Starting phenix.real_space_refine on Mon Sep 30 02:14:10 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9ayc_43985/09_2024/9ayc_43985.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9ayc_43985/09_2024/9ayc_43985.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.23 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9ayc_43985/09_2024/9ayc_43985.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9ayc_43985/09_2024/9ayc_43985.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9ayc_43985/09_2024/9ayc_43985.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9ayc_43985/09_2024/9ayc_43985.cif" } resolution = 3.23 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.012 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: 6 Type Number sf(0) Gaussians P 4 5.49 5 S 54 5.16 5 C 7599 2.51 5 N 1983 2.21 5 O 2136 1.98 5 H 11947 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 23723 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 23723 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1481, 23723 Classifications: {'peptide': 1481} Link IDs: {'PCIS': 2, 'PTRANS': 41, 'TRANS': 1437} Chain breaks: 3 Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 3, 'TPO:plan-1': 1} Unresolved non-hydrogen planarities: 25 Time building chain proxies: 12.50, per 1000 atoms: 0.53 Number of scatterers: 23723 At special positions: 0 Unit cell: (88.776, 133.986, 152.892, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 54 16.00 P 4 15.00 O 2136 8.00 N 1983 7.00 C 7599 6.00 H 11947 1.00 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: 6.26 Conformation dependent library (CDL) restraints added in 1.8 seconds 2922 Ramachandran restraints generated. 1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2800 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 7 sheets defined 72.2% alpha, 9.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.57 Creating SS restraints... Processing helix chain 'A' and resid 2 through 13 removed outlier: 3.706A pdb=" N CYS A 10 " --> pdb=" O VAL A 6 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LYS A 11 " --> pdb=" O SER A 7 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU A 12 " --> pdb=" O TRP A 8 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N CYS A 13 " --> pdb=" O ALA A 9 " (cutoff:3.500A) Processing helix chain 'A' and resid 29 through 36 Processing helix chain 'A' and resid 36 through 59 Processing helix chain 'A' and resid 69 through 92 removed outlier: 3.727A pdb=" N VAL A 73 " --> pdb=" O ASN A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 99 Processing helix chain 'A' and resid 100 through 128 removed outlier: 3.631A pdb=" N VAL A 104 " --> pdb=" O ASN A 100 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N PHE A 115 " --> pdb=" O MET A 111 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N VAL A 116 " --> pdb=" O LEU A 112 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N TRP A 122 " --> pdb=" O LEU A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 161 Processing helix chain 'A' and resid 165 through 189 Processing helix chain 'A' and resid 196 through 204 removed outlier: 3.609A pdb=" N HIS A 199 " --> pdb=" O PRO A 196 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ILE A 200 " --> pdb=" O HIS A 197 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N THR A 203 " --> pdb=" O ILE A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 223 Processing helix chain 'A' and resid 225 through 236 removed outlier: 4.551A pdb=" N LEU A 229 " --> pdb=" O TRP A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 239 through 243 Processing helix chain 'A' and resid 247 through 250 Processing helix chain 'A' and resid 251 through 270 Processing helix chain 'A' and resid 274 through 283 Processing helix chain 'A' and resid 284 through 302 Processing helix chain 'A' and resid 303 through 327 Processing helix chain 'A' and resid 342 through 391 removed outlier: 3.585A pdb=" N PHE A 346 " --> pdb=" O ILE A 342 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N PHE A 353 " --> pdb=" O ALA A 349 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N VAL A 391 " --> pdb=" O GLN A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 393 through 400 Processing helix chain 'A' and resid 401 through 411 removed outlier: 3.709A pdb=" N MET A 409 " --> pdb=" O ILE A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 423 removed outlier: 3.813A pdb=" N GLN A 421 " --> pdb=" O GLN A 417 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N TRP A 422 " --> pdb=" O ASP A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 424 through 445 Proline residue: A 430 - end of helix Processing helix chain 'A' and resid 447 through 493 removed outlier: 4.097A pdb=" N GLY A 451 " --> pdb=" O SER A 447 " (cutoff:3.500A) Proline residue: A 460 - end of helix Processing helix chain 'A' and resid 493 through 500 Processing helix chain 'A' and resid 502 through 555 removed outlier: 3.544A pdb=" N TYR A 506 " --> pdb=" O TRP A 502 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N LEU A 519 " --> pdb=" O ASN A 515 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N LYS A 520 " --> pdb=" O ASN A 516 " (cutoff:3.500A) Proline residue: A 540 - end of helix removed outlier: 3.886A pdb=" N SER A 544 " --> pdb=" O PRO A 540 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N TYR A 553 " --> pdb=" O ALA A 549 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 563 Processing helix chain 'A' and resid 564 through 603 removed outlier: 4.086A pdb=" N PHE A 576 " --> pdb=" O ASN A 572 " (cutoff:3.500A) Proline residue: A 577 - end of helix removed outlier: 3.984A pdb=" N ILE A 581 " --> pdb=" O PRO A 577 " (cutoff:3.500A) Proline residue: A 582 - end of helix Processing helix chain 'A' and resid 608 through 612 removed outlier: 4.499A pdb=" N VAL A 612 " --> pdb=" O PRO A 609 " (cutoff:3.500A) Processing helix chain 'A' and resid 668 through 677 Processing helix chain 'A' and resid 706 through 713 Processing helix chain 'A' and resid 718 through 729 Processing helix chain 'A' and resid 731 through 738 Processing helix chain 'A' and resid 740 through 744 Processing helix chain 'A' and resid 754 through 770 removed outlier: 3.518A pdb=" N ALA A 766 " --> pdb=" O SER A 762 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ARG A 770 " --> pdb=" O ALA A 766 " (cutoff:3.500A) Processing helix chain 'A' and resid 778 through 783 removed outlier: 3.685A pdb=" N ALA A 781 " --> pdb=" O ASP A 778 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N ALA A 782 " --> pdb=" O PRO A 779 " (cutoff:3.500A) Processing helix chain 'A' and resid 784 through 795 Processing helix chain 'A' and resid 800 through 805 removed outlier: 3.554A pdb=" N HIS A 803 " --> pdb=" O GLY A 800 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N THR A 804 " --> pdb=" O LEU A 801 " (cutoff:3.500A) Processing helix chain 'A' and resid 813 through 820 removed outlier: 3.739A pdb=" N ILE A 819 " --> pdb=" O SER A 815 " (cutoff:3.500A) Processing helix chain 'A' and resid 837 through 843 Processing helix chain 'A' and resid 846 through 856 removed outlier: 3.728A pdb=" N LYS A 850 " --> pdb=" O SER A 846 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N LEU A 852 " --> pdb=" O LEU A 848 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N TYR A 855 " --> pdb=" O LEU A 851 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLY A 856 " --> pdb=" O LEU A 852 " (cutoff:3.500A) Processing helix chain 'A' and resid 883 through 889 Processing helix chain 'A' and resid 919 through 926 Processing helix chain 'A' and resid 935 through 946 removed outlier: 3.872A pdb=" N TYR A 939 " --> pdb=" O LYS A 935 " (cutoff:3.500A) Processing helix chain 'A' and resid 947 through 983 Processing helix chain 'A' and resid 987 through 1016 Processing helix chain 'A' and resid 1017 through 1036 Processing helix chain 'A' and resid 1037 through 1044 removed outlier: 3.779A pdb=" N PHE A1041 " --> pdb=" O PRO A1037 " (cutoff:3.500A) Processing helix chain 'A' and resid 1045 through 1063 removed outlier: 3.565A pdb=" N ASP A1056 " --> pdb=" O ARG A1052 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N ILE A1057 " --> pdb=" O PHE A1053 " (cutoff:3.500A) Processing helix chain 'A' and resid 1063 through 1089 Processing helix chain 'A' and resid 1092 through 1138 Proline residue: A1098 - end of helix removed outlier: 3.925A pdb=" N SER A1126 " --> pdb=" O SER A1122 " (cutoff:3.500A) Proline residue: A1127 - end of helix removed outlier: 3.604A pdb=" N GLY A1138 " --> pdb=" O GLU A1134 " (cutoff:3.500A) Processing helix chain 'A' and resid 1138 through 1146 Processing helix chain 'A' and resid 1147 through 1201 Proline residue: A1168 - end of helix removed outlier: 3.944A pdb=" N ASN A1173 " --> pdb=" O SER A1169 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ARG A1174 " --> pdb=" O ILE A1170 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ARG A1179 " --> pdb=" O TRP A1175 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLN A1201 " --> pdb=" O PHE A1197 " (cutoff:3.500A) Processing helix chain 'A' and resid 1205 through 1218 removed outlier: 3.533A pdb=" N VAL A1209 " --> pdb=" O THR A1205 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N GLN A1218 " --> pdb=" O SER A1214 " (cutoff:3.500A) Processing helix chain 'A' and resid 1218 through 1248 removed outlier: 3.895A pdb=" N THR A1222 " --> pdb=" O GLN A1218 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N VAL A1238 " --> pdb=" O GLU A1234 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N SER A1239 " --> pdb=" O THR A1235 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N VAL A1240 " --> pdb=" O ASN A1236 " (cutoff:3.500A) Processing helix chain 'A' and resid 1313 through 1320 removed outlier: 3.955A pdb=" N LEU A1317 " --> pdb=" O SER A1313 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N PHE A1320 " --> pdb=" O THR A1316 " (cutoff:3.500A) Processing helix chain 'A' and resid 1341 through 1348 removed outlier: 3.760A pdb=" N LYS A1348 " --> pdb=" O ASP A1344 " (cutoff:3.500A) Processing helix chain 'A' and resid 1374 through 1385 Processing helix chain 'A' and resid 1387 through 1395 removed outlier: 3.711A pdb=" N SER A1395 " --> pdb=" O VAL A1391 " (cutoff:3.500A) Processing helix chain 'A' and resid 1397 through 1400 removed outlier: 4.184A pdb=" N ASP A1400 " --> pdb=" O ASP A1397 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1397 through 1400' Processing helix chain 'A' and resid 1404 through 1408 removed outlier: 3.644A pdb=" N GLY A1408 " --> pdb=" O GLU A1405 " (cutoff:3.500A) Processing helix chain 'A' and resid 1411 through 1426 removed outlier: 3.610A pdb=" N VAL A1426 " --> pdb=" O ARG A1422 " (cutoff:3.500A) Processing helix chain 'A' and resid 1442 through 1456 removed outlier: 3.567A pdb=" N PHE A1456 " --> pdb=" O ILE A1452 " (cutoff:3.500A) Processing helix chain 'A' and resid 1467 through 1471 removed outlier: 3.637A pdb=" N THR A1470 " --> pdb=" O ARG A1467 " (cutoff:3.500A) Processing helix chain 'A' and resid 1490 through 1497 Processing helix chain 'A' and resid 1500 through 1509 Processing helix chain 'A' and resid 1510 through 1515 removed outlier: 3.587A pdb=" N GLU A1514 " --> pdb=" O GLY A1510 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 613 through 615 removed outlier: 6.609A pdb=" N THR A 633 " --> pdb=" O VAL A 683 " (cutoff:3.500A) removed outlier: 5.158A pdb=" N GLY A 685 " --> pdb=" O ASP A 631 " (cutoff:3.500A) removed outlier: 7.897A pdb=" N ASP A 631 " --> pdb=" O GLY A 685 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N ALA A 687 " --> pdb=" O GLY A 629 " (cutoff:3.500A) removed outlier: 7.809A pdb=" N GLY A 629 " --> pdb=" O ALA A 687 " (cutoff:3.500A) removed outlier: 5.652A pdb=" N VAL A 689 " --> pdb=" O ASN A 627 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N ASN A 627 " --> pdb=" O VAL A 689 " (cutoff:3.500A) removed outlier: 5.427A pdb=" N ALA A 632 " --> pdb=" O ASN A 648 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 613 through 615 removed outlier: 6.609A pdb=" N THR A 633 " --> pdb=" O VAL A 683 " (cutoff:3.500A) removed outlier: 5.158A pdb=" N GLY A 685 " --> pdb=" O ASP A 631 " (cutoff:3.500A) removed outlier: 7.897A pdb=" N ASP A 631 " --> pdb=" O GLY A 685 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N ALA A 687 " --> pdb=" O GLY A 629 " (cutoff:3.500A) removed outlier: 7.809A pdb=" N GLY A 629 " --> pdb=" O ALA A 687 " (cutoff:3.500A) removed outlier: 5.652A pdb=" N VAL A 689 " --> pdb=" O ASN A 627 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N ASN A 627 " --> pdb=" O VAL A 689 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 693 through 696 removed outlier: 6.118A pdb=" N TYR A 774 " --> pdb=" O VAL A 808 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N THR A 659 " --> pdb=" O LEU A 809 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N LEU A 658 " --> pdb=" O SER A 822 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N ALA A 824 " --> pdb=" O LEU A 658 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N CYS A 660 " --> pdb=" O ALA A 824 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N LEU A 826 " --> pdb=" O CYS A 660 " (cutoff:3.500A) removed outlier: 5.873A pdb=" N VAL A 662 " --> pdb=" O LEU A 826 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N ILE A 823 " --> pdb=" O GLN A 834 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N GLN A 834 " --> pdb=" O ILE A 823 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N LEU A 825 " --> pdb=" O THR A 832 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1287 through 1292 removed outlier: 6.518A pdb=" N THR A1279 " --> pdb=" O VAL A1288 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N LYS A1290 " --> pdb=" O TYR A1277 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N TYR A1277 " --> pdb=" O LYS A1290 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N ILE A1292 " --> pdb=" O ASN A1275 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ASN A1275 " --> pdb=" O ILE A1292 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ILE A1272 " --> pdb=" O ILE A1296 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1287 through 1292 removed outlier: 6.518A pdb=" N THR A1279 " --> pdb=" O VAL A1288 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N LYS A1290 " --> pdb=" O TYR A1277 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N TYR A1277 " --> pdb=" O LYS A1290 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N ILE A1292 " --> pdb=" O ASN A1275 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ASN A1275 " --> pdb=" O ILE A1292 " (cutoff:3.500A) removed outlier: 5.387A pdb=" N PHE A1274 " --> pdb=" O VAL A1331 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N VAL A1331 " --> pdb=" O PHE A1274 " (cutoff:3.500A) removed outlier: 5.248A pdb=" N ASN A1276 " --> pdb=" O ASN A1329 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N ASN A1329 " --> pdb=" O ASN A1276 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1350 through 1352 removed outlier: 6.527A pdb=" N VAL A1302 " --> pdb=" O THR A1463 " (cutoff:3.500A) removed outlier: 7.552A pdb=" N ALA A1465 " --> pdb=" O VAL A1302 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N ILE A1304 " --> pdb=" O ALA A1465 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N LYS A1301 " --> pdb=" O ARG A1476 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N ILE A1478 " --> pdb=" O LYS A1301 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N GLY A1303 " --> pdb=" O ILE A1478 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N LEU A1480 " --> pdb=" O GLY A1303 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N VAL A1305 " --> pdb=" O LEU A1480 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ASP A1489 " --> pdb=" O ILE A1477 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N ASP A1481 " --> pdb=" O VAL A1485 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N VAL A1485 " --> pdb=" O ASP A1481 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1361 through 1362 771 hydrogen bonds defined for protein. 2244 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: 9.64 Time building geometry restraints manager: 7.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 11925 1.03 - 1.23: 22 1.23 - 1.42: 4986 1.42 - 1.62: 6946 1.62 - 1.81: 89 Bond restraints: 23968 Sorted by residual: bond pdb=" CG2 TPO A 911 " pdb="HG21 TPO A 911 " ideal model delta sigma weight residual 0.970 1.090 -0.120 2.00e-02 2.50e+03 3.61e+01 bond pdb=" CG2 TPO A 911 " pdb="HG23 TPO A 911 " ideal model delta sigma weight residual 0.970 1.090 -0.120 2.00e-02 2.50e+03 3.58e+01 bond pdb=" CG2 TPO A 911 " pdb="HG22 TPO A 911 " ideal model delta sigma weight residual 0.970 1.089 -0.119 2.00e-02 2.50e+03 3.56e+01 bond pdb=" CB TPO A 911 " pdb=" HB TPO A 911 " ideal model delta sigma weight residual 0.970 1.089 -0.119 2.00e-02 2.50e+03 3.53e+01 bond pdb=" OG1 TPO A 911 " pdb=" P TPO A 911 " ideal model delta sigma weight residual 1.717 1.612 0.105 2.00e-02 2.50e+03 2.74e+01 ... (remaining 23963 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.47: 43087 2.47 - 4.94: 253 4.94 - 7.41: 22 7.41 - 9.88: 0 9.88 - 12.35: 1 Bond angle restraints: 43363 Sorted by residual: angle pdb=" OG1 TPO A 911 " pdb=" P TPO A 911 " pdb=" O1P TPO A 911 " ideal model delta sigma weight residual 100.43 112.78 -12.35 3.00e+00 1.11e-01 1.70e+01 angle pdb=" N ILE A1367 " pdb=" CA ILE A1367 " pdb=" C ILE A1367 " ideal model delta sigma weight residual 111.62 109.39 2.23 7.90e-01 1.60e+00 7.94e+00 angle pdb=" N GLY A1398 " pdb=" CA GLY A1398 " pdb=" C GLY A1398 " ideal model delta sigma weight residual 111.67 114.21 -2.54 9.20e-01 1.18e+00 7.64e+00 angle pdb=" C ASP A1333 " pdb=" N ASN A1334 " pdb=" CA ASN A1334 " ideal model delta sigma weight residual 122.08 125.47 -3.39 1.47e+00 4.63e-01 5.32e+00 angle pdb=" O1P TPO A 911 " pdb=" P TPO A 911 " pdb=" O2P TPO A 911 " ideal model delta sigma weight residual 114.94 108.24 6.70 3.00e+00 1.11e-01 4.98e+00 ... (remaining 43358 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.63: 10198 17.63 - 35.25: 701 35.25 - 52.87: 182 52.87 - 70.50: 113 70.50 - 88.12: 16 Dihedral angle restraints: 11210 sinusoidal: 6056 harmonic: 5154 Sorted by residual: dihedral pdb=" CA GLU A 930 " pdb=" C GLU A 930 " pdb=" N GLN A 931 " pdb=" CA GLN A 931 " ideal model delta harmonic sigma weight residual 180.00 155.78 24.22 0 5.00e+00 4.00e-02 2.35e+01 dihedral pdb=" CA GLN A 931 " pdb=" C GLN A 931 " pdb=" N GLY A 932 " pdb=" CA GLY A 932 " ideal model delta harmonic sigma weight residual 180.00 161.24 18.76 0 5.00e+00 4.00e-02 1.41e+01 dihedral pdb=" CA LEU A 189 " pdb=" C LEU A 189 " pdb=" N PRO A 190 " pdb=" CA PRO A 190 " ideal model delta harmonic sigma weight residual -180.00 -161.79 -18.21 0 5.00e+00 4.00e-02 1.33e+01 ... (remaining 11207 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 1289 0.034 - 0.068: 438 0.068 - 0.101: 104 0.101 - 0.135: 45 0.135 - 0.169: 7 Chirality restraints: 1883 Sorted by residual: chirality pdb=" CA ILE A 628 " pdb=" N ILE A 628 " pdb=" C ILE A 628 " pdb=" CB ILE A 628 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 7.15e-01 chirality pdb=" CA ILE A 661 " pdb=" N ILE A 661 " pdb=" C ILE A 661 " pdb=" CB ILE A 661 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 6.83e-01 chirality pdb=" CA ILE A 626 " pdb=" N ILE A 626 " pdb=" C ILE A 626 " pdb=" CB ILE A 626 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.19e-01 ... (remaining 1880 not shown) Planarity restraints: 3469 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER A1126 " -0.030 5.00e-02 4.00e+02 4.46e-02 3.19e+00 pdb=" N PRO A1127 " 0.077 5.00e-02 4.00e+02 pdb=" CA PRO A1127 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO A1127 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A 565 " -0.027 5.00e-02 4.00e+02 4.01e-02 2.57e+00 pdb=" N PRO A 566 " 0.069 5.00e-02 4.00e+02 pdb=" CA PRO A 566 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 566 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 429 " -0.026 5.00e-02 4.00e+02 3.91e-02 2.45e+00 pdb=" N PRO A 430 " 0.068 5.00e-02 4.00e+02 pdb=" CA PRO A 430 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 430 " -0.022 5.00e-02 4.00e+02 ... (remaining 3466 not shown) Histogram of nonbonded interaction distances: 1.75 - 2.32: 4906 2.32 - 2.89: 54539 2.89 - 3.46: 61060 3.46 - 4.03: 81233 4.03 - 4.60: 126402 Nonbonded interactions: 328140 Sorted by model distance: nonbonded pdb="HH11 ARG A 716 " pdb=" O3P SEP A 908 " model vdw 1.747 2.450 nonbonded pdb=" HZ3 LYS A 617 " pdb=" O1P SEP A 903 " model vdw 1.752 2.450 nonbonded pdb=" O GLN A1070 " pdb="HD21 ASN A1074 " model vdw 1.757 2.450 nonbonded pdb=" O ARG A 67 " pdb=" HH TYR A 125 " model vdw 1.761 2.450 nonbonded pdb=" H VAL A 239 " pdb=" OD2 ASP A 242 " model vdw 1.767 2.450 ... (remaining 328135 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 8.000 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: 0.420 Extract box with map and model: 0.900 Check model and map are aligned: 0.160 Set scattering table: 0.210 Process input model: 53.030 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.105 12021 Z= 0.266 Angle : 0.610 12.354 16297 Z= 0.318 Chirality : 0.039 0.169 1883 Planarity : 0.004 0.045 2035 Dihedral : 11.285 88.124 4375 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 0.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.21), residues: 1461 helix: 0.94 (0.16), residues: 968 sheet: 0.31 (0.58), residues: 66 loop : 0.65 (0.31), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 636 HIS 0.006 0.001 HIS A 364 PHE 0.013 0.001 PHE A 431 TYR 0.014 0.001 TYR A 506 ARG 0.003 0.000 ARG A 485 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2922 Ramachandran restraints generated. 1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2922 Ramachandran restraints generated. 1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 203 is missing expected H atoms. Skipping. Residue LEU 204 is missing expected H atoms. Skipping. Residue THR 205 is missing expected H atoms. Skipping. Residue LEU 885 is missing expected H atoms. Skipping. Residue LEU 888 is missing expected H atoms. Skipping. Residue LYS 890 is missing expected H atoms. Skipping. Residue LEU 891 is missing expected H atoms. Skipping. Evaluate side-chains 217 residues out of total 1297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 217 time to evaluate : 1.770 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 260 GLU cc_start: 0.8737 (tt0) cc_final: 0.8405 (tm-30) REVERT: A 528 TYR cc_start: 0.7768 (m-80) cc_final: 0.7513 (m-80) REVERT: A 684 LYS cc_start: 0.9036 (tppt) cc_final: 0.8807 (ttpt) REVERT: A 1038 MET cc_start: 0.8327 (mmm) cc_final: 0.8110 (mmm) REVERT: A 1241 GLU cc_start: 0.8844 (tp30) cc_final: 0.8602 (tp30) REVERT: A 1350 SER cc_start: 0.8954 (t) cc_final: 0.8747 (p) REVERT: A 1372 GLN cc_start: 0.8965 (tp40) cc_final: 0.8374 (tm-30) REVERT: A 1376 GLU cc_start: 0.8631 (mp0) cc_final: 0.8323 (mp0) REVERT: A 1481 ASP cc_start: 0.8470 (t0) cc_final: 0.8197 (t70) outliers start: 0 outliers final: 0 residues processed: 217 average time/residue: 0.7009 time to fit residues: 205.4470 Evaluate side-chains 124 residues out of total 1297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 124 time to evaluate : 2.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 124 optimal weight: 2.9990 chunk 112 optimal weight: 1.9990 chunk 62 optimal weight: 0.6980 chunk 38 optimal weight: 1.9990 chunk 75 optimal weight: 4.9990 chunk 59 optimal weight: 0.9980 chunk 116 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 86 optimal weight: 10.0000 chunk 134 optimal weight: 4.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 ASN A 106 GLN ** A1334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1416 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.2265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 12021 Z= 0.281 Angle : 0.547 5.320 16297 Z= 0.308 Chirality : 0.038 0.145 1883 Planarity : 0.004 0.043 2035 Dihedral : 4.905 73.961 1607 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 2.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 0.47 % Allowed : 4.91 % Favored : 94.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.22 (0.22), residues: 1461 helix: 1.91 (0.16), residues: 976 sheet: 0.34 (0.56), residues: 75 loop : 0.81 (0.32), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 849 HIS 0.008 0.001 HIS A 364 PHE 0.013 0.001 PHE A1502 TYR 0.018 0.001 TYR A1105 ARG 0.003 0.000 ARG A1115 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2922 Ramachandran restraints generated. 1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2922 Ramachandran restraints generated. 1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 203 is missing expected H atoms. Skipping. Residue LEU 204 is missing expected H atoms. Skipping. Residue THR 205 is missing expected H atoms. Skipping. Residue LEU 885 is missing expected H atoms. Skipping. Residue LEU 888 is missing expected H atoms. Skipping. Residue LYS 890 is missing expected H atoms. Skipping. Residue LEU 891 is missing expected H atoms. Skipping. Evaluate side-chains 133 residues out of total 1297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 127 time to evaluate : 1.928 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 260 GLU cc_start: 0.8787 (tt0) cc_final: 0.8576 (tm-30) REVERT: A 412 ASP cc_start: 0.8505 (m-30) cc_final: 0.8277 (m-30) REVERT: A 528 TYR cc_start: 0.7710 (m-80) cc_final: 0.7437 (m-80) REVERT: A 642 TYR cc_start: 0.6984 (OUTLIER) cc_final: 0.6425 (t80) REVERT: A 684 LYS cc_start: 0.9023 (tppt) cc_final: 0.8770 (ttpt) REVERT: A 1038 MET cc_start: 0.8359 (mmm) cc_final: 0.7971 (mmm) REVERT: A 1241 GLU cc_start: 0.9000 (tp30) cc_final: 0.8773 (tp30) REVERT: A 1372 GLN cc_start: 0.9026 (tp40) cc_final: 0.8394 (tm-30) REVERT: A 1376 GLU cc_start: 0.8695 (mp0) cc_final: 0.8480 (mp0) outliers start: 6 outliers final: 4 residues processed: 130 average time/residue: 0.7283 time to fit residues: 132.4145 Evaluate side-chains 113 residues out of total 1297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 108 time to evaluate : 1.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 642 TYR Chi-restraints excluded: chain A residue 1096 ILE Chi-restraints excluded: chain A residue 1187 ILE Chi-restraints excluded: chain A residue 1316 THR Chi-restraints excluded: chain A residue 1384 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 74 optimal weight: 8.9990 chunk 41 optimal weight: 1.9990 chunk 111 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 134 optimal weight: 4.9990 chunk 145 optimal weight: 6.9990 chunk 119 optimal weight: 0.9980 chunk 133 optimal weight: 1.9990 chunk 45 optimal weight: 0.6980 chunk 108 optimal weight: 1.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 854 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.2778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 12021 Z= 0.267 Angle : 0.512 6.792 16297 Z= 0.282 Chirality : 0.037 0.139 1883 Planarity : 0.003 0.038 2035 Dihedral : 4.811 75.767 1607 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 2.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 1.09 % Allowed : 5.76 % Favored : 93.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.33 (0.22), residues: 1461 helix: 2.03 (0.16), residues: 986 sheet: 0.13 (0.55), residues: 75 loop : 0.78 (0.33), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 849 HIS 0.008 0.001 HIS A 364 PHE 0.015 0.001 PHE A 576 TYR 0.018 0.001 TYR A1105 ARG 0.004 0.000 ARG A1115 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2922 Ramachandran restraints generated. 1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2922 Ramachandran restraints generated. 1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 203 is missing expected H atoms. Skipping. Residue LEU 204 is missing expected H atoms. Skipping. Residue THR 205 is missing expected H atoms. Skipping. Residue LEU 885 is missing expected H atoms. Skipping. Residue LEU 888 is missing expected H atoms. Skipping. Residue LYS 890 is missing expected H atoms. Skipping. Residue LEU 891 is missing expected H atoms. Skipping. Evaluate side-chains 127 residues out of total 1297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 113 time to evaluate : 1.881 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 412 ASP cc_start: 0.8552 (m-30) cc_final: 0.8318 (m-30) REVERT: A 528 TYR cc_start: 0.7685 (m-80) cc_final: 0.7415 (m-80) REVERT: A 642 TYR cc_start: 0.6944 (OUTLIER) cc_final: 0.6476 (t80) REVERT: A 684 LYS cc_start: 0.9039 (tppt) cc_final: 0.8789 (ttpt) REVERT: A 1241 GLU cc_start: 0.9045 (tp30) cc_final: 0.8811 (tp30) REVERT: A 1372 GLN cc_start: 0.9015 (tp40) cc_final: 0.8670 (tp40) REVERT: A 1376 GLU cc_start: 0.8722 (mp0) cc_final: 0.8452 (mp0) outliers start: 14 outliers final: 7 residues processed: 121 average time/residue: 0.6278 time to fit residues: 106.1797 Evaluate side-chains 117 residues out of total 1297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 109 time to evaluate : 1.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 PHE Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 642 TYR Chi-restraints excluded: chain A residue 848 LEU Chi-restraints excluded: chain A residue 1006 THR Chi-restraints excluded: chain A residue 1316 THR Chi-restraints excluded: chain A residue 1350 SER Chi-restraints excluded: chain A residue 1384 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 133 optimal weight: 0.6980 chunk 101 optimal weight: 0.9980 chunk 69 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 chunk 64 optimal weight: 3.9990 chunk 90 optimal weight: 1.9990 chunk 135 optimal weight: 5.9990 chunk 143 optimal weight: 6.9990 chunk 70 optimal weight: 2.9990 chunk 128 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1334 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.3045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 12021 Z= 0.239 Angle : 0.491 5.630 16297 Z= 0.269 Chirality : 0.037 0.154 1883 Planarity : 0.003 0.034 2035 Dihedral : 4.753 75.655 1607 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 1.25 % Allowed : 5.92 % Favored : 92.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.42 (0.22), residues: 1461 helix: 2.12 (0.16), residues: 986 sheet: 0.00 (0.56), residues: 75 loop : 0.76 (0.33), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 849 HIS 0.007 0.001 HIS A 364 PHE 0.014 0.001 PHE A 576 TYR 0.018 0.001 TYR A1105 ARG 0.003 0.000 ARG A1380 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2922 Ramachandran restraints generated. 1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2922 Ramachandran restraints generated. 1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 203 is missing expected H atoms. Skipping. Residue LEU 204 is missing expected H atoms. Skipping. Residue THR 205 is missing expected H atoms. Skipping. Residue LEU 885 is missing expected H atoms. Skipping. Residue LEU 888 is missing expected H atoms. Skipping. Residue LYS 890 is missing expected H atoms. Skipping. Residue LEU 891 is missing expected H atoms. Skipping. Evaluate side-chains 125 residues out of total 1297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 109 time to evaluate : 1.914 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 412 ASP cc_start: 0.8553 (m-30) cc_final: 0.8281 (m-30) REVERT: A 642 TYR cc_start: 0.7093 (OUTLIER) cc_final: 0.6572 (t80) REVERT: A 684 LYS cc_start: 0.9024 (tppt) cc_final: 0.8787 (ttpt) REVERT: A 1241 GLU cc_start: 0.9053 (tp30) cc_final: 0.8801 (tp30) REVERT: A 1372 GLN cc_start: 0.8992 (tp40) cc_final: 0.8686 (tp40) REVERT: A 1507 MET cc_start: 0.8176 (tpt) cc_final: 0.7756 (mpp) outliers start: 16 outliers final: 9 residues processed: 118 average time/residue: 0.6149 time to fit residues: 102.3210 Evaluate side-chains 113 residues out of total 1297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 103 time to evaluate : 2.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 PHE Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 642 TYR Chi-restraints excluded: chain A residue 706 THR Chi-restraints excluded: chain A residue 848 LEU Chi-restraints excluded: chain A residue 931 GLN Chi-restraints excluded: chain A residue 1011 ILE Chi-restraints excluded: chain A residue 1350 SER Chi-restraints excluded: chain A residue 1358 VAL Chi-restraints excluded: chain A residue 1480 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 119 optimal weight: 0.9980 chunk 81 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 106 optimal weight: 0.9990 chunk 59 optimal weight: 1.9990 chunk 122 optimal weight: 0.6980 chunk 98 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 73 optimal weight: 3.9990 chunk 128 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.3258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 12021 Z= 0.205 Angle : 0.474 6.325 16297 Z= 0.258 Chirality : 0.036 0.149 1883 Planarity : 0.003 0.031 2035 Dihedral : 4.690 76.403 1607 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 0.78 % Allowed : 6.46 % Favored : 92.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.62 (0.22), residues: 1461 helix: 2.28 (0.16), residues: 987 sheet: 0.11 (0.57), residues: 75 loop : 0.83 (0.33), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1014 HIS 0.007 0.001 HIS A 364 PHE 0.016 0.001 PHE A 576 TYR 0.016 0.001 TYR A1105 ARG 0.004 0.000 ARG A1380 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2922 Ramachandran restraints generated. 1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2922 Ramachandran restraints generated. 1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 203 is missing expected H atoms. Skipping. Residue LEU 204 is missing expected H atoms. Skipping. Residue THR 205 is missing expected H atoms. Skipping. Residue LEU 885 is missing expected H atoms. Skipping. Residue LEU 888 is missing expected H atoms. Skipping. Residue LYS 890 is missing expected H atoms. Skipping. Residue LEU 891 is missing expected H atoms. Skipping. Evaluate side-chains 117 residues out of total 1297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 107 time to evaluate : 1.799 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 412 ASP cc_start: 0.8598 (m-30) cc_final: 0.8358 (m-30) REVERT: A 642 TYR cc_start: 0.7274 (OUTLIER) cc_final: 0.6733 (t80) REVERT: A 684 LYS cc_start: 0.9032 (tppt) cc_final: 0.8783 (ttpt) REVERT: A 1241 GLU cc_start: 0.9065 (tp30) cc_final: 0.8813 (tp30) REVERT: A 1372 GLN cc_start: 0.8985 (tp40) cc_final: 0.8683 (tp40) outliers start: 10 outliers final: 9 residues processed: 112 average time/residue: 0.6515 time to fit residues: 104.6131 Evaluate side-chains 113 residues out of total 1297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 103 time to evaluate : 1.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 PHE Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 409 MET Chi-restraints excluded: chain A residue 642 TYR Chi-restraints excluded: chain A residue 848 LEU Chi-restraints excluded: chain A residue 931 GLN Chi-restraints excluded: chain A residue 1011 ILE Chi-restraints excluded: chain A residue 1350 SER Chi-restraints excluded: chain A residue 1384 LEU Chi-restraints excluded: chain A residue 1480 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 48 optimal weight: 2.9990 chunk 128 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 83 optimal weight: 0.4980 chunk 35 optimal weight: 1.9990 chunk 143 optimal weight: 0.9980 chunk 118 optimal weight: 1.9990 chunk 66 optimal weight: 4.9990 chunk 11 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 75 optimal weight: 4.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 521 ASN A1354 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.3447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 12021 Z= 0.260 Angle : 0.490 7.798 16297 Z= 0.268 Chirality : 0.037 0.175 1883 Planarity : 0.003 0.030 2035 Dihedral : 4.698 76.297 1607 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 1.17 % Allowed : 7.01 % Favored : 91.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.62 (0.22), residues: 1461 helix: 2.28 (0.16), residues: 992 sheet: -0.01 (0.58), residues: 75 loop : 0.82 (0.33), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1014 HIS 0.007 0.001 HIS A 364 PHE 0.019 0.001 PHE A 576 TYR 0.018 0.001 TYR A1105 ARG 0.004 0.000 ARG A1380 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2922 Ramachandran restraints generated. 1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2922 Ramachandran restraints generated. 1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 203 is missing expected H atoms. Skipping. Residue LEU 204 is missing expected H atoms. Skipping. Residue THR 205 is missing expected H atoms. Skipping. Residue LEU 885 is missing expected H atoms. Skipping. Residue LEU 888 is missing expected H atoms. Skipping. Residue LYS 890 is missing expected H atoms. Skipping. Residue LEU 891 is missing expected H atoms. Skipping. Evaluate side-chains 121 residues out of total 1297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 106 time to evaluate : 1.823 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 412 ASP cc_start: 0.8629 (m-30) cc_final: 0.8382 (m-30) REVERT: A 642 TYR cc_start: 0.7371 (OUTLIER) cc_final: 0.6856 (t80) REVERT: A 684 LYS cc_start: 0.9022 (tppt) cc_final: 0.8754 (ttpt) REVERT: A 1241 GLU cc_start: 0.9070 (tp30) cc_final: 0.8818 (tp30) REVERT: A 1372 GLN cc_start: 0.8990 (tp40) cc_final: 0.8693 (tp40) outliers start: 15 outliers final: 12 residues processed: 116 average time/residue: 0.6282 time to fit residues: 102.3238 Evaluate side-chains 117 residues out of total 1297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 104 time to evaluate : 2.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 PHE Chi-restraints excluded: chain A residue 409 MET Chi-restraints excluded: chain A residue 533 SER Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 642 TYR Chi-restraints excluded: chain A residue 821 ASP Chi-restraints excluded: chain A residue 848 LEU Chi-restraints excluded: chain A residue 931 GLN Chi-restraints excluded: chain A residue 1006 THR Chi-restraints excluded: chain A residue 1011 ILE Chi-restraints excluded: chain A residue 1350 SER Chi-restraints excluded: chain A residue 1384 LEU Chi-restraints excluded: chain A residue 1480 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 138 optimal weight: 4.9990 chunk 16 optimal weight: 2.9990 chunk 81 optimal weight: 0.8980 chunk 104 optimal weight: 0.9990 chunk 120 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 142 optimal weight: 3.9990 chunk 89 optimal weight: 6.9990 chunk 86 optimal weight: 9.9990 chunk 65 optimal weight: 2.9990 chunk 88 optimal weight: 4.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 476 GLN A 757 GLN A 854 ASN A1390 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.3672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 12021 Z= 0.326 Angle : 0.515 7.276 16297 Z= 0.286 Chirality : 0.038 0.243 1883 Planarity : 0.003 0.028 2035 Dihedral : 4.785 76.199 1607 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 1.17 % Allowed : 7.17 % Favored : 91.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.48 (0.22), residues: 1461 helix: 2.18 (0.16), residues: 987 sheet: -0.42 (0.55), residues: 85 loop : 0.90 (0.34), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1014 HIS 0.008 0.001 HIS A 364 PHE 0.018 0.001 PHE A 576 TYR 0.021 0.001 TYR A1105 ARG 0.005 0.000 ARG A1380 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2922 Ramachandran restraints generated. 1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2922 Ramachandran restraints generated. 1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 203 is missing expected H atoms. Skipping. Residue LEU 204 is missing expected H atoms. Skipping. Residue THR 205 is missing expected H atoms. Skipping. Residue LEU 885 is missing expected H atoms. Skipping. Residue LEU 888 is missing expected H atoms. Skipping. Residue LYS 890 is missing expected H atoms. Skipping. Residue LEU 891 is missing expected H atoms. Skipping. Evaluate side-chains 118 residues out of total 1297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 103 time to evaluate : 1.963 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 412 ASP cc_start: 0.8664 (m-30) cc_final: 0.8433 (m-30) REVERT: A 642 TYR cc_start: 0.7446 (OUTLIER) cc_final: 0.6896 (t80) REVERT: A 684 LYS cc_start: 0.9018 (tppt) cc_final: 0.8743 (ttpt) REVERT: A 1241 GLU cc_start: 0.9059 (tp30) cc_final: 0.8812 (tp30) REVERT: A 1372 GLN cc_start: 0.8974 (tp40) cc_final: 0.8756 (tp-100) outliers start: 15 outliers final: 13 residues processed: 114 average time/residue: 0.6345 time to fit residues: 102.1692 Evaluate side-chains 116 residues out of total 1297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 102 time to evaluate : 1.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 PHE Chi-restraints excluded: chain A residue 409 MET Chi-restraints excluded: chain A residue 533 SER Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 642 TYR Chi-restraints excluded: chain A residue 821 ASP Chi-restraints excluded: chain A residue 848 LEU Chi-restraints excluded: chain A residue 854 ASN Chi-restraints excluded: chain A residue 931 GLN Chi-restraints excluded: chain A residue 1006 THR Chi-restraints excluded: chain A residue 1011 ILE Chi-restraints excluded: chain A residue 1350 SER Chi-restraints excluded: chain A residue 1384 LEU Chi-restraints excluded: chain A residue 1480 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 56 optimal weight: 0.9980 chunk 85 optimal weight: 20.0000 chunk 42 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 27 optimal weight: 0.5980 chunk 90 optimal weight: 1.9990 chunk 97 optimal weight: 0.7980 chunk 70 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 112 optimal weight: 1.9990 chunk 129 optimal weight: 5.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.3719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 12021 Z= 0.230 Angle : 0.488 8.955 16297 Z= 0.266 Chirality : 0.037 0.141 1883 Planarity : 0.003 0.029 2035 Dihedral : 4.770 76.606 1607 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 1.32 % Allowed : 7.09 % Favored : 91.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.59 (0.22), residues: 1461 helix: 2.26 (0.16), residues: 989 sheet: -0.18 (0.60), residues: 75 loop : 0.85 (0.33), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1014 HIS 0.007 0.001 HIS A 364 PHE 0.012 0.001 PHE A 576 TYR 0.018 0.001 TYR A1105 ARG 0.004 0.000 ARG A1380 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2922 Ramachandran restraints generated. 1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2922 Ramachandran restraints generated. 1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 203 is missing expected H atoms. Skipping. Residue LEU 204 is missing expected H atoms. Skipping. Residue THR 205 is missing expected H atoms. Skipping. Residue LEU 885 is missing expected H atoms. Skipping. Residue LEU 888 is missing expected H atoms. Skipping. Residue LYS 890 is missing expected H atoms. Skipping. Residue LEU 891 is missing expected H atoms. Skipping. Evaluate side-chains 120 residues out of total 1297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 103 time to evaluate : 2.070 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 412 ASP cc_start: 0.8651 (m-30) cc_final: 0.8410 (m-30) REVERT: A 642 TYR cc_start: 0.7429 (OUTLIER) cc_final: 0.6929 (t80) REVERT: A 684 LYS cc_start: 0.9020 (tppt) cc_final: 0.8710 (ttpt) REVERT: A 1241 GLU cc_start: 0.9047 (tp30) cc_final: 0.8797 (tp30) REVERT: A 1372 GLN cc_start: 0.8971 (tp40) cc_final: 0.8366 (tm-30) outliers start: 17 outliers final: 13 residues processed: 116 average time/residue: 0.6307 time to fit residues: 102.9361 Evaluate side-chains 117 residues out of total 1297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 103 time to evaluate : 2.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 PHE Chi-restraints excluded: chain A residue 409 MET Chi-restraints excluded: chain A residue 533 SER Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 642 TYR Chi-restraints excluded: chain A residue 795 VAL Chi-restraints excluded: chain A residue 821 ASP Chi-restraints excluded: chain A residue 931 GLN Chi-restraints excluded: chain A residue 1006 THR Chi-restraints excluded: chain A residue 1011 ILE Chi-restraints excluded: chain A residue 1350 SER Chi-restraints excluded: chain A residue 1384 LEU Chi-restraints excluded: chain A residue 1466 HIS Chi-restraints excluded: chain A residue 1480 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 136 optimal weight: 4.9990 chunk 124 optimal weight: 0.7980 chunk 132 optimal weight: 0.7980 chunk 80 optimal weight: 4.9990 chunk 57 optimal weight: 0.9980 chunk 104 optimal weight: 0.8980 chunk 40 optimal weight: 0.9980 chunk 120 optimal weight: 1.9990 chunk 125 optimal weight: 0.9990 chunk 87 optimal weight: 4.9990 chunk 140 optimal weight: 8.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 521 ASN A1354 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.3781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 12021 Z= 0.174 Angle : 0.464 8.235 16297 Z= 0.248 Chirality : 0.036 0.142 1883 Planarity : 0.003 0.030 2035 Dihedral : 4.711 77.394 1607 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 0.86 % Allowed : 7.55 % Favored : 91.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.76 (0.22), residues: 1461 helix: 2.40 (0.16), residues: 990 sheet: -0.26 (0.61), residues: 74 loop : 0.89 (0.33), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1014 HIS 0.006 0.001 HIS A 364 PHE 0.020 0.001 PHE A 576 TYR 0.015 0.001 TYR A1105 ARG 0.006 0.000 ARG A1380 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2922 Ramachandran restraints generated. 1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2922 Ramachandran restraints generated. 1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 203 is missing expected H atoms. Skipping. Residue LEU 204 is missing expected H atoms. Skipping. Residue THR 205 is missing expected H atoms. Skipping. Residue LEU 885 is missing expected H atoms. Skipping. Residue LEU 888 is missing expected H atoms. Skipping. Residue LYS 890 is missing expected H atoms. Skipping. Residue LEU 891 is missing expected H atoms. Skipping. Evaluate side-chains 114 residues out of total 1297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 103 time to evaluate : 2.130 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 412 ASP cc_start: 0.8646 (m-30) cc_final: 0.8384 (m-30) REVERT: A 642 TYR cc_start: 0.7455 (OUTLIER) cc_final: 0.6954 (t80) REVERT: A 684 LYS cc_start: 0.9022 (tppt) cc_final: 0.8706 (ttpt) REVERT: A 1241 GLU cc_start: 0.9042 (tp30) cc_final: 0.8808 (tp30) REVERT: A 1372 GLN cc_start: 0.8971 (tp40) cc_final: 0.8685 (tp40) outliers start: 11 outliers final: 10 residues processed: 110 average time/residue: 0.6294 time to fit residues: 97.3246 Evaluate side-chains 112 residues out of total 1297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 101 time to evaluate : 2.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 PHE Chi-restraints excluded: chain A residue 409 MET Chi-restraints excluded: chain A residue 533 SER Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 642 TYR Chi-restraints excluded: chain A residue 931 GLN Chi-restraints excluded: chain A residue 1011 ILE Chi-restraints excluded: chain A residue 1350 SER Chi-restraints excluded: chain A residue 1384 LEU Chi-restraints excluded: chain A residue 1466 HIS Chi-restraints excluded: chain A residue 1480 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 85 optimal weight: 0.9980 chunk 66 optimal weight: 2.9990 chunk 97 optimal weight: 0.9980 chunk 147 optimal weight: 2.9990 chunk 135 optimal weight: 4.9990 chunk 117 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 93 optimal weight: 0.7980 chunk 125 optimal weight: 2.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.3828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 12021 Z= 0.236 Angle : 0.480 8.896 16297 Z= 0.260 Chirality : 0.037 0.145 1883 Planarity : 0.003 0.029 2035 Dihedral : 4.671 77.346 1607 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 0.93 % Allowed : 7.48 % Favored : 91.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.71 (0.22), residues: 1461 helix: 2.38 (0.16), residues: 990 sheet: -0.30 (0.61), residues: 74 loop : 0.84 (0.33), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1014 HIS 0.007 0.001 HIS A 364 PHE 0.011 0.001 PHE A 954 TYR 0.017 0.001 TYR A1105 ARG 0.005 0.000 ARG A1380 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2922 Ramachandran restraints generated. 1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2922 Ramachandran restraints generated. 1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 203 is missing expected H atoms. Skipping. Residue LEU 204 is missing expected H atoms. Skipping. Residue THR 205 is missing expected H atoms. Skipping. Residue LEU 885 is missing expected H atoms. Skipping. Residue LEU 888 is missing expected H atoms. Skipping. Residue LYS 890 is missing expected H atoms. Skipping. Residue LEU 891 is missing expected H atoms. Skipping. Evaluate side-chains 111 residues out of total 1297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 99 time to evaluate : 2.146 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 412 ASP cc_start: 0.8667 (m-30) cc_final: 0.8403 (m-30) REVERT: A 642 TYR cc_start: 0.7496 (OUTLIER) cc_final: 0.6989 (t80) REVERT: A 684 LYS cc_start: 0.9028 (tppt) cc_final: 0.8714 (ttpt) REVERT: A 1241 GLU cc_start: 0.9055 (tp30) cc_final: 0.8824 (tp30) REVERT: A 1372 GLN cc_start: 0.8972 (tp40) cc_final: 0.8352 (tm-30) outliers start: 12 outliers final: 11 residues processed: 107 average time/residue: 0.6231 time to fit residues: 93.6577 Evaluate side-chains 111 residues out of total 1297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 99 time to evaluate : 1.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 PHE Chi-restraints excluded: chain A residue 409 MET Chi-restraints excluded: chain A residue 533 SER Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 642 TYR Chi-restraints excluded: chain A residue 821 ASP Chi-restraints excluded: chain A residue 931 GLN Chi-restraints excluded: chain A residue 1011 ILE Chi-restraints excluded: chain A residue 1350 SER Chi-restraints excluded: chain A residue 1384 LEU Chi-restraints excluded: chain A residue 1466 HIS Chi-restraints excluded: chain A residue 1480 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 35 optimal weight: 1.9990 chunk 108 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 117 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 120 optimal weight: 0.9990 chunk 14 optimal weight: 0.9990 chunk 21 optimal weight: 0.5980 chunk 103 optimal weight: 1.9990 chunk 6 optimal weight: 0.5980 overall best weight: 1.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.101452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.071608 restraints weight = 71385.300| |-----------------------------------------------------------------------------| r_work (start): 0.3106 rms_B_bonded: 2.73 r_work: 0.2995 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2875 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.3892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 12021 Z= 0.189 Angle : 0.463 8.942 16297 Z= 0.248 Chirality : 0.036 0.156 1883 Planarity : 0.003 0.029 2035 Dihedral : 4.614 77.874 1607 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 0.93 % Allowed : 7.48 % Favored : 91.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.82 (0.22), residues: 1461 helix: 2.46 (0.16), residues: 990 sheet: -0.22 (0.62), residues: 74 loop : 0.88 (0.33), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1014 HIS 0.006 0.001 HIS A 364 PHE 0.011 0.001 PHE A 576 TYR 0.015 0.001 TYR A1105 ARG 0.005 0.000 ARG A1380 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5230.14 seconds wall clock time: 95 minutes 32.37 seconds (5732.37 seconds total)