Starting phenix.real_space_refine on Sun Jan 19 07:46:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8r6u_18963/01_2025/8r6u_18963.cif Found real_map, /net/cci-nas-00/data/ceres_data/8r6u_18963/01_2025/8r6u_18963.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.98 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8r6u_18963/01_2025/8r6u_18963.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8r6u_18963/01_2025/8r6u_18963.map" model { file = "/net/cci-nas-00/data/ceres_data/8r6u_18963/01_2025/8r6u_18963.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8r6u_18963/01_2025/8r6u_18963.cif" } resolution = 2.98 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= 0.001 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 41 5.49 5 Mg 1 5.21 5 S 72 5.16 5 C 8346 2.51 5 N 2338 2.21 5 O 2610 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 13408 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 12495 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1566, 12479 Classifications: {'peptide': 1566} Link IDs: {'PCIS': 2, 'PTRANS': 57, 'TRANS': 1506} Chain breaks: 4 Conformer: "B" Number of residues, atoms: 1566, 12479 Classifications: {'peptide': 1566} Link IDs: {'PCIS': 2, 'PTRANS': 57, 'TRANS': 1506} Chain breaks: 4 bond proxies already assigned to first conformer: 12726 Chain: "P" Number of atoms: 341 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 341 Classifications: {'RNA': 16} Modifications used: {'5*END': 1, 'rna2p_pur': 4, 'rna3p_pur': 6, 'rna3p_pyr': 6} Link IDs: {'rna2p': 3, 'rna3p': 12} Chain: "T" Number of atoms: 361 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 361 Classifications: {'RNA': 17} Modifications used: {'rna2p_pur': 2, 'rna2p_pyr': 4, 'rna3p_pur': 5, 'rna3p_pyr': 6} Link IDs: {'rna2p': 6, 'rna3p': 10} Chain: "G" Number of atoms: 81 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 81 Classifications: {'RNA': 4} Modifications used: {'5*END': 1, 'rna3p_pur': 2, 'rna3p_pyr': 2} Link IDs: {'rna3p': 3} Chain: "E" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 129 Classifications: {'RNA': 6} Modifications used: {'rna2p_pur': 2, 'rna3p_pur': 2, 'rna3p_pyr': 2} Link IDs: {'rna2p': 1, 'rna3p': 4} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 14.86, per 1000 atoms: 1.11 Number of scatterers: 13408 At special positions: 0 Unit cell: (101.15, 109.65, 127.5, 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 72 16.00 P 41 15.00 Mg 1 11.99 O 2610 8.00 N 2338 7.00 C 8346 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: 3.43 Conformation dependent library (CDL) restraints added in 3.2 seconds 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2948 Finding SS restraints... Secondary structure from input PDB file: 76 helices and 14 sheets defined 55.1% alpha, 11.0% beta 10 base pairs and 21 stacking pairs defined. Time for finding SS restraints: 5.04 Creating SS restraints... Processing helix chain 'A' and resid 2 through 8 Processing helix chain 'A' and resid 71 through 76 removed outlier: 5.138A pdb=" N TYR A 76 " --> pdb=" O SER A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 85 removed outlier: 3.851A pdb=" N PHE A 84 " --> pdb=" O HIS A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 149 removed outlier: 3.945A pdb=" N LEU A 138 " --> pdb=" O ASN A 134 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N TYR A 149 " --> pdb=" O LYS A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 157 removed outlier: 3.728A pdb=" N ARG A 156 " --> pdb=" O PRO A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 209 removed outlier: 3.512A pdb=" N MET A 208 " --> pdb=" O LYS A 204 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ASP A 209 " --> pdb=" O ALA A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 234 Processing helix chain 'A' and resid 237 through 245 Processing helix chain 'A' and resid 249 through 259 removed outlier: 4.196A pdb=" N LEU A 253 " --> pdb=" O GLU A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 285 Processing helix chain 'A' and resid 292 through 317 removed outlier: 3.774A pdb=" N ILE A 299 " --> pdb=" O GLU A 295 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N CYS A 302 " --> pdb=" O GLU A 298 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALA A 317 " --> pdb=" O ALA A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 355 Processing helix chain 'A' and resid 359 through 375 Processing helix chain 'A' and resid 383 through 393 removed outlier: 3.808A pdb=" N GLU A 387 " --> pdb=" O ASP A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 425 Processing helix chain 'A' and resid 436 through 446 removed outlier: 3.710A pdb=" N GLN A 440 " --> pdb=" O MET A 436 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 466 removed outlier: 3.853A pdb=" N THR A 464 " --> pdb=" O GLY A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 491 Processing helix chain 'A' and resid 496 through 510 Processing helix chain 'A' and resid 512 through 532 removed outlier: 3.984A pdb=" N TRP A 520 " --> pdb=" O GLN A 516 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 575 No H-bonds generated for 'chain 'A' and resid 573 through 575' Processing helix chain 'A' and resid 606 through 611 Processing helix chain 'A' and resid 611 through 627 Processing helix chain 'A' and resid 639 through 655 Processing helix chain 'A' and resid 656 through 665 Processing helix chain 'A' and resid 665 through 671 removed outlier: 3.562A pdb=" N THR A 669 " --> pdb=" O LEU A 665 " (cutoff:3.500A) Processing helix chain 'A' and resid 672 through 675 removed outlier: 3.535A pdb=" N VAL A 675 " --> pdb=" O GLU A 672 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 672 through 675' Processing helix chain 'A' and resid 682 through 689 removed outlier: 3.783A pdb=" N LYS A 685 " --> pdb=" O LYS A 682 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N MET A 686 " --> pdb=" O PRO A 683 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LEU A 687 " --> pdb=" O GLN A 684 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N GLY A 688 " --> pdb=" O LYS A 685 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LYS A 689 " --> pdb=" O MET A 686 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 682 through 689' Processing helix chain 'A' and resid 696 through 716 Processing helix chain 'A' and resid 742 through 749 Processing helix chain 'A' and resid 750 through 756 removed outlier: 4.821A pdb=" N GLY A 753 " --> pdb=" O TRP A 750 " (cutoff:3.500A) Processing helix chain 'A' and resid 763 through 766 Processing helix chain 'A' and resid 767 through 776 Processing helix chain 'A' and resid 777 through 781 Processing helix chain 'A' and resid 802 through 822 Processing helix chain 'A' and resid 824 through 839 removed outlier: 3.573A pdb=" N ASN A 828 " --> pdb=" O GLN A 824 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLU A 831 " --> pdb=" O GLN A 827 " (cutoff:3.500A) Processing helix chain 'A' and resid 841 through 846 removed outlier: 3.825A pdb=" N LEU A 845 " --> pdb=" O ASN A 841 " (cutoff:3.500A) Processing helix chain 'A' and resid 860 through 865 Processing helix chain 'A' and resid 874 through 885 Processing helix chain 'A' and resid 889 through 903 removed outlier: 4.041A pdb=" N GLY A 894 " --> pdb=" O ILE A 890 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N GLN A 895 " --> pdb=" O ASP A 891 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LYS A 898 " --> pdb=" O GLY A 894 " (cutoff:3.500A) Processing helix chain 'A' and resid 926 through 945 removed outlier: 4.151A pdb=" N GLY A 935 " --> pdb=" O LEU A 931 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N VAL A 936 " --> pdb=" O VAL A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 956 through 974 removed outlier: 5.601A pdb=" N ILE A 962 " --> pdb=" O LYS A 958 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N GLU A 963 " --> pdb=" O ASN A 959 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N GLY A 966 " --> pdb=" O ILE A 962 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N LEU A 967 " --> pdb=" O GLU A 963 " (cutoff:3.500A) Processing helix chain 'A' and resid 988 through 993 removed outlier: 3.944A pdb=" N HIS A 993 " --> pdb=" O TRP A 989 " (cutoff:3.500A) Processing helix chain 'A' and resid 994 through 1005 removed outlier: 4.088A pdb=" N LEU A 998 " --> pdb=" O TYR A 994 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N PHE A1005 " --> pdb=" O VAL A1001 " (cutoff:3.500A) Processing helix chain 'A' and resid 1010 through 1020 removed outlier: 3.888A pdb=" N MET A1020 " --> pdb=" O ALA A1016 " (cutoff:3.500A) Processing helix chain 'A' and resid 1021 through 1023 No H-bonds generated for 'chain 'A' and resid 1021 through 1023' Processing helix chain 'A' and resid 1029 through 1039 removed outlier: 3.635A pdb=" N LYS A1039 " --> pdb=" O HIS A1035 " (cutoff:3.500A) Processing helix chain 'A' and resid 1046 through 1058 removed outlier: 3.946A pdb=" N GLU A1050 " --> pdb=" O ASP A1046 " (cutoff:3.500A) Processing helix chain 'A' and resid 1083 through 1108 Processing helix chain 'A' and resid 1109 through 1113 removed outlier: 3.521A pdb=" N GLY A1112 " --> pdb=" O GLY A1109 " (cutoff:3.500A) Processing helix chain 'A' and resid 1138 through 1155 removed outlier: 3.999A pdb=" N VAL A1143 " --> pdb=" O ASP A1139 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N ARG A1144 " --> pdb=" O MET A1140 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N SER A1155 " --> pdb=" O ASN A1151 " (cutoff:3.500A) Processing helix chain 'A' and resid 1155 through 1160 Processing helix chain 'A' and resid 1161 through 1164 Processing helix chain 'A' and resid 1194 through 1200 removed outlier: 4.311A pdb=" N TRP A1198 " --> pdb=" O PRO A1194 " (cutoff:3.500A) Processing helix chain 'A' and resid 1210 through 1212 No H-bonds generated for 'chain 'A' and resid 1210 through 1212' Processing helix chain 'A' and resid 1213 through 1228 removed outlier: 3.855A pdb=" N ASP A1217 " --> pdb=" O SER A1213 " (cutoff:3.500A) Processing helix chain 'A' and resid 1231 through 1250 Processing helix chain 'A' and resid 1257 through 1266 Processing helix chain 'A' and resid 1280 through 1284 removed outlier: 3.602A pdb=" N ALA A1284 " --> pdb=" O PRO A1281 " (cutoff:3.500A) Processing helix chain 'A' and resid 1288 through 1297 Processing helix chain 'A' and resid 1302 through 1315 removed outlier: 3.521A pdb=" N ILE A1313 " --> pdb=" O TYR A1309 " (cutoff:3.500A) Processing helix chain 'A' and resid 1345 through 1356 removed outlier: 3.746A pdb=" N MET A1355 " --> pdb=" O LEU A1351 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N GLY A1356 " --> pdb=" O LEU A1352 " (cutoff:3.500A) Processing helix chain 'A' and resid 1360 through 1368 Processing helix chain 'A' and resid 1369 through 1373 Processing helix chain 'A' and resid 1378 through 1390 Processing helix chain 'A' and resid 1392 through 1397 removed outlier: 3.854A pdb=" N SER A1397 " --> pdb=" O PRO A1393 " (cutoff:3.500A) Processing helix chain 'A' and resid 1403 through 1411 removed outlier: 3.581A pdb=" N ARG A1407 " --> pdb=" O HIS A1403 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ALA A1411 " --> pdb=" O ARG A1407 " (cutoff:3.500A) Processing helix chain 'A' and resid 1437 through 1448 Processing helix chain 'A' and resid 1449 through 1451 No H-bonds generated for 'chain 'A' and resid 1449 through 1451' Processing helix chain 'A' and resid 1457 through 1465 removed outlier: 3.955A pdb=" N MET A1463 " --> pdb=" O ASN A1459 " (cutoff:3.500A) Processing helix chain 'A' and resid 1469 through 1478 Processing helix chain 'A' and resid 1512 through 1522 Processing helix chain 'A' and resid 1534 through 1546 removed outlier: 3.587A pdb=" N ALA A1543 " --> pdb=" O ASP A1539 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N SER A1544 " --> pdb=" O LYS A1540 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N PHE A1545 " --> pdb=" O LEU A1541 " (cutoff:3.500A) Processing helix chain 'A' and resid 1551 through 1559 removed outlier: 3.625A pdb=" N ASP A1558 " --> pdb=" O GLU A1554 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLY A1559 " --> pdb=" O THR A1555 " (cutoff:3.500A) Processing helix chain 'A' and resid 1563 through 1575 removed outlier: 3.871A pdb=" N ASN A1569 " --> pdb=" O VAL A1565 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ASP A1575 " --> pdb=" O ILE A1571 " (cutoff:3.500A) Processing helix chain 'A' and resid 1595 through 1604 Processing sheet with id=AA1, first strand: chain 'A' and resid 22 through 24 removed outlier: 6.748A pdb=" N ILE A 122 " --> pdb=" O PHE A 166 " (cutoff:3.500A) removed outlier: 7.908A pdb=" N GLY A 168 " --> pdb=" O ILE A 122 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N VAL A 124 " --> pdb=" O GLY A 168 " (cutoff:3.500A) removed outlier: 7.890A pdb=" N ILE A 170 " --> pdb=" O VAL A 124 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N GLU A 126 " --> pdb=" O ILE A 170 " (cutoff:3.500A) removed outlier: 7.879A pdb=" N VAL A 172 " --> pdb=" O GLU A 126 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N SER A 128 " --> pdb=" O VAL A 172 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N VAL A 113 " --> pdb=" O VAL A 125 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 36 through 40 removed outlier: 3.674A pdb=" N GLY A 66 " --> pdb=" O ILE A 49 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 335 through 336 Processing sheet with id=AA4, first strand: chain 'A' and resid 409 through 411 removed outlier: 4.615A pdb=" N ARG A 409 " --> pdb=" O ILE A 543 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 409 through 411 removed outlier: 4.615A pdb=" N ARG A 409 " --> pdb=" O ILE A 543 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 719 through 722 Processing sheet with id=AA7, first strand: chain 'A' and resid 850 through 851 Processing sheet with id=AA8, first strand: chain 'A' and resid 921 through 924 removed outlier: 7.529A pdb=" N ILE A 908 " --> pdb=" O MET A1027 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N THR A1074 " --> pdb=" O LYS A1024 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 1117 through 1123 removed outlier: 4.600A pdb=" N TYR A1166 " --> pdb=" O LYS A 987 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 1117 through 1123 removed outlier: 6.923A pdb=" N SER A 983 " --> pdb=" O VAL A1173 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N VAL A1173 " --> pdb=" O SER A 983 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 1178 through 1180 removed outlier: 3.918A pdb=" N PHE A1187 " --> pdb=" O HIS A1190 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 1338 through 1340 removed outlier: 4.239A pdb=" N MET A1339 " --> pdb=" O ARG A1422 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 1486 through 1488 Processing sheet with id=AB5, first strand: chain 'A' and resid 1496 through 1503 removed outlier: 3.651A pdb=" N LEU A1502 " --> pdb=" O ARG A1579 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N ARG A1579 " --> pdb=" O LEU A1502 " (cutoff:3.500A) 623 hydrogen bonds defined for protein. 1773 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 28 hydrogen bonds 56 hydrogen bond angles 0 basepair planarities 10 basepair parallelities 21 stacking parallelities Total time for adding SS restraints: 6.36 Time building geometry restraints manager: 3.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3816 1.33 - 1.45: 2471 1.45 - 1.57: 7294 1.57 - 1.69: 80 1.69 - 1.81: 118 Bond restraints: 13779 Sorted by residual: bond pdb=" N ASN A 14 " pdb=" CA ASN A 14 " ideal model delta sigma weight residual 1.457 1.483 -0.026 1.29e-02 6.01e+03 4.01e+00 bond pdb=" CB ASN A 765 " pdb=" CG ASN A 765 " ideal model delta sigma weight residual 1.516 1.478 0.038 2.50e-02 1.60e+03 2.32e+00 bond pdb=" CB LYS A 997 " pdb=" CG LYS A 997 " ideal model delta sigma weight residual 1.520 1.477 0.043 3.00e-02 1.11e+03 2.08e+00 bond pdb=" CG GLN A 670 " pdb=" CD GLN A 670 " ideal model delta sigma weight residual 1.516 1.481 0.035 2.50e-02 1.60e+03 1.97e+00 bond pdb=" CB TRP A1198 " pdb=" CG TRP A1198 " ideal model delta sigma weight residual 1.498 1.455 0.043 3.10e-02 1.04e+03 1.94e+00 ... (remaining 13774 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.95: 18311 1.95 - 3.89: 432 3.89 - 5.84: 43 5.84 - 7.78: 16 7.78 - 9.73: 1 Bond angle restraints: 18803 Sorted by residual: angle pdb=" N GLU A 290 " pdb=" CA GLU A 290 " pdb=" C GLU A 290 " ideal model delta sigma weight residual 111.02 117.20 -6.18 1.25e+00 6.40e-01 2.45e+01 angle pdb=" C THR A 91 " pdb=" CA THR A 91 " pdb=" CB THR A 91 " ideal model delta sigma weight residual 115.89 109.37 6.52 1.32e+00 5.74e-01 2.44e+01 angle pdb=" CA TRP A 520 " pdb=" CB TRP A 520 " pdb=" CG TRP A 520 " ideal model delta sigma weight residual 113.60 121.31 -7.71 1.90e+00 2.77e-01 1.65e+01 angle pdb=" P C G 4 " pdb=" O5' C G 4 " pdb=" C5' C G 4 " ideal model delta sigma weight residual 120.90 126.80 -5.90 1.50e+00 4.44e-01 1.55e+01 angle pdb=" N SER A 96 " pdb=" CA SER A 96 " pdb=" C SER A 96 " ideal model delta sigma weight residual 114.62 110.51 4.11 1.14e+00 7.69e-01 1.30e+01 ... (remaining 18798 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.43: 8017 33.43 - 66.85: 332 66.85 - 100.28: 33 100.28 - 133.71: 1 133.71 - 167.14: 1 Dihedral angle restraints: 8384 sinusoidal: 3828 harmonic: 4556 Sorted by residual: dihedral pdb=" O4' U T 22 " pdb=" C1' U T 22 " pdb=" N1 U T 22 " pdb=" C2 U T 22 " ideal model delta sinusoidal sigma weight residual 232.00 64.86 167.14 1 1.70e+01 3.46e-03 6.56e+01 dihedral pdb=" CA LEU A 546 " pdb=" C LEU A 546 " pdb=" N LYS A 547 " pdb=" CA LYS A 547 " ideal model delta harmonic sigma weight residual 180.00 153.36 26.64 0 5.00e+00 4.00e-02 2.84e+01 dihedral pdb=" O4' G P 16 " pdb=" C1' G P 16 " pdb=" N9 G P 16 " pdb=" C4 G P 16 " ideal model delta sinusoidal sigma weight residual -106.00 -174.98 68.98 1 1.70e+01 3.46e-03 2.13e+01 ... (remaining 8381 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 1303 0.038 - 0.075: 594 0.075 - 0.113: 172 0.113 - 0.151: 41 0.151 - 0.189: 4 Chirality restraints: 2114 Sorted by residual: chirality pdb=" CA PRO A1007 " pdb=" N PRO A1007 " pdb=" C PRO A1007 " pdb=" CB PRO A1007 " both_signs ideal model delta sigma weight residual False 2.72 2.53 0.19 2.00e-01 2.50e+01 8.90e-01 chirality pdb=" CB ILE A 479 " pdb=" CA ILE A 479 " pdb=" CG1 ILE A 479 " pdb=" CG2 ILE A 479 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.18 2.00e-01 2.50e+01 7.69e-01 chirality pdb=" C1' A E 5 " pdb=" O4' A E 5 " pdb=" C2' A E 5 " pdb=" N9 A E 5 " both_signs ideal model delta sigma weight residual False 2.46 2.29 0.16 2.00e-01 2.50e+01 6.64e-01 ... (remaining 2111 not shown) Planarity restraints: 2242 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER A 639 " -0.016 2.00e-02 2.50e+03 3.14e-02 9.86e+00 pdb=" C SER A 639 " 0.054 2.00e-02 2.50e+03 pdb=" O SER A 639 " -0.020 2.00e-02 2.50e+03 pdb=" N GLU A 640 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C MET A1006 " 0.050 5.00e-02 4.00e+02 7.59e-02 9.21e+00 pdb=" N PRO A1007 " -0.131 5.00e-02 4.00e+02 pdb=" CA PRO A1007 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO A1007 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU A 235 " 0.034 5.00e-02 4.00e+02 5.10e-02 4.17e+00 pdb=" N PRO A 236 " -0.088 5.00e-02 4.00e+02 pdb=" CA PRO A 236 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 236 " 0.028 5.00e-02 4.00e+02 ... (remaining 2239 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.55: 75 2.55 - 3.14: 10023 3.14 - 3.73: 20569 3.73 - 4.31: 28616 4.31 - 4.90: 47778 Nonbonded interactions: 107061 Sorted by model distance: nonbonded pdb=" OD1 ASP A 985 " pdb="MG MG A2101 " model vdw 1.964 2.170 nonbonded pdb=" OD1 ASP A1127 " pdb="MG MG A2101 " model vdw 2.033 2.170 nonbonded pdb=" O LYS A 798 " pdb=" OH TYR A1166 " model vdw 2.108 3.040 nonbonded pdb=" O2' G T 16 " pdb=" OP2 U T 18 " model vdw 2.213 3.040 nonbonded pdb=" OH TYR A1110 " pdb=" OD1 ASP A1141 " model vdw 2.231 3.040 ... (remaining 107056 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.37 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: 6.550 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 44.570 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.080 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:14.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.061 13779 Z= 0.461 Angle : 0.734 9.727 18803 Z= 0.394 Chirality : 0.046 0.189 2114 Planarity : 0.006 0.076 2242 Dihedral : 17.129 167.137 5436 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.62 % Favored : 93.38 % Rotamer: Outliers : 6.46 % Allowed : 12.63 % Favored : 80.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % 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: -1.04 (0.20), residues: 1558 helix: 0.46 (0.18), residues: 771 sheet: -0.30 (0.46), residues: 137 loop : -2.24 (0.21), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP A 520 HIS 0.007 0.001 HIS A1246 PHE 0.028 0.002 PHE A 649 TYR 0.017 0.002 TYR A 668 ARG 0.007 0.001 ARG A1579 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 139 time to evaluate : 1.693 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 93 ARG cc_start: 0.6831 (OUTLIER) cc_final: 0.6546 (mtm-85) REVERT: A 134 ASN cc_start: 0.7227 (p0) cc_final: 0.6646 (p0) REVERT: A 543 ILE cc_start: 0.9058 (OUTLIER) cc_final: 0.8695 (tp) REVERT: A 636 LYS cc_start: 0.8476 (mttt) cc_final: 0.8226 (mtmt) REVERT: A 851 THR cc_start: 0.8985 (OUTLIER) cc_final: 0.8722 (p) REVERT: A 884 LYS cc_start: 0.7807 (OUTLIER) cc_final: 0.7148 (tmtt) REVERT: A 919 LEU cc_start: 0.7409 (OUTLIER) cc_final: 0.7143 (tt) REVERT: A 1205 ILE cc_start: 0.8992 (OUTLIER) cc_final: 0.8668 (pp) REVERT: A 1215 GLN cc_start: 0.8449 (OUTLIER) cc_final: 0.7495 (mt0) REVERT: A 1217 ASP cc_start: 0.8200 (m-30) cc_final: 0.7795 (m-30) REVERT: A 1290 ARG cc_start: 0.8120 (OUTLIER) cc_final: 0.7116 (mmp-170) REVERT: A 1414 TYR cc_start: 0.7400 (p90) cc_final: 0.7141 (p90) outliers start: 88 outliers final: 40 residues processed: 216 average time/residue: 1.3014 time to fit residues: 307.5975 Evaluate side-chains 175 residues out of total 1374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 127 time to evaluate : 1.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 ARG Chi-restraints excluded: chain A residue 139 GLU Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 458 ASP Chi-restraints excluded: chain A residue 496 THR Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 603 THR Chi-restraints excluded: chain A residue 659 THR Chi-restraints excluded: chain A residue 765 ASN Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain A residue 851 THR Chi-restraints excluded: chain A residue 862 SER Chi-restraints excluded: chain A residue 865 GLN Chi-restraints excluded: chain A residue 881 LEU Chi-restraints excluded: chain A residue 884 LYS Chi-restraints excluded: chain A residue 893 VAL Chi-restraints excluded: chain A residue 919 LEU Chi-restraints excluded: chain A residue 926 ASP Chi-restraints excluded: chain A residue 938 THR Chi-restraints excluded: chain A residue 990 ASN Chi-restraints excluded: chain A residue 995 THR Chi-restraints excluded: chain A residue 1120 ASP Chi-restraints excluded: chain A residue 1122 ILE Chi-restraints excluded: chain A residue 1143 VAL Chi-restraints excluded: chain A residue 1205 ILE Chi-restraints excluded: chain A residue 1215 GLN Chi-restraints excluded: chain A residue 1248 MET Chi-restraints excluded: chain A residue 1260 THR Chi-restraints excluded: chain A residue 1290 ARG Chi-restraints excluded: chain A residue 1340 VAL Chi-restraints excluded: chain A residue 1360 ASP Chi-restraints excluded: chain A residue 1371 VAL Chi-restraints excluded: chain A residue 1395 VAL Chi-restraints excluded: chain A residue 1399 LEU Chi-restraints excluded: chain A residue 1409 VAL Chi-restraints excluded: chain A residue 1435 LYS Chi-restraints excluded: chain A residue 1447 ILE Chi-restraints excluded: chain A residue 1459 ASN Chi-restraints excluded: chain A residue 1485 THR Chi-restraints excluded: chain A residue 1511 CYS Chi-restraints excluded: chain A residue 1516 LEU Chi-restraints excluded: chain A residue 1570 PHE Chi-restraints excluded: chain A residue 1582 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 133 optimal weight: 9.9990 chunk 119 optimal weight: 0.7980 chunk 66 optimal weight: 0.8980 chunk 40 optimal weight: 0.9980 chunk 80 optimal weight: 7.9990 chunk 63 optimal weight: 0.9980 chunk 123 optimal weight: 0.5980 chunk 47 optimal weight: 4.9990 chunk 75 optimal weight: 8.9990 chunk 92 optimal weight: 0.9980 chunk 143 optimal weight: 9.9990 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 322 GLN A 467 ASN A 765 ASN A 870 HIS A 915 GLN A 964 ASN A1242 GLN A1353 ASN ** A1467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1599 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.142485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.108149 restraints weight = 33664.576| |-----------------------------------------------------------------------------| r_work (start): 0.3355 rms_B_bonded: 2.70 r_work: 0.3177 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3177 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3177 r_free = 0.3177 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3177 r_free = 0.3177 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3177 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.1070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13779 Z= 0.165 Angle : 0.556 7.177 18803 Z= 0.296 Chirality : 0.039 0.166 2114 Planarity : 0.004 0.069 2242 Dihedral : 14.771 171.414 2450 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 3.27 % Allowed : 17.42 % Favored : 79.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.21), residues: 1558 helix: 1.02 (0.19), residues: 762 sheet: 0.37 (0.47), residues: 122 loop : -2.09 (0.21), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 520 HIS 0.004 0.001 HIS A1246 PHE 0.019 0.001 PHE A1567 TYR 0.016 0.001 TYR A 28 ARG 0.003 0.000 ARG A1197 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 142 time to evaluate : 1.485 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 3 LEU cc_start: 0.6997 (pp) cc_final: 0.6744 (pp) REVERT: A 93 ARG cc_start: 0.7040 (OUTLIER) cc_final: 0.6513 (mtm-85) REVERT: A 134 ASN cc_start: 0.7247 (p0) cc_final: 0.6738 (p0) REVERT: A 153 ILE cc_start: 0.8105 (mt) cc_final: 0.7731 (tt) REVERT: A 183 LEU cc_start: 0.7977 (OUTLIER) cc_final: 0.7736 (mp) REVERT: A 422 GLU cc_start: 0.8462 (OUTLIER) cc_final: 0.7733 (tm-30) REVERT: A 636 LYS cc_start: 0.8608 (mttt) cc_final: 0.8298 (mtmt) REVERT: A 689 LYS cc_start: 0.8701 (OUTLIER) cc_final: 0.8046 (mptt) REVERT: A 723 ARG cc_start: 0.7239 (OUTLIER) cc_final: 0.7019 (ppp80) REVERT: A 919 LEU cc_start: 0.7260 (OUTLIER) cc_final: 0.6870 (tm) REVERT: A 1215 GLN cc_start: 0.8172 (OUTLIER) cc_final: 0.6942 (mt0) REVERT: A 1290 ARG cc_start: 0.8374 (OUTLIER) cc_final: 0.7671 (mtp180) REVERT: A 1422 ARG cc_start: 0.6917 (OUTLIER) cc_final: 0.6694 (ptp90) REVERT: A 1460 GLN cc_start: 0.5788 (pm20) cc_final: 0.5555 (pm20) outliers start: 44 outliers final: 18 residues processed: 175 average time/residue: 1.3947 time to fit residues: 265.9573 Evaluate side-chains 152 residues out of total 1374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 125 time to evaluate : 1.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 ARG Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 422 GLU Chi-restraints excluded: chain A residue 496 THR Chi-restraints excluded: chain A residue 560 SER Chi-restraints excluded: chain A residue 689 LYS Chi-restraints excluded: chain A residue 723 ARG Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain A residue 865 GLN Chi-restraints excluded: chain A residue 893 VAL Chi-restraints excluded: chain A residue 919 LEU Chi-restraints excluded: chain A residue 938 THR Chi-restraints excluded: chain A residue 995 THR Chi-restraints excluded: chain A residue 1044 SER Chi-restraints excluded: chain A residue 1120 ASP Chi-restraints excluded: chain A residue 1215 GLN Chi-restraints excluded: chain A residue 1260 THR Chi-restraints excluded: chain A residue 1290 ARG Chi-restraints excluded: chain A residue 1340 VAL Chi-restraints excluded: chain A residue 1364 GLN Chi-restraints excluded: chain A residue 1371 VAL Chi-restraints excluded: chain A residue 1422 ARG Chi-restraints excluded: chain A residue 1447 ILE Chi-restraints excluded: chain A residue 1516 LEU Chi-restraints excluded: chain A residue 1570 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 99 optimal weight: 0.1980 chunk 92 optimal weight: 3.9990 chunk 115 optimal weight: 5.9990 chunk 109 optimal weight: 3.9990 chunk 50 optimal weight: 5.9990 chunk 149 optimal weight: 2.9990 chunk 150 optimal weight: 4.9990 chunk 46 optimal weight: 3.9990 chunk 72 optimal weight: 6.9990 chunk 61 optimal weight: 5.9990 chunk 13 optimal weight: 9.9990 overall best weight: 3.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 2 ASN A 915 GLN ** A1467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.139251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.105277 restraints weight = 49187.387| |-----------------------------------------------------------------------------| r_work (start): 0.3308 rms_B_bonded: 3.60 r_work: 0.3073 rms_B_bonded: 4.46 restraints_weight: 0.5000 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3072 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3072 r_free = 0.3072 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3072 r_free = 0.3072 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3072 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.0959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 13779 Z= 0.316 Angle : 0.608 7.261 18803 Z= 0.323 Chirality : 0.042 0.166 2114 Planarity : 0.005 0.066 2242 Dihedral : 14.523 168.795 2398 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.30 % Favored : 93.70 % Rotamer: Outliers : 4.28 % Allowed : 17.49 % Favored : 78.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.21), residues: 1558 helix: 1.00 (0.19), residues: 761 sheet: 0.23 (0.46), residues: 122 loop : -2.12 (0.21), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 520 HIS 0.005 0.001 HIS A1246 PHE 0.022 0.002 PHE A 649 TYR 0.012 0.002 TYR A1166 ARG 0.007 0.000 ARG A1557 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 129 time to evaluate : 1.441 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 ARG cc_start: 0.7107 (OUTLIER) cc_final: 0.6467 (mtm-85) REVERT: A 134 ASN cc_start: 0.7115 (p0) cc_final: 0.6583 (p0) REVERT: A 143 ARG cc_start: 0.7684 (ttm110) cc_final: 0.7239 (ttt180) REVERT: A 636 LYS cc_start: 0.8702 (mttt) cc_final: 0.8386 (mtmt) REVERT: A 689 LYS cc_start: 0.8756 (OUTLIER) cc_final: 0.8226 (mmtp) REVERT: A 919 LEU cc_start: 0.7564 (OUTLIER) cc_final: 0.7288 (tt) REVERT: A 1215 GLN cc_start: 0.8311 (OUTLIER) cc_final: 0.7074 (mt0) REVERT: A 1416 LEU cc_start: 0.7467 (OUTLIER) cc_final: 0.6687 (mt) REVERT: A 1460 GLN cc_start: 0.5854 (pm20) cc_final: 0.5582 (pm20) outliers start: 58 outliers final: 26 residues processed: 174 average time/residue: 1.3854 time to fit residues: 263.4903 Evaluate side-chains 153 residues out of total 1374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 122 time to evaluate : 1.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 93 ARG Chi-restraints excluded: chain A residue 107 ASP Chi-restraints excluded: chain A residue 139 GLU Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 458 ASP Chi-restraints excluded: chain A residue 496 THR Chi-restraints excluded: chain A residue 560 SER Chi-restraints excluded: chain A residue 603 THR Chi-restraints excluded: chain A residue 689 LYS Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain A residue 865 GLN Chi-restraints excluded: chain A residue 893 VAL Chi-restraints excluded: chain A residue 919 LEU Chi-restraints excluded: chain A residue 938 THR Chi-restraints excluded: chain A residue 995 THR Chi-restraints excluded: chain A residue 1044 SER Chi-restraints excluded: chain A residue 1120 ASP Chi-restraints excluded: chain A residue 1215 GLN Chi-restraints excluded: chain A residue 1243 LEU Chi-restraints excluded: chain A residue 1260 THR Chi-restraints excluded: chain A residue 1340 VAL Chi-restraints excluded: chain A residue 1364 GLN Chi-restraints excluded: chain A residue 1371 VAL Chi-restraints excluded: chain A residue 1416 LEU Chi-restraints excluded: chain A residue 1422 ARG Chi-restraints excluded: chain A residue 1447 ILE Chi-restraints excluded: chain A residue 1565 VAL Chi-restraints excluded: chain A residue 1570 PHE Chi-restraints excluded: chain A residue 1596 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 13 optimal weight: 8.9990 chunk 37 optimal weight: 6.9990 chunk 116 optimal weight: 5.9990 chunk 27 optimal weight: 8.9990 chunk 155 optimal weight: 1.9990 chunk 15 optimal weight: 4.9990 chunk 108 optimal weight: 0.8980 chunk 131 optimal weight: 10.0000 chunk 19 optimal weight: 6.9990 chunk 98 optimal weight: 5.9990 chunk 59 optimal weight: 6.9990 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 199 ASN A 358 HIS A1174 ASN A1467 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.136952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.103357 restraints weight = 41720.425| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 3.03 r_work: 0.3089 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3093 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3093 r_free = 0.3093 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3093 r_free = 0.3093 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3093 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.1064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 13779 Z= 0.397 Angle : 0.661 8.017 18803 Z= 0.350 Chirality : 0.044 0.182 2114 Planarity : 0.005 0.068 2242 Dihedral : 14.517 165.814 2390 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.62 % Favored : 93.38 % Rotamer: Outliers : 4.57 % Allowed : 18.00 % Favored : 77.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.21), residues: 1558 helix: 0.80 (0.19), residues: 766 sheet: 0.07 (0.46), residues: 122 loop : -2.28 (0.21), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 520 HIS 0.006 0.001 HIS A1246 PHE 0.024 0.002 PHE A 649 TYR 0.021 0.002 TYR A1414 ARG 0.007 0.001 ARG A1557 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 128 time to evaluate : 1.436 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 LEU cc_start: 0.7047 (pp) cc_final: 0.6773 (pp) REVERT: A 93 ARG cc_start: 0.7095 (OUTLIER) cc_final: 0.6383 (mtm-85) REVERT: A 134 ASN cc_start: 0.7184 (p0) cc_final: 0.6659 (p0) REVERT: A 143 ARG cc_start: 0.7669 (ttm110) cc_final: 0.7232 (ttt180) REVERT: A 636 LYS cc_start: 0.8616 (mttt) cc_final: 0.8358 (mtmt) REVERT: A 689 LYS cc_start: 0.8762 (OUTLIER) cc_final: 0.8226 (mmtp) REVERT: A 919 LEU cc_start: 0.7580 (OUTLIER) cc_final: 0.7334 (tt) REVERT: A 1215 GLN cc_start: 0.8340 (OUTLIER) cc_final: 0.7212 (mt0) REVERT: A 1416 LEU cc_start: 0.7482 (OUTLIER) cc_final: 0.6717 (mt) REVERT: A 1460 GLN cc_start: 0.5914 (pm20) cc_final: 0.5562 (pm20) outliers start: 62 outliers final: 31 residues processed: 181 average time/residue: 1.3265 time to fit residues: 262.9840 Evaluate side-chains 155 residues out of total 1374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 119 time to evaluate : 1.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 93 ARG Chi-restraints excluded: chain A residue 107 ASP Chi-restraints excluded: chain A residue 139 GLU Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 295 GLU Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 458 ASP Chi-restraints excluded: chain A residue 496 THR Chi-restraints excluded: chain A residue 560 SER Chi-restraints excluded: chain A residue 603 THR Chi-restraints excluded: chain A residue 689 LYS Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain A residue 862 SER Chi-restraints excluded: chain A residue 890 ILE Chi-restraints excluded: chain A residue 893 VAL Chi-restraints excluded: chain A residue 919 LEU Chi-restraints excluded: chain A residue 995 THR Chi-restraints excluded: chain A residue 1033 LEU Chi-restraints excluded: chain A residue 1044 SER Chi-restraints excluded: chain A residue 1120 ASP Chi-restraints excluded: chain A residue 1215 GLN Chi-restraints excluded: chain A residue 1243 LEU Chi-restraints excluded: chain A residue 1260 THR Chi-restraints excluded: chain A residue 1340 VAL Chi-restraints excluded: chain A residue 1364 GLN Chi-restraints excluded: chain A residue 1371 VAL Chi-restraints excluded: chain A residue 1399 LEU Chi-restraints excluded: chain A residue 1416 LEU Chi-restraints excluded: chain A residue 1422 ARG Chi-restraints excluded: chain A residue 1447 ILE Chi-restraints excluded: chain A residue 1459 ASN Chi-restraints excluded: chain A residue 1565 VAL Chi-restraints excluded: chain A residue 1570 PHE Chi-restraints excluded: chain A residue 1595 THR Chi-restraints excluded: chain A residue 1596 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 37 optimal weight: 0.4980 chunk 126 optimal weight: 1.9990 chunk 67 optimal weight: 0.8980 chunk 157 optimal weight: 10.0000 chunk 146 optimal weight: 6.9990 chunk 30 optimal weight: 0.8980 chunk 145 optimal weight: 10.0000 chunk 2 optimal weight: 0.6980 chunk 57 optimal weight: 0.8980 chunk 109 optimal weight: 0.6980 chunk 61 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 526 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.142123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.108806 restraints weight = 41971.342| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 3.04 r_work: 0.3173 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3173 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3173 r_free = 0.3173 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3173 r_free = 0.3173 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3173 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.1472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.081 13779 Z= 0.162 Angle : 0.532 8.543 18803 Z= 0.284 Chirality : 0.038 0.160 2114 Planarity : 0.004 0.064 2242 Dihedral : 14.230 172.178 2386 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 3.19 % Allowed : 19.67 % Favored : 77.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.21), residues: 1558 helix: 1.26 (0.19), residues: 763 sheet: 0.45 (0.47), residues: 122 loop : -2.05 (0.21), residues: 673 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 520 HIS 0.005 0.001 HIS A1246 PHE 0.016 0.001 PHE A 649 TYR 0.011 0.001 TYR A 889 ARG 0.007 0.000 ARG A1557 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 133 time to evaluate : 1.507 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 ARG cc_start: 0.7169 (OUTLIER) cc_final: 0.6564 (mtm-85) REVERT: A 134 ASN cc_start: 0.7216 (p0) cc_final: 0.6662 (p0) REVERT: A 214 LEU cc_start: 0.6992 (OUTLIER) cc_final: 0.6767 (mm) REVERT: A 636 LYS cc_start: 0.8622 (mttt) cc_final: 0.8320 (mtmt) REVERT: A 689 LYS cc_start: 0.8688 (OUTLIER) cc_final: 0.8067 (mptt) REVERT: A 919 LEU cc_start: 0.7399 (OUTLIER) cc_final: 0.7127 (tt) REVERT: A 1215 GLN cc_start: 0.8153 (OUTLIER) cc_final: 0.6330 (mm-40) REVERT: A 1422 ARG cc_start: 0.6842 (OUTLIER) cc_final: 0.6522 (ptp90) REVERT: A 1460 GLN cc_start: 0.6006 (pm20) cc_final: 0.5664 (pm20) REVERT: A 1505 GLU cc_start: 0.5435 (OUTLIER) cc_final: 0.3302 (tm-30) REVERT: A 1570 PHE cc_start: 0.7606 (OUTLIER) cc_final: 0.7284 (t80) outliers start: 43 outliers final: 21 residues processed: 169 average time/residue: 1.4091 time to fit residues: 260.0886 Evaluate side-chains 151 residues out of total 1374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 122 time to evaluate : 1.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 ARG Chi-restraints excluded: chain A residue 139 GLU Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 295 GLU Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 496 THR Chi-restraints excluded: chain A residue 560 SER Chi-restraints excluded: chain A residue 689 LYS Chi-restraints excluded: chain A residue 721 ILE Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain A residue 893 VAL Chi-restraints excluded: chain A residue 919 LEU Chi-restraints excluded: chain A residue 995 THR Chi-restraints excluded: chain A residue 1044 SER Chi-restraints excluded: chain A residue 1050 GLU Chi-restraints excluded: chain A residue 1120 ASP Chi-restraints excluded: chain A residue 1143 VAL Chi-restraints excluded: chain A residue 1215 GLN Chi-restraints excluded: chain A residue 1260 THR Chi-restraints excluded: chain A residue 1340 VAL Chi-restraints excluded: chain A residue 1364 GLN Chi-restraints excluded: chain A residue 1371 VAL Chi-restraints excluded: chain A residue 1399 LEU Chi-restraints excluded: chain A residue 1422 ARG Chi-restraints excluded: chain A residue 1447 ILE Chi-restraints excluded: chain A residue 1505 GLU Chi-restraints excluded: chain A residue 1570 PHE Chi-restraints excluded: chain A residue 1596 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 47 optimal weight: 2.9990 chunk 95 optimal weight: 0.0020 chunk 39 optimal weight: 10.0000 chunk 89 optimal weight: 5.9990 chunk 118 optimal weight: 0.9990 chunk 140 optimal weight: 10.0000 chunk 13 optimal weight: 8.9990 chunk 10 optimal weight: 0.9990 chunk 46 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 76 optimal weight: 0.7980 overall best weight: 0.9594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 358 HIS A 915 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.142685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.109021 restraints weight = 42895.234| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 3.18 r_work: 0.3169 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3166 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3166 r_free = 0.3166 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3166 r_free = 0.3166 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3166 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.1607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 13779 Z= 0.164 Angle : 0.521 8.905 18803 Z= 0.276 Chirality : 0.038 0.167 2114 Planarity : 0.004 0.060 2242 Dihedral : 14.138 173.343 2386 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 3.19 % Allowed : 19.96 % Favored : 76.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.21), residues: 1558 helix: 1.42 (0.19), residues: 766 sheet: 0.60 (0.48), residues: 122 loop : -2.02 (0.22), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 520 HIS 0.005 0.001 HIS A1246 PHE 0.025 0.001 PHE A1567 TYR 0.012 0.001 TYR A 193 ARG 0.006 0.000 ARG A1557 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 130 time to evaluate : 1.388 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 ARG cc_start: 0.7169 (OUTLIER) cc_final: 0.6588 (mtm-85) REVERT: A 134 ASN cc_start: 0.7246 (p0) cc_final: 0.6709 (p0) REVERT: A 214 LEU cc_start: 0.6946 (OUTLIER) cc_final: 0.6710 (mm) REVERT: A 636 LYS cc_start: 0.8616 (mttt) cc_final: 0.8311 (mtmt) REVERT: A 689 LYS cc_start: 0.8648 (OUTLIER) cc_final: 0.8038 (mptt) REVERT: A 919 LEU cc_start: 0.7313 (OUTLIER) cc_final: 0.7056 (tt) REVERT: A 1422 ARG cc_start: 0.6807 (OUTLIER) cc_final: 0.6363 (ptp90) REVERT: A 1505 GLU cc_start: 0.5503 (OUTLIER) cc_final: 0.3429 (tm-30) outliers start: 43 outliers final: 20 residues processed: 166 average time/residue: 1.3763 time to fit residues: 249.3373 Evaluate side-chains 153 residues out of total 1374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 127 time to evaluate : 1.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 ARG Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 295 GLU Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 496 THR Chi-restraints excluded: chain A residue 560 SER Chi-restraints excluded: chain A residue 689 LYS Chi-restraints excluded: chain A residue 721 ILE Chi-restraints excluded: chain A residue 893 VAL Chi-restraints excluded: chain A residue 919 LEU Chi-restraints excluded: chain A residue 938 THR Chi-restraints excluded: chain A residue 995 THR Chi-restraints excluded: chain A residue 1044 SER Chi-restraints excluded: chain A residue 1050 GLU Chi-restraints excluded: chain A residue 1120 ASP Chi-restraints excluded: chain A residue 1143 VAL Chi-restraints excluded: chain A residue 1340 VAL Chi-restraints excluded: chain A residue 1364 GLN Chi-restraints excluded: chain A residue 1371 VAL Chi-restraints excluded: chain A residue 1399 LEU Chi-restraints excluded: chain A residue 1409 VAL Chi-restraints excluded: chain A residue 1422 ARG Chi-restraints excluded: chain A residue 1447 ILE Chi-restraints excluded: chain A residue 1505 GLU Chi-restraints excluded: chain A residue 1596 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 156 optimal weight: 7.9990 chunk 130 optimal weight: 9.9990 chunk 143 optimal weight: 5.9990 chunk 50 optimal weight: 4.9990 chunk 118 optimal weight: 0.9990 chunk 1 optimal weight: 20.0000 chunk 78 optimal weight: 10.0000 chunk 101 optimal weight: 8.9990 chunk 106 optimal weight: 0.9990 chunk 28 optimal weight: 3.9990 chunk 108 optimal weight: 5.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 954 ASN ** A1080 GLN ** 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 = 0.3776 r_free = 0.3776 target = 0.138306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.104615 restraints weight = 51665.935| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 3.91 r_work: 0.3076 rms_B_bonded: 4.41 restraints_weight: 0.5000 r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3074 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3074 r_free = 0.3074 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3074 r_free = 0.3074 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3074 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.1290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 13779 Z= 0.354 Angle : 0.633 8.522 18803 Z= 0.334 Chirality : 0.043 0.221 2114 Planarity : 0.005 0.062 2242 Dihedral : 14.176 168.516 2378 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 3.92 % Allowed : 19.38 % Favored : 76.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.21), residues: 1558 helix: 1.15 (0.19), residues: 765 sheet: 0.39 (0.47), residues: 122 loop : -2.07 (0.22), residues: 671 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A1538 HIS 0.005 0.001 HIS A1246 PHE 0.021 0.002 PHE A 649 TYR 0.020 0.002 TYR A1247 ARG 0.005 0.000 ARG A1345 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 124 time to evaluate : 1.603 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 LEU cc_start: 0.6929 (pp) cc_final: 0.6673 (pp) REVERT: A 93 ARG cc_start: 0.7238 (OUTLIER) cc_final: 0.6627 (mtm-85) REVERT: A 134 ASN cc_start: 0.7263 (p0) cc_final: 0.6698 (p0) REVERT: A 214 LEU cc_start: 0.7021 (OUTLIER) cc_final: 0.6819 (mm) REVERT: A 443 GLU cc_start: 0.8858 (OUTLIER) cc_final: 0.8240 (tm-30) REVERT: A 636 LYS cc_start: 0.8677 (mttt) cc_final: 0.8377 (mtmt) REVERT: A 689 LYS cc_start: 0.8754 (OUTLIER) cc_final: 0.8088 (mptt) REVERT: A 919 LEU cc_start: 0.7589 (OUTLIER) cc_final: 0.7322 (tt) REVERT: A 1207 GLU cc_start: 0.7390 (pm20) cc_final: 0.7076 (tt0) REVERT: A 1416 LEU cc_start: 0.7412 (OUTLIER) cc_final: 0.6654 (mt) REVERT: A 1447 ILE cc_start: 0.7771 (OUTLIER) cc_final: 0.7498 (tp) REVERT: A 1460 GLN cc_start: 0.5954 (pm20) cc_final: 0.5638 (pm20) REVERT: A 1505 GLU cc_start: 0.5415 (OUTLIER) cc_final: 0.3353 (tm-30) outliers start: 53 outliers final: 28 residues processed: 167 average time/residue: 1.4340 time to fit residues: 262.7602 Evaluate side-chains 159 residues out of total 1374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 123 time to evaluate : 1.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 93 ARG Chi-restraints excluded: chain A residue 107 ASP Chi-restraints excluded: chain A residue 139 GLU Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 295 GLU Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 443 GLU Chi-restraints excluded: chain A residue 496 THR Chi-restraints excluded: chain A residue 560 SER Chi-restraints excluded: chain A residue 603 THR Chi-restraints excluded: chain A residue 689 LYS Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain A residue 862 SER Chi-restraints excluded: chain A residue 893 VAL Chi-restraints excluded: chain A residue 919 LEU Chi-restraints excluded: chain A residue 936 VAL Chi-restraints excluded: chain A residue 938 THR Chi-restraints excluded: chain A residue 995 THR Chi-restraints excluded: chain A residue 1044 SER Chi-restraints excluded: chain A residue 1050 GLU Chi-restraints excluded: chain A residue 1120 ASP Chi-restraints excluded: chain A residue 1143 VAL Chi-restraints excluded: chain A residue 1340 VAL Chi-restraints excluded: chain A residue 1364 GLN Chi-restraints excluded: chain A residue 1371 VAL Chi-restraints excluded: chain A residue 1399 LEU Chi-restraints excluded: chain A residue 1409 VAL Chi-restraints excluded: chain A residue 1416 LEU Chi-restraints excluded: chain A residue 1422 ARG Chi-restraints excluded: chain A residue 1447 ILE Chi-restraints excluded: chain A residue 1459 ASN Chi-restraints excluded: chain A residue 1505 GLU Chi-restraints excluded: chain A residue 1511 CYS Chi-restraints excluded: chain A residue 1596 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 66 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 chunk 150 optimal weight: 5.9990 chunk 45 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 29 optimal weight: 0.0470 chunk 103 optimal weight: 0.6980 chunk 107 optimal weight: 2.9990 chunk 40 optimal weight: 9.9990 chunk 148 optimal weight: 2.9990 overall best weight: 0.9482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.142132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.108063 restraints weight = 48879.944| |-----------------------------------------------------------------------------| r_work (start): 0.3359 rms_B_bonded: 3.57 r_work: 0.3134 rms_B_bonded: 4.46 restraints_weight: 0.5000 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3132 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3132 r_free = 0.3132 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3132 r_free = 0.3132 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3132 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.1604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.097 13779 Z= 0.177 Angle : 0.543 9.360 18803 Z= 0.287 Chirality : 0.039 0.174 2114 Planarity : 0.004 0.062 2242 Dihedral : 14.028 172.600 2378 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 2.69 % Allowed : 20.90 % Favored : 76.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.21), residues: 1558 helix: 1.35 (0.19), residues: 768 sheet: 0.25 (0.46), residues: 135 loop : -1.94 (0.22), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 520 HIS 0.005 0.001 HIS A1246 PHE 0.029 0.001 PHE A1567 TYR 0.017 0.001 TYR A1247 ARG 0.009 0.000 ARG A1557 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 127 time to evaluate : 1.411 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 ARG cc_start: 0.7278 (OUTLIER) cc_final: 0.6644 (mtm-85) REVERT: A 134 ASN cc_start: 0.7213 (p0) cc_final: 0.6673 (p0) REVERT: A 214 LEU cc_start: 0.6984 (OUTLIER) cc_final: 0.6740 (mm) REVERT: A 443 GLU cc_start: 0.8742 (OUTLIER) cc_final: 0.8126 (tm-30) REVERT: A 636 LYS cc_start: 0.8642 (mttt) cc_final: 0.8325 (mtmt) REVERT: A 689 LYS cc_start: 0.8676 (OUTLIER) cc_final: 0.8050 (mptt) REVERT: A 919 LEU cc_start: 0.7397 (OUTLIER) cc_final: 0.7127 (tt) REVERT: A 1207 GLU cc_start: 0.7316 (pm20) cc_final: 0.7062 (tt0) REVERT: A 1422 ARG cc_start: 0.6792 (OUTLIER) cc_final: 0.6303 (ptp90) REVERT: A 1447 ILE cc_start: 0.7708 (OUTLIER) cc_final: 0.7431 (tp) REVERT: A 1460 GLN cc_start: 0.6017 (pm20) cc_final: 0.5767 (pm20) REVERT: A 1505 GLU cc_start: 0.5493 (OUTLIER) cc_final: 0.3397 (tm-30) outliers start: 36 outliers final: 22 residues processed: 156 average time/residue: 1.4552 time to fit residues: 247.2733 Evaluate side-chains 153 residues out of total 1374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 123 time to evaluate : 1.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 93 ARG Chi-restraints excluded: chain A residue 139 GLU Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 295 GLU Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 443 GLU Chi-restraints excluded: chain A residue 496 THR Chi-restraints excluded: chain A residue 560 SER Chi-restraints excluded: chain A residue 689 LYS Chi-restraints excluded: chain A residue 721 ILE Chi-restraints excluded: chain A residue 893 VAL Chi-restraints excluded: chain A residue 905 CYS Chi-restraints excluded: chain A residue 919 LEU Chi-restraints excluded: chain A residue 938 THR Chi-restraints excluded: chain A residue 995 THR Chi-restraints excluded: chain A residue 1044 SER Chi-restraints excluded: chain A residue 1050 GLU Chi-restraints excluded: chain A residue 1120 ASP Chi-restraints excluded: chain A residue 1143 VAL Chi-restraints excluded: chain A residue 1340 VAL Chi-restraints excluded: chain A residue 1364 GLN Chi-restraints excluded: chain A residue 1371 VAL Chi-restraints excluded: chain A residue 1399 LEU Chi-restraints excluded: chain A residue 1409 VAL Chi-restraints excluded: chain A residue 1422 ARG Chi-restraints excluded: chain A residue 1447 ILE Chi-restraints excluded: chain A residue 1505 GLU Chi-restraints excluded: chain A residue 1596 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 90 optimal weight: 4.9990 chunk 139 optimal weight: 10.0000 chunk 147 optimal weight: 0.9990 chunk 97 optimal weight: 7.9990 chunk 20 optimal weight: 1.9990 chunk 65 optimal weight: 4.9990 chunk 6 optimal weight: 9.9990 chunk 3 optimal weight: 10.0000 chunk 47 optimal weight: 2.9990 chunk 136 optimal weight: 0.5980 chunk 99 optimal weight: 0.9990 overall best weight: 1.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 915 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.141682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.108067 restraints weight = 49888.276| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 3.62 r_work: 0.3136 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3137 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3137 r_free = 0.3137 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3137 r_free = 0.3137 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3137 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.1597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 13779 Z= 0.204 Angle : 0.561 10.145 18803 Z= 0.293 Chirality : 0.039 0.183 2114 Planarity : 0.004 0.060 2242 Dihedral : 13.992 172.240 2378 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 2.69 % Allowed : 20.97 % Favored : 76.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.21), residues: 1558 helix: 1.37 (0.19), residues: 768 sheet: 0.29 (0.46), residues: 135 loop : -1.93 (0.22), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A1538 HIS 0.005 0.001 HIS A1246 PHE 0.018 0.001 PHE A 649 TYR 0.019 0.001 TYR A1247 ARG 0.003 0.000 ARG A1345 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 127 time to evaluate : 1.462 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 ARG cc_start: 0.7361 (OUTLIER) cc_final: 0.6725 (mtm-85) REVERT: A 134 ASN cc_start: 0.7196 (p0) cc_final: 0.6677 (p0) REVERT: A 214 LEU cc_start: 0.7003 (OUTLIER) cc_final: 0.6781 (mm) REVERT: A 422 GLU cc_start: 0.8535 (OUTLIER) cc_final: 0.7783 (tm-30) REVERT: A 443 GLU cc_start: 0.8726 (OUTLIER) cc_final: 0.8105 (tm-30) REVERT: A 636 LYS cc_start: 0.8617 (mttt) cc_final: 0.8308 (mtmt) REVERT: A 689 LYS cc_start: 0.8683 (OUTLIER) cc_final: 0.8058 (mptt) REVERT: A 919 LEU cc_start: 0.7387 (OUTLIER) cc_final: 0.7126 (tt) REVERT: A 1207 GLU cc_start: 0.7338 (pm20) cc_final: 0.7059 (tt0) REVERT: A 1422 ARG cc_start: 0.6787 (OUTLIER) cc_final: 0.6155 (ptp90) REVERT: A 1447 ILE cc_start: 0.7696 (OUTLIER) cc_final: 0.7427 (tp) REVERT: A 1460 GLN cc_start: 0.6031 (pm20) cc_final: 0.5763 (pm20) REVERT: A 1505 GLU cc_start: 0.5437 (OUTLIER) cc_final: 0.3388 (tm-30) outliers start: 36 outliers final: 22 residues processed: 158 average time/residue: 1.4340 time to fit residues: 246.9468 Evaluate side-chains 158 residues out of total 1374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 127 time to evaluate : 1.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 93 ARG Chi-restraints excluded: chain A residue 139 GLU Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 295 GLU Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 422 GLU Chi-restraints excluded: chain A residue 443 GLU Chi-restraints excluded: chain A residue 496 THR Chi-restraints excluded: chain A residue 560 SER Chi-restraints excluded: chain A residue 689 LYS Chi-restraints excluded: chain A residue 721 ILE Chi-restraints excluded: chain A residue 893 VAL Chi-restraints excluded: chain A residue 905 CYS Chi-restraints excluded: chain A residue 919 LEU Chi-restraints excluded: chain A residue 938 THR Chi-restraints excluded: chain A residue 995 THR Chi-restraints excluded: chain A residue 1044 SER Chi-restraints excluded: chain A residue 1050 GLU Chi-restraints excluded: chain A residue 1120 ASP Chi-restraints excluded: chain A residue 1143 VAL Chi-restraints excluded: chain A residue 1340 VAL Chi-restraints excluded: chain A residue 1364 GLN Chi-restraints excluded: chain A residue 1371 VAL Chi-restraints excluded: chain A residue 1399 LEU Chi-restraints excluded: chain A residue 1409 VAL Chi-restraints excluded: chain A residue 1422 ARG Chi-restraints excluded: chain A residue 1447 ILE Chi-restraints excluded: chain A residue 1505 GLU Chi-restraints excluded: chain A residue 1596 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 42 optimal weight: 3.9990 chunk 132 optimal weight: 1.9990 chunk 54 optimal weight: 0.8980 chunk 142 optimal weight: 9.9990 chunk 110 optimal weight: 0.0370 chunk 79 optimal weight: 3.9990 chunk 133 optimal weight: 9.9990 chunk 96 optimal weight: 0.0170 chunk 55 optimal weight: 1.9990 chunk 5 optimal weight: 20.0000 chunk 29 optimal weight: 0.9990 overall best weight: 0.7900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 358 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.143890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.110324 restraints weight = 36454.512| |-----------------------------------------------------------------------------| r_work (start): 0.3391 rms_B_bonded: 2.81 r_work: 0.3206 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3208 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3208 r_free = 0.3208 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3208 r_free = 0.3208 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3208 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.1848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.080 13779 Z= 0.164 Angle : 0.535 9.075 18803 Z= 0.282 Chirality : 0.038 0.208 2114 Planarity : 0.004 0.061 2242 Dihedral : 13.892 174.093 2378 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 2.32 % Allowed : 21.34 % Favored : 76.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.22), residues: 1558 helix: 1.48 (0.19), residues: 770 sheet: 0.46 (0.47), residues: 130 loop : -1.85 (0.22), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP A1538 HIS 0.004 0.001 HIS A1246 PHE 0.033 0.001 PHE A1567 TYR 0.020 0.001 TYR A1110 ARG 0.007 0.000 ARG A1345 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 139 time to evaluate : 1.562 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 VAL cc_start: 0.7720 (OUTLIER) cc_final: 0.7435 (t) REVERT: A 93 ARG cc_start: 0.7353 (OUTLIER) cc_final: 0.6782 (mtm-85) REVERT: A 134 ASN cc_start: 0.7190 (p0) cc_final: 0.6656 (p0) REVERT: A 155 ARG cc_start: 0.7507 (ttm110) cc_final: 0.6853 (mtp-110) REVERT: A 214 LEU cc_start: 0.6905 (OUTLIER) cc_final: 0.6117 (pt) REVERT: A 280 ASP cc_start: 0.8666 (t0) cc_final: 0.8447 (t0) REVERT: A 422 GLU cc_start: 0.8466 (OUTLIER) cc_final: 0.7695 (tm-30) REVERT: A 636 LYS cc_start: 0.8545 (mttt) cc_final: 0.8241 (mtmt) REVERT: A 689 LYS cc_start: 0.8629 (OUTLIER) cc_final: 0.8044 (mptt) REVERT: A 919 LEU cc_start: 0.7235 (OUTLIER) cc_final: 0.7024 (tt) REVERT: A 1207 GLU cc_start: 0.7191 (pm20) cc_final: 0.6898 (tt0) REVERT: A 1304 ARG cc_start: 0.6227 (tpt170) cc_final: 0.5924 (tpt170) REVERT: A 1422 ARG cc_start: 0.6686 (OUTLIER) cc_final: 0.6114 (ptp90) REVERT: A 1447 ILE cc_start: 0.7693 (OUTLIER) cc_final: 0.7434 (tp) REVERT: A 1505 GLU cc_start: 0.5518 (OUTLIER) cc_final: 0.3548 (tm-30) outliers start: 31 outliers final: 17 residues processed: 165 average time/residue: 1.4925 time to fit residues: 268.2848 Evaluate side-chains 155 residues out of total 1374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 129 time to evaluate : 1.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 93 ARG Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 422 GLU Chi-restraints excluded: chain A residue 496 THR Chi-restraints excluded: chain A residue 560 SER Chi-restraints excluded: chain A residue 689 LYS Chi-restraints excluded: chain A residue 721 ILE Chi-restraints excluded: chain A residue 893 VAL Chi-restraints excluded: chain A residue 905 CYS Chi-restraints excluded: chain A residue 919 LEU Chi-restraints excluded: chain A residue 938 THR Chi-restraints excluded: chain A residue 1044 SER Chi-restraints excluded: chain A residue 1120 ASP Chi-restraints excluded: chain A residue 1143 VAL Chi-restraints excluded: chain A residue 1340 VAL Chi-restraints excluded: chain A residue 1364 GLN Chi-restraints excluded: chain A residue 1371 VAL Chi-restraints excluded: chain A residue 1399 LEU Chi-restraints excluded: chain A residue 1409 VAL Chi-restraints excluded: chain A residue 1422 ARG Chi-restraints excluded: chain A residue 1447 ILE Chi-restraints excluded: chain A residue 1505 GLU Chi-restraints excluded: chain A residue 1596 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 152 optimal weight: 7.9990 chunk 100 optimal weight: 6.9990 chunk 15 optimal weight: 0.8980 chunk 103 optimal weight: 0.9980 chunk 42 optimal weight: 0.3980 chunk 9 optimal weight: 9.9990 chunk 131 optimal weight: 2.9990 chunk 139 optimal weight: 9.9990 chunk 35 optimal weight: 0.2980 chunk 153 optimal weight: 5.9990 chunk 93 optimal weight: 0.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 915 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.144331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.111111 restraints weight = 43864.023| |-----------------------------------------------------------------------------| r_work (start): 0.3403 rms_B_bonded: 3.04 r_work: 0.3204 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3207 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3207 r_free = 0.3207 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3207 r_free = 0.3207 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3207 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.1931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 13779 Z= 0.157 Angle : 0.530 9.420 18803 Z= 0.279 Chirality : 0.038 0.203 2114 Planarity : 0.004 0.059 2242 Dihedral : 13.827 173.936 2377 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 2.25 % Allowed : 21.55 % Favored : 76.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.22), residues: 1558 helix: 1.58 (0.19), residues: 764 sheet: 0.60 (0.48), residues: 130 loop : -1.79 (0.22), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP A1538 HIS 0.004 0.001 HIS A1246 PHE 0.018 0.001 PHE A 649 TYR 0.014 0.001 TYR A1247 ARG 0.004 0.000 ARG A1304 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8824.85 seconds wall clock time: 157 minutes 3.91 seconds (9423.91 seconds total)