimal weight: 20.0000 chunk 127 optimal weight: 9.9990 chunk 111 optimal weight: 20.0000 chunk 1 optimal weight: 0.8980 chunk 96 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 78 optimal weight: 0.8980 chunk 17 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 382 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.160842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.115519 restraints weight = 14754.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.113230 restraints weight = 13649.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.114683 restraints weight = 13838.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.115703 restraints weight = 8157.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.116479 restraints weight = 6966.430| |-----------------------------------------------------------------------------| r_work (final): 0.3489 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7457 moved from start: 0.5026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 10924 Z= 0.224 Angle : 0.668 15.812 14841 Z= 0.333 Chirality : 0.043 0.216 1729 Planarity : 0.004 0.045 1830 Dihedral : 9.417 89.362 1497 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 3.06 % Allowed : 23.11 % Favored : 73.83 % 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: 1.32 (0.23), residues: 1320 helix: 1.69 (0.18), residues: 877 sheet: -0.28 (0.63), residues: 64 loop : -0.80 (0.30), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 128 TYR 0.016 0.002 TYR A 318 PHE 0.020 0.002 PHE A1062 TRP 0.020 0.002 TRP A1275 HIS 0.006 0.001 HIS A 985 Details of bonding type rmsd covalent geometry : bond 0.00529 (10924) covalent geometry : angle 0.66850 (14841) hydrogen bonds : bond 0.04934 ( 686) hydrogen bonds : angle 4.10919 ( 2019) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 124 time to evaluate : 0.305 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 TRP cc_start: 0.7362 (t-100) cc_final: 0.7132 (t-100) REVERT: A 118 LEU cc_start: 0.8286 (tp) cc_final: 0.7637 (tt) REVERT: A 419 THR cc_start: 0.7949 (OUTLIER) cc_final: 0.7619 (p) REVERT: A 473 MET cc_start: 0.7745 (mtt) cc_final: 0.7334 (mtp) REVERT: A 491 GLN cc_start: 0.8848 (tp40) cc_final: 0.8561 (tp-100) REVERT: A 534 GLU cc_start: 0.8433 (mm-30) cc_final: 0.7650 (mt-10) REVERT: A 793 ASP cc_start: 0.8149 (t0) cc_final: 0.7738 (t0) REVERT: A 835 MET cc_start: 0.7438 (mmm) cc_final: 0.7059 (mmp) REVERT: A 836 ASP cc_start: 0.7321 (m-30) cc_final: 0.7117 (t0) REVERT: A 849 MET cc_start: 0.7368 (tmm) cc_final: 0.6774 (tpt) REVERT: A 963 TRP cc_start: 0.8222 (t-100) cc_final: 0.7398 (t60) REVERT: A 1077 LYS cc_start: 0.8248 (ptpt) cc_final: 0.7785 (ptmt) REVERT: A 1085 MET cc_start: 0.7550 (mmm) cc_final: 0.7203 (tpt) REVERT: A 1113 MET cc_start: 0.6839 (OUTLIER) cc_final: 0.6469 (tpp) outliers start: 36 outliers final: 31 residues processed: 156 average time/residue: 0.0890 time to fit residues: 20.5069 Evaluate side-chains 151 residues out of total 1177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 118 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 212 SER Chi-restraints excluded: chain A residue 312 SER Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 338 MET Chi-restraints excluded: chain A residue 339 MET Chi-restraints excluded: chain A residue 375 CYS Chi-restraints excluded: chain A residue 385 PHE Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 611 VAL Chi-restraints excluded: chain A residue 618 VAL Chi-restraints excluded: chain A residue 650 THR Chi-restraints excluded: chain A residue 761 ILE Chi-restraints excluded: chain A residue 811 ILE Chi-restraints excluded: chain A residue 821 THR Chi-restraints excluded: chain A residue 831 TYR Chi-restraints excluded: chain A residue 840 VAL Chi-restraints excluded: chain A residue 1011 THR Chi-restraints excluded: chain A residue 1032 TYR Chi-restraints excluded: chain A residue 1041 ILE Chi-restraints excluded: chain A residue 1072 VAL Chi-restraints excluded: chain A residue 1113 MET Chi-restraints excluded: chain A residue 1239 VAL Chi-restraints excluded: chain A residue 1371 ILE Chi-restraints excluded: chain A residue 1408 LYS Chi-restraints excluded: chain A residue 1414 LEU Chi-restraints excluded: chain A residue 1431 VAL Chi-restraints excluded: chain A residue 1514 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 132 optimal weight: 0.9980 chunk 130 optimal weight: 5.9990 chunk 120 optimal weight: 5.9990 chunk 37 optimal weight: 0.9990 chunk 121 optimal weight: 0.6980 chunk 38 optimal weight: 0.8980 chunk 50 optimal weight: 2.9990 chunk 100 optimal weight: 0.8980 chunk 65 optimal weight: 0.8980 chunk 6 optimal weight: 0.8980 chunk 54 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 GLN A1155 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.163289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.118158 restraints weight = 14919.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.114999 restraints weight = 12642.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.116297 restraints weight = 14303.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.117885 restraints weight = 8122.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.119144 restraints weight = 6606.112| |-----------------------------------------------------------------------------| r_work (final): 0.3512 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7391 moved from start: 0.5129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 10924 Z= 0.155 Angle : 0.621 16.432 14841 Z= 0.304 Chirality : 0.041 0.212 1729 Planarity : 0.004 0.044 1830 Dihedral : 9.315 86.319 1497 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 2.80 % Allowed : 23.53 % Favored : 73.66 % 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: 1.46 (0.23), residues: 1320 helix: 1.80 (0.18), residues: 877 sheet: -0.09 (0.64), residues: 63 loop : -0.78 (0.30), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 128 TYR 0.013 0.001 TYR A 318 PHE 0.019 0.001 PHE A 50 TRP 0.022 0.002 TRP A1275 HIS 0.006 0.001 HIS A 985 Details of bonding type rmsd covalent geometry : bond 0.00358 (10924) covalent geometry : angle 0.62092 (14841) hydrogen bonds : bond 0.04529 ( 686) hydrogen bonds : angle 4.02446 ( 2019) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1683.02 seconds wall clock time: 29 minutes 54.83 seconds (1794.83 seconds total)