Starting phenix.real_space_refine on Thu Aug 6 04:22:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8r6u_18963/08_2026/8r6u_18963.cif Found real_map, /net/cci-nas-00/data/ceres_data/8r6u_18963/08_2026/8r6u_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 { model { file = "/net/cci-nas-00/data/ceres_data/8r6u_18963/08_2026/8r6u_18963.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8r6u_18963/08_2026/8r6u_18963.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8r6u_18963/08_2026/8r6u_18963.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8r6u_18963/08_2026/8r6u_18963.map" } resolution = 2.98 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/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: 3.89, per 1000 atoms: 0.29 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: 0.98 Conformation dependent library (CDL) restraints added in 859.4 milliseconds 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: 1.44 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: 2.35 Time building geometry restraints manager: 1.29 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=" N7 A P 9 " pdb=" C5 A P 9 " ideal model delta sigma weight residual 1.388 1.371 0.017 6.00e-03 2.78e+04 8.24e+00 bond pdb=" N9 A P 9 " pdb=" C4 A P 9 " ideal model delta sigma weight residual 1.374 1.361 0.013 6.00e-03 2.78e+04 4.63e+00 bond pdb=" C6 A P 3 " pdb=" N1 A P 3 " ideal model delta sigma weight residual 1.351 1.336 0.015 7.00e-03 2.04e+04 4.50e+00 bond pdb=" C6 A P 9 " pdb=" N1 A P 9 " ideal model delta sigma weight residual 1.351 1.337 0.014 7.00e-03 2.04e+04 4.25e+00 bond pdb=" N3 A P 3 " pdb=" C4 A P 3 " ideal model delta sigma weight residual 1.344 1.332 0.012 6.00e-03 2.78e+04 4.11e+00 ... (remaining 13774 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.95: 18221 1.95 - 3.89: 519 3.89 - 5.84: 46 5.84 - 7.78: 16 7.78 - 9.73: 1 Bond angle restraints: 18803 Sorted by residual: angle pdb=" O5' C G 4 " pdb=" C5' C G 4 " pdb=" C4' C G 4 " ideal model delta sigma weight residual 109.40 114.34 -4.94 8.00e-01 1.56e+00 3.81e+01 angle pdb=" O5' U T 20 " pdb=" C5' U T 20 " pdb=" C4' U T 20 " ideal model delta sigma weight residual 109.40 113.59 -4.19 8.00e-01 1.56e+00 2.75e+01 angle pdb=" N1 U T 22 " pdb=" C2 U T 22 " pdb=" O2 U T 22 " ideal model delta sigma weight residual 122.80 126.40 -3.60 7.00e-01 2.04e+00 2.65e+01 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 ... (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: 1258 0.038 - 0.075: 596 0.075 - 0.113: 183 0.113 - 0.151: 73 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=" 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 2.47 2.29 0.18 2.00e-01 2.50e+01 7.77e-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 ... (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: 1.850 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.150 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 14.860 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:5.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8663 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= 0.331 Angle : 0.758 9.727 18803 Z= 0.463 Chirality : 0.050 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.04 (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 ARG 0.007 0.001 ARG A1579 TYR 0.017 0.002 TYR A 668 PHE 0.028 0.002 PHE A 649 TRP 0.031 0.003 TRP A 520 HIS 0.007 0.001 HIS A1246 Details of bonding type rmsd/Z covalent geometry : bond 0.00707 / 0.33 (13779) covalent geometry : angle 0.75817 / 0.46 (18803) hydrogen bonds : bond 0.14670 / 9.63 ( 624) hydrogen bonds : angle 5.25549 / 3.69 ( 1829) *********************** 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 : 0.314 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: 0.4973 time to fit residues: 117.5403 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 : 0.303 ------------------------------------------------------------------------------- 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 98 optimal weight: 3.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 9.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 6.9990 chunk 77 optimal weight: 0.0070 chunk 122 optimal weight: 0.8980 chunk 91 optimal weight: 6.9990 chunk 149 optimal weight: 10.0000 overall best weight: 1.9602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 199 ASN 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: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.139264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.105828 restraints weight = 44295.642| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 3.21 r_work: 0.3119 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3116 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3116 r_free = 0.3116 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3116 r_free = 0.3116 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3116 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8648 moved from start: 0.0751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 13779 Z= 0.165 Angle : 0.606 7.420 18803 Z= 0.328 Chirality : 0.042 0.183 2114 Planarity : 0.005 0.073 2242 Dihedral : 15.009 171.678 2450 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 4.14 % Allowed : 16.84 % Favored : 79.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.70 (0.21), residues: 1558 helix: 0.84 (0.19), residues: 764 sheet: 0.21 (0.47), residues: 122 loop : -2.22 (0.21), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 971 TYR 0.022 0.002 TYR A 28 PHE 0.020 0.002 PHE A 649 TRP 0.027 0.002 TRP A 520 HIS 0.005 0.001 HIS A1246 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.17 (13779) covalent geometry : angle 0.60552 / 0.33 (18803) hydrogen bonds : bond 0.06243 / 4.19 ( 624) hydrogen bonds : angle 4.48715 / 3.15 ( 1829) *********************** 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: 56 poor density : 130 time to evaluate : 0.321 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 3 LEU cc_start: 0.7006 (pp) cc_final: 0.6720 (pp) REVERT: A 93 ARG cc_start: 0.7037 (OUTLIER) cc_final: 0.6427 (mtm-85) REVERT: A 134 ASN cc_start: 0.7223 (p0) cc_final: 0.6701 (p0) REVERT: A 153 ILE cc_start: 0.8104 (mt) cc_final: 0.7717 (tt) REVERT: A 183 LEU cc_start: 0.8074 (OUTLIER) cc_final: 0.7812 (mp) REVERT: A 636 LYS cc_start: 0.8631 (mttt) cc_final: 0.8354 (mtmt) REVERT: A 689 LYS cc_start: 0.8753 (OUTLIER) cc_final: 0.8211 (mmtp) REVERT: A 723 ARG cc_start: 0.7361 (OUTLIER) cc_final: 0.7120 (ppp80) REVERT: A 919 LEU cc_start: 0.7380 (OUTLIER) cc_final: 0.6961 (tt) REVERT: A 1215 GLN cc_start: 0.8304 (OUTLIER) cc_final: 0.7195 (mt0) REVERT: A 1422 ARG cc_start: 0.6964 (OUTLIER) cc_final: 0.6739 (ptp90) REVERT: A 1460 GLN cc_start: 0.5615 (pm20) cc_final: 0.5371 (pm20) outliers start: 56 outliers final: 26 residues processed: 172 average time/residue: 0.5336 time to fit residues: 100.0901 Evaluate side-chains 155 residues out of total 1374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 122 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 ARG Chi-restraints excluded: chain A residue 107 ASP 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 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 723 ARG Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain A residue 862 SER 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 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 1422 ARG Chi-restraints excluded: chain A residue 1447 ILE Chi-restraints excluded: chain A residue 1459 ASN Chi-restraints excluded: chain A residue 1511 CYS Chi-restraints excluded: chain A residue 1516 LEU 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 50 optimal weight: 2.9990 chunk 155 optimal weight: 3.9990 chunk 88 optimal weight: 0.8980 chunk 14 optimal weight: 0.8980 chunk 46 optimal weight: 2.9990 chunk 134 optimal weight: 10.0000 chunk 146 optimal weight: 10.0000 chunk 115 optimal weight: 0.4980 chunk 152 optimal weight: 0.9990 chunk 18 optimal weight: 0.9980 chunk 133 optimal weight: 8.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.141317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.107962 restraints weight = 33380.316| |-----------------------------------------------------------------------------| r_work (start): 0.3363 rms_B_bonded: 2.63 r_work: 0.3182 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3182 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3182 r_free = 0.3182 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3182 r_free = 0.3182 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3182 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8587 moved from start: 0.1137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.059 13779 Z= 0.115 Angle : 0.540 10.144 18803 Z= 0.290 Chirality : 0.039 0.214 2114 Planarity : 0.004 0.065 2242 Dihedral : 14.541 175.856 2402 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 3.63 % Allowed : 18.00 % Favored : 78.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.37 (0.21), residues: 1558 helix: 1.16 (0.19), residues: 759 sheet: 0.39 (0.47), residues: 122 loop : -2.10 (0.21), residues: 677 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1304 TYR 0.015 0.001 TYR A1414 PHE 0.016 0.001 PHE A 649 TRP 0.024 0.001 TRP A 520 HIS 0.004 0.001 HIS A1246 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.11 (13779) covalent geometry : angle 0.54049 / 0.29 (18803) hydrogen bonds : bond 0.04746 / 3.20 ( 624) hydrogen bonds : angle 4.21336 / 2.95 ( 1829) *********************** 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 185 residues out of total 1374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 136 time to evaluate : 0.397 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 ARG cc_start: 0.7000 (OUTLIER) cc_final: 0.6398 (mtm-85) REVERT: A 134 ASN cc_start: 0.7278 (p0) cc_final: 0.6735 (p0) REVERT: A 422 GLU cc_start: 0.8487 (OUTLIER) cc_final: 0.7785 (tm-30) REVERT: A 636 LYS cc_start: 0.8598 (mttt) cc_final: 0.8303 (mtmt) REVERT: A 689 LYS cc_start: 0.8689 (OUTLIER) cc_final: 0.8052 (mptt) REVERT: A 919 LEU cc_start: 0.7344 (OUTLIER) cc_final: 0.7077 (tt) REVERT: A 1205 ILE cc_start: 0.8880 (OUTLIER) cc_final: 0.8520 (pp) REVERT: A 1215 GLN cc_start: 0.8138 (OUTLIER) cc_final: 0.6820 (mt0) REVERT: A 1290 ARG cc_start: 0.8378 (OUTLIER) cc_final: 0.7713 (mtp180) REVERT: A 1422 ARG cc_start: 0.6966 (OUTLIER) cc_final: 0.6729 (ptp90) REVERT: A 1460 GLN cc_start: 0.5804 (pm20) cc_final: 0.5577 (pm20) REVERT: A 1570 PHE cc_start: 0.7582 (OUTLIER) cc_final: 0.7230 (t80) REVERT: A 1582 ARG cc_start: 0.7997 (OUTLIER) cc_final: 0.7448 (mtp85) outliers start: 49 outliers final: 20 residues processed: 172 average time/residue: 0.5205 time to fit residues: 97.8635 Evaluate side-chains 155 residues out of total 1374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 125 time to evaluate : 0.370 ------------------------------------------------------------------------------- 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 139 GLU 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 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 1205 ILE 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 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 1570 PHE Chi-restraints excluded: chain A residue 1582 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 129 optimal weight: 5.9990 chunk 150 optimal weight: 0.7980 chunk 22 optimal weight: 7.9990 chunk 110 optimal weight: 6.9990 chunk 70 optimal weight: 7.9990 chunk 59 optimal weight: 8.9990 chunk 9 optimal weight: 1.9990 chunk 98 optimal weight: 3.9990 chunk 96 optimal weight: 4.9990 chunk 111 optimal weight: 0.9980 chunk 31 optimal weight: 8.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 915 GLN ** A1467 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 = 0.3789 r_free = 0.3789 target = 0.139400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.106093 restraints weight = 41143.512| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 2.95 r_work: 0.3131 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3136 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3136 r_free = 0.3136 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 = 0.3136 r_free = 0.3136 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3136 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8631 moved from start: 0.1086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 13779 Z= 0.177 Angle : 0.578 7.842 18803 Z= 0.310 Chirality : 0.041 0.223 2114 Planarity : 0.005 0.066 2242 Dihedral : 14.442 173.907 2390 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 4.35 % Allowed : 17.78 % Favored : 77.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.39 (0.21), residues: 1558 helix: 1.15 (0.19), residues: 761 sheet: 0.37 (0.47), residues: 122 loop : -2.12 (0.21), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A1557 TYR 0.015 0.002 TYR A1414 PHE 0.021 0.002 PHE A1567 TRP 0.020 0.002 TRP A 520 HIS 0.006 0.001 HIS A1246 Details of bonding type rmsd/Z covalent geometry : bond 0.00416 / 0.18 (13779) covalent geometry : angle 0.57790 / 0.31 (18803) hydrogen bonds : bond 0.05512 / 3.72 ( 624) hydrogen bonds : angle 4.22350 / 2.95 ( 1829) *********************** 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 187 residues out of total 1374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 128 time to evaluate : 0.394 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 ARG cc_start: 0.7147 (OUTLIER) cc_final: 0.6530 (mtm-85) REVERT: A 134 ASN cc_start: 0.7220 (p0) cc_final: 0.6672 (p0) REVERT: A 636 LYS cc_start: 0.8629 (mttt) cc_final: 0.8328 (mtmt) REVERT: A 689 LYS cc_start: 0.8724 (OUTLIER) cc_final: 0.8083 (mptt) REVERT: A 919 LEU cc_start: 0.7539 (OUTLIER) cc_final: 0.7265 (tt) REVERT: A 1215 GLN cc_start: 0.8218 (OUTLIER) cc_final: 0.6943 (mt0) REVERT: A 1290 ARG cc_start: 0.8413 (OUTLIER) cc_final: 0.7757 (mtp180) REVERT: A 1460 GLN cc_start: 0.5796 (pm20) cc_final: 0.5549 (pm20) REVERT: A 1582 ARG cc_start: 0.8058 (OUTLIER) cc_final: 0.7302 (mtp85) outliers start: 59 outliers final: 32 residues processed: 173 average time/residue: 0.4795 time to fit residues: 90.9492 Evaluate side-chains 160 residues out of total 1374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 122 time to evaluate : 0.369 ------------------------------------------------------------------------------- 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 721 ILE Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain A residue 865 GLN Chi-restraints excluded: chain A residue 890 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 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 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 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 1565 VAL Chi-restraints excluded: chain A residue 1570 PHE Chi-restraints excluded: chain A residue 1582 ARG 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 111 optimal weight: 0.9990 chunk 28 optimal weight: 3.9990 chunk 101 optimal weight: 6.9990 chunk 52 optimal weight: 4.9990 chunk 130 optimal weight: 10.0000 chunk 108 optimal weight: 2.9990 chunk 151 optimal weight: 0.0170 chunk 34 optimal weight: 9.9990 chunk 6 optimal weight: 0.9990 chunk 122 optimal weight: 0.7980 chunk 131 optimal weight: 10.0000 overall best weight: 1.1624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 358 HIS A 526 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 = 0.3819 r_free = 0.3819 target = 0.141892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.107024 restraints weight = 55578.053| |-----------------------------------------------------------------------------| r_work (start): 0.3348 rms_B_bonded: 4.04 r_work: 0.3139 rms_B_bonded: 4.34 restraints_weight: 0.5000 r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3134 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3134 r_free = 0.3134 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3134 r_free = 0.3134 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3134 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8609 moved from start: 0.1325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 13779 Z= 0.117 Angle : 0.521 8.393 18803 Z= 0.280 Chirality : 0.039 0.216 2114 Planarity : 0.004 0.062 2242 Dihedral : 14.329 176.396 2390 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 3.48 % Allowed : 18.51 % Favored : 78.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.20 (0.21), residues: 1558 helix: 1.33 (0.19), residues: 758 sheet: 0.54 (0.48), residues: 122 loop : -2.08 (0.21), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1557 TYR 0.011 0.001 TYR A1414 PHE 0.016 0.001 PHE A 649 TRP 0.024 0.001 TRP A 520 HIS 0.004 0.001 HIS A1246 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 (13779) covalent geometry : angle 0.52115 / 0.28 (18803) hydrogen bonds : bond 0.04438 / 2.99 ( 624) hydrogen bonds : angle 4.09255 / 2.85 ( 1829) *********************** 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 178 residues out of total 1374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 131 time to evaluate : 0.554 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 LEU cc_start: 0.6874 (pp) cc_final: 0.6618 (pp) REVERT: A 93 ARG cc_start: 0.7104 (OUTLIER) cc_final: 0.6452 (mtm-85) REVERT: A 134 ASN cc_start: 0.7215 (p0) cc_final: 0.6672 (p0) REVERT: A 422 GLU cc_start: 0.8568 (OUTLIER) cc_final: 0.7830 (tm-30) REVERT: A 636 LYS cc_start: 0.8637 (mttt) cc_final: 0.8314 (mtmt) REVERT: A 689 LYS cc_start: 0.8700 (OUTLIER) cc_final: 0.8052 (mptt) REVERT: A 865 GLN cc_start: 0.8582 (OUTLIER) cc_final: 0.8238 (pt0) REVERT: A 919 LEU cc_start: 0.7362 (OUTLIER) cc_final: 0.7079 (tt) REVERT: A 1215 GLN cc_start: 0.8233 (OUTLIER) cc_final: 0.6370 (mm-40) REVERT: A 1290 ARG cc_start: 0.8456 (OUTLIER) cc_final: 0.7775 (mtp180) REVERT: A 1422 ARG cc_start: 0.6966 (OUTLIER) cc_final: 0.6663 (ptp90) REVERT: A 1460 GLN cc_start: 0.5826 (pm20) cc_final: 0.5537 (pm20) REVERT: A 1570 PHE cc_start: 0.7593 (OUTLIER) cc_final: 0.7266 (t80) outliers start: 47 outliers final: 18 residues processed: 170 average time/residue: 0.5309 time to fit residues: 98.9889 Evaluate side-chains 149 residues out of total 1374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 122 time to evaluate : 0.493 ------------------------------------------------------------------------------- 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 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 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 865 GLN 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 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 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 1409 VAL Chi-restraints excluded: chain A residue 1422 ARG Chi-restraints excluded: chain A residue 1447 ILE Chi-restraints excluded: chain A residue 1570 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 101 optimal weight: 8.9990 chunk 5 optimal weight: 0.0270 chunk 33 optimal weight: 0.9990 chunk 63 optimal weight: 0.1980 chunk 24 optimal weight: 0.4980 chunk 120 optimal weight: 1.9990 chunk 52 optimal weight: 7.9990 chunk 94 optimal weight: 3.9990 chunk 40 optimal weight: 10.0000 chunk 57 optimal weight: 4.9990 chunk 108 optimal weight: 4.9990 overall best weight: 0.7442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 915 GLN ** A1467 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 = 0.3831 r_free = 0.3831 target = 0.142851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.109407 restraints weight = 45155.939| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 3.38 r_work: 0.3170 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3170 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3170 r_free = 0.3170 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 = 0.3170 r_free = 0.3170 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3170 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8585 moved from start: 0.1500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.071 13779 Z= 0.105 Angle : 0.511 9.035 18803 Z= 0.274 Chirality : 0.038 0.219 2114 Planarity : 0.004 0.061 2242 Dihedral : 14.234 176.640 2388 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 2.98 % Allowed : 19.23 % Favored : 77.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.06 (0.21), residues: 1558 helix: 1.43 (0.19), residues: 762 sheet: 0.70 (0.48), residues: 122 loop : -2.03 (0.22), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1557 TYR 0.013 0.001 TYR A 193 PHE 0.023 0.001 PHE A1567 TRP 0.022 0.001 TRP A 520 HIS 0.005 0.001 HIS A1246 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.11 (13779) covalent geometry : angle 0.51106 / 0.27 (18803) hydrogen bonds : bond 0.04098 / 2.77 ( 624) hydrogen bonds : angle 3.99399 / 2.78 ( 1829) *********************** 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 176 residues out of total 1374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 136 time to evaluate : 0.428 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 ARG cc_start: 0.7168 (OUTLIER) cc_final: 0.6604 (mtm-85) REVERT: A 134 ASN cc_start: 0.7223 (p0) cc_final: 0.6676 (p0) REVERT: A 280 ASP cc_start: 0.8718 (t0) cc_final: 0.8474 (t0) REVERT: A 422 GLU cc_start: 0.8485 (OUTLIER) cc_final: 0.7731 (tm-30) REVERT: A 636 LYS cc_start: 0.8594 (mttt) cc_final: 0.8277 (mtmt) REVERT: A 689 LYS cc_start: 0.8657 (OUTLIER) cc_final: 0.8048 (mptt) REVERT: A 919 LEU cc_start: 0.7325 (OUTLIER) cc_final: 0.7081 (tt) REVERT: A 1264 MET cc_start: 0.8395 (ttm) cc_final: 0.8131 (ptt) REVERT: A 1290 ARG cc_start: 0.8417 (OUTLIER) cc_final: 0.7743 (mtp180) REVERT: A 1422 ARG cc_start: 0.6895 (OUTLIER) cc_final: 0.6609 (ptp90) REVERT: A 1460 GLN cc_start: 0.5904 (pm20) cc_final: 0.5603 (pm20) REVERT: A 1570 PHE cc_start: 0.7622 (OUTLIER) cc_final: 0.7413 (t80) outliers start: 40 outliers final: 23 residues processed: 168 average time/residue: 0.4916 time to fit residues: 90.1647 Evaluate side-chains 161 residues out of total 1374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 131 time to evaluate : 0.498 ------------------------------------------------------------------------------- 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 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 458 ASP 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 905 CYS Chi-restraints excluded: chain A residue 919 LEU Chi-restraints excluded: chain A residue 995 THR Chi-restraints excluded: chain A residue 1050 GLU Chi-restraints excluded: chain A residue 1120 ASP 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 1395 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 1570 PHE 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 96 optimal weight: 1.9990 chunk 34 optimal weight: 8.9990 chunk 99 optimal weight: 2.9990 chunk 2 optimal weight: 4.9990 chunk 130 optimal weight: 9.9990 chunk 8 optimal weight: 5.9990 chunk 133 optimal weight: 10.0000 chunk 11 optimal weight: 8.9990 chunk 139 optimal weight: 4.9990 chunk 42 optimal weight: 0.1980 chunk 144 optimal weight: 9.9990 overall best weight: 3.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 915 GLN A 954 ASN ** A1080 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3784 r_free = 0.3784 target = 0.139038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.105923 restraints weight = 50352.732| |-----------------------------------------------------------------------------| r_work (start): 0.3332 rms_B_bonded: 3.80 r_work: 0.3101 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3097 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3097 r_free = 0.3097 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3097 r_free = 0.3097 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3097 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8650 moved from start: 0.1236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 13779 Z= 0.203 Angle : 0.596 8.863 18803 Z= 0.317 Chirality : 0.042 0.223 2114 Planarity : 0.005 0.061 2242 Dihedral : 14.271 173.401 2382 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 3.48 % Allowed : 19.30 % Favored : 77.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.29 (0.21), residues: 1558 helix: 1.24 (0.19), residues: 760 sheet: 0.49 (0.47), residues: 122 loop : -2.09 (0.21), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1557 TYR 0.015 0.002 TYR A1414 PHE 0.021 0.002 PHE A 649 TRP 0.024 0.002 TRP A1538 HIS 0.006 0.001 HIS A1246 Details of bonding type rmsd/Z covalent geometry : bond 0.00483 / 0.20 (13779) covalent geometry : angle 0.59609 / 0.32 (18803) hydrogen bonds : bond 0.05580 / 3.76 ( 624) hydrogen bonds : angle 4.16142 / 2.90 ( 1829) *********************** 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 171 residues out of total 1374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 124 time to evaluate : 0.407 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 ARG cc_start: 0.7181 (OUTLIER) cc_final: 0.6592 (mtm-85) REVERT: A 134 ASN cc_start: 0.7253 (p0) cc_final: 0.6680 (p0) REVERT: A 636 LYS cc_start: 0.8641 (mttt) cc_final: 0.8319 (mtmt) REVERT: A 689 LYS cc_start: 0.8720 (OUTLIER) cc_final: 0.8074 (mptt) REVERT: A 919 LEU cc_start: 0.7545 (OUTLIER) cc_final: 0.7272 (tt) REVERT: A 1207 GLU cc_start: 0.7111 (pm20) cc_final: 0.6890 (tt0) REVERT: A 1416 LEU cc_start: 0.7442 (OUTLIER) cc_final: 0.6706 (mt) REVERT: A 1460 GLN cc_start: 0.5945 (pm20) cc_final: 0.5578 (pm20) REVERT: A 1505 GLU cc_start: 0.5405 (OUTLIER) cc_final: 0.3292 (tm-30) REVERT: A 1570 PHE cc_start: 0.7660 (OUTLIER) cc_final: 0.7311 (t80) outliers start: 47 outliers final: 27 residues processed: 166 average time/residue: 0.5102 time to fit residues: 92.6953 Evaluate side-chains 154 residues out of total 1374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 121 time to evaluate : 0.321 ------------------------------------------------------------------------------- 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 689 LYS Chi-restraints excluded: chain A residue 845 LEU 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 1340 VAL Chi-restraints excluded: chain A residue 1364 GLN 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 1416 LEU Chi-restraints excluded: chain A residue 1422 ARG Chi-restraints excluded: chain A residue 1447 ILE Chi-restraints excluded: chain A residue 1490 VAL 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 93 optimal weight: 5.9990 chunk 15 optimal weight: 4.9990 chunk 102 optimal weight: 1.9990 chunk 74 optimal weight: 0.7980 chunk 7 optimal weight: 0.8980 chunk 148 optimal weight: 10.0000 chunk 73 optimal weight: 2.9990 chunk 24 optimal weight: 0.7980 chunk 1 optimal weight: 8.9990 chunk 29 optimal weight: 0.0030 chunk 153 optimal weight: 10.0000 overall best weight: 0.8992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 358 HIS ** A1467 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 = 0.3818 r_free = 0.3818 target = 0.141919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.108371 restraints weight = 47564.085| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 3.52 r_work: 0.3151 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3149 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3149 r_free = 0.3149 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3149 r_free = 0.3149 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3149 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8600 moved from start: 0.1500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 13779 Z= 0.111 Angle : 0.530 9.216 18803 Z= 0.283 Chirality : 0.039 0.209 2114 Planarity : 0.004 0.061 2242 Dihedral : 14.187 176.546 2382 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 2.83 % Allowed : 19.81 % Favored : 77.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.07 (0.21), residues: 1558 helix: 1.42 (0.19), residues: 761 sheet: 0.63 (0.48), residues: 122 loop : -2.01 (0.22), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A1557 TYR 0.011 0.001 TYR A 193 PHE 0.026 0.001 PHE A1567 TRP 0.028 0.001 TRP A1538 HIS 0.004 0.001 HIS A1246 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.11 (13779) covalent geometry : angle 0.53024 / 0.28 (18803) hydrogen bonds : bond 0.04274 / 2.88 ( 624) hydrogen bonds : angle 4.01841 / 2.80 ( 1829) *********************** 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 170 residues out of total 1374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 132 time to evaluate : 0.301 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 VAL cc_start: 0.7660 (OUTLIER) cc_final: 0.7385 (t) REVERT: A 93 ARG cc_start: 0.7181 (OUTLIER) cc_final: 0.6600 (mtm-85) REVERT: A 134 ASN cc_start: 0.7336 (p0) cc_final: 0.6769 (p0) REVERT: A 443 GLU cc_start: 0.8742 (OUTLIER) cc_final: 0.8121 (tm-30) REVERT: A 636 LYS cc_start: 0.8615 (mttt) cc_final: 0.8297 (mtmt) REVERT: A 689 LYS cc_start: 0.8667 (OUTLIER) cc_final: 0.8054 (mptt) REVERT: A 919 LEU cc_start: 0.7346 (OUTLIER) cc_final: 0.7075 (tt) REVERT: A 1422 ARG cc_start: 0.6863 (OUTLIER) cc_final: 0.6501 (ptp90) REVERT: A 1460 GLN cc_start: 0.6041 (pm20) cc_final: 0.5695 (pm20) outliers start: 38 outliers final: 23 residues processed: 165 average time/residue: 0.5381 time to fit residues: 96.7906 Evaluate side-chains 152 residues out of total 1374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 123 time to evaluate : 0.484 ------------------------------------------------------------------------------- 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 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 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 1172 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 1409 VAL Chi-restraints excluded: chain A residue 1422 ARG Chi-restraints excluded: chain A residue 1447 ILE 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 147 optimal weight: 0.6980 chunk 100 optimal weight: 6.9990 chunk 125 optimal weight: 0.0980 chunk 124 optimal weight: 3.9990 chunk 92 optimal weight: 1.9990 chunk 122 optimal weight: 1.9990 chunk 19 optimal weight: 8.9990 chunk 42 optimal weight: 0.9980 chunk 6 optimal weight: 0.8980 chunk 53 optimal weight: 6.9990 chunk 23 optimal weight: 0.0060 overall best weight: 0.5396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.143548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.109760 restraints weight = 52699.002| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 3.94 r_work: 0.3154 rms_B_bonded: 4.53 restraints_weight: 0.5000 r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3154 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3154 r_free = 0.3154 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3154 r_free = 0.3154 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3154 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.1660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.077 13779 Z= 0.105 Angle : 0.533 9.909 18803 Z= 0.282 Chirality : 0.039 0.217 2114 Planarity : 0.004 0.060 2242 Dihedral : 14.084 177.007 2378 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.56 % Favored : 95.37 % Rotamer: Outliers : 2.32 % Allowed : 20.03 % Favored : 77.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.08 (0.22), residues: 1558 helix: 1.49 (0.19), residues: 767 sheet: 0.80 (0.48), residues: 122 loop : -1.92 (0.22), residues: 669 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1557 TYR 0.012 0.001 TYR A1110 PHE 0.016 0.001 PHE A 911 TRP 0.034 0.001 TRP A1538 HIS 0.004 0.001 HIS A1246 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.11 (13779) covalent geometry : angle 0.53257 / 0.28 (18803) hydrogen bonds : bond 0.03902 / 2.63 ( 624) hydrogen bonds : angle 3.96052 / 2.75 ( 1829) *********************** 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 165 residues out of total 1374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 134 time to evaluate : 0.459 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 VAL cc_start: 0.7646 (OUTLIER) cc_final: 0.7375 (t) REVERT: A 93 ARG cc_start: 0.7209 (OUTLIER) cc_final: 0.6608 (mtm-85) REVERT: A 134 ASN cc_start: 0.7297 (p0) cc_final: 0.6746 (p0) REVERT: A 280 ASP cc_start: 0.8749 (t0) cc_final: 0.8492 (t0) REVERT: A 422 GLU cc_start: 0.8549 (OUTLIER) cc_final: 0.7770 (tm-30) REVERT: A 636 LYS cc_start: 0.8578 (mttt) cc_final: 0.8238 (mtmt) REVERT: A 689 LYS cc_start: 0.8620 (OUTLIER) cc_final: 0.7986 (mptt) REVERT: A 919 LEU cc_start: 0.7308 (OUTLIER) cc_final: 0.7055 (tt) REVERT: A 1422 ARG cc_start: 0.6806 (OUTLIER) cc_final: 0.6417 (ptp90) REVERT: A 1460 GLN cc_start: 0.5957 (pm20) cc_final: 0.5611 (pm20) REVERT: A 1505 GLU cc_start: 0.5450 (OUTLIER) cc_final: 0.3383 (tm-30) outliers start: 31 outliers final: 19 residues processed: 159 average time/residue: 0.5615 time to fit residues: 97.3723 Evaluate side-chains 156 residues out of total 1374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 130 time to evaluate : 0.324 ------------------------------------------------------------------------------- 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 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 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 1050 GLU Chi-restraints excluded: chain A residue 1120 ASP Chi-restraints excluded: chain A residue 1172 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 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 117 optimal weight: 6.9990 chunk 16 optimal weight: 10.0000 chunk 55 optimal weight: 7.9990 chunk 35 optimal weight: 1.9990 chunk 77 optimal weight: 5.9990 chunk 135 optimal weight: 9.9990 chunk 148 optimal weight: 8.9990 chunk 153 optimal weight: 5.9990 chunk 143 optimal weight: 7.9990 chunk 69 optimal weight: 5.9990 chunk 102 optimal weight: 0.6980 overall best weight: 4.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 915 GLN A1080 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 = 0.3775 r_free = 0.3775 target = 0.138313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.104715 restraints weight = 45771.213| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 3.25 r_work: 0.3095 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3094 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3094 r_free = 0.3094 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3094 r_free = 0.3094 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3094 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8661 moved from start: 0.1291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 13779 Z= 0.266 Angle : 0.667 9.973 18803 Z= 0.353 Chirality : 0.046 0.328 2114 Planarity : 0.005 0.061 2242 Dihedral : 14.227 172.077 2377 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 2.54 % Allowed : 19.81 % Favored : 77.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.36 (0.21), residues: 1558 helix: 1.14 (0.19), residues: 760 sheet: 0.40 (0.47), residues: 122 loop : -2.07 (0.21), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A1557 TYR 0.019 0.002 TYR A 755 PHE 0.026 0.002 PHE A1567 TRP 0.045 0.002 TRP A1538 HIS 0.006 0.001 HIS A1246 Details of bonding type rmsd/Z covalent geometry : bond 0.00641 / 0.27 (13779) covalent geometry : angle 0.66718 / 0.35 (18803) hydrogen bonds : bond 0.06201 / 4.19 ( 624) hydrogen bonds : angle 4.25088 / 2.96 ( 1829) ********************** 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 158 residues out of total 1374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 124 time to evaluate : 0.367 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 ARG cc_start: 0.7250 (OUTLIER) cc_final: 0.6717 (mtm-85) REVERT: A 134 ASN cc_start: 0.7342 (p0) cc_final: 0.6758 (p0) REVERT: A 443 GLU cc_start: 0.8886 (OUTLIER) cc_final: 0.8254 (tm-30) REVERT: A 636 LYS cc_start: 0.8633 (mttt) cc_final: 0.8324 (mtmt) REVERT: A 689 LYS cc_start: 0.8736 (OUTLIER) cc_final: 0.8098 (mptt) REVERT: A 919 LEU cc_start: 0.7548 (OUTLIER) cc_final: 0.7272 (tt) REVERT: A 1460 GLN cc_start: 0.6044 (pm20) cc_final: 0.5617 (pm20) REVERT: A 1505 GLU cc_start: 0.5445 (OUTLIER) cc_final: 0.3372 (tm-30) outliers start: 34 outliers final: 22 residues processed: 153 average time/residue: 0.5654 time to fit residues: 94.4423 Evaluate side-chains 150 residues out of total 1374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 123 time to evaluate : 0.389 ------------------------------------------------------------------------------- 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 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 659 THR Chi-restraints excluded: chain A residue 671 MET Chi-restraints excluded: chain A residue 689 LYS 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 1044 SER Chi-restraints excluded: chain A residue 1050 GLU Chi-restraints excluded: chain A residue 1120 ASP 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 47 optimal weight: 0.6980 chunk 72 optimal weight: 0.6980 chunk 156 optimal weight: 10.0000 chunk 12 optimal weight: 5.9990 chunk 84 optimal weight: 0.3980 chunk 68 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 27 optimal weight: 7.9990 chunk 20 optimal weight: 10.0000 chunk 42 optimal weight: 0.1980 chunk 112 optimal weight: 0.3980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.143347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.110136 restraints weight = 39694.755| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 2.90 r_work: 0.3191 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3194 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3194 r_free = 0.3194 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3194 r_free = 0.3194 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3194 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.1635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.101 13779 Z= 0.110 Angle : 0.551 9.739 18803 Z= 0.293 Chirality : 0.039 0.199 2114 Planarity : 0.004 0.058 2242 Dihedral : 14.085 177.421 2377 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 1.67 % Allowed : 21.12 % Favored : 77.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.03 (0.21), residues: 1558 helix: 1.35 (0.19), residues: 773 sheet: 0.68 (0.48), residues: 122 loop : -1.91 (0.22), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A1557 TYR 0.013 0.001 TYR A 193 PHE 0.018 0.001 PHE A 934 TRP 0.046 0.002 TRP A1538 HIS 0.003 0.001 HIS A 706 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.11 (13779) covalent geometry : angle 0.55065 / 0.29 (18803) hydrogen bonds : bond 0.04084 / 2.76 ( 624) hydrogen bonds : angle 4.04271 / 2.81 ( 1829) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3598.22 seconds wall clock time: 62 minutes 3.64 seconds (3723.64 seconds total)