Starting phenix.real_space_refine on Mon Aug 25 18:44:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8psa_17848/08_2025/8psa_17848.cif Found real_map, /net/cci-nas-00/data/ceres_data/8psa_17848/08_2025/8psa_17848.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8psa_17848/08_2025/8psa_17848.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8psa_17848/08_2025/8psa_17848.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8psa_17848/08_2025/8psa_17848.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8psa_17848/08_2025/8psa_17848.map" } resolution = 3.6 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= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 107 5.16 5 C 18912 2.51 5 N 4967 2.21 5 O 5694 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 101 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 29681 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 12409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1589, 12409 Classifications: {'peptide': 1589} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 61, 'TRANS': 1527} Chain breaks: 3 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 1223 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1223 Classifications: {'peptide': 163} Link IDs: {'PTRANS': 8, 'TRANS': 154} Chain: "G" Number of atoms: 16018 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2036, 16018 Classifications: {'peptide': 2036} Link IDs: {'PCIS': 1, 'PTRANS': 108, 'TRANS': 1926} Chain breaks: 1 Chain: "G" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'FMN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.74, per 1000 atoms: 0.19 Number of scatterers: 29681 At special positions: 0 Unit cell: (183.57, 181.46, 176.185, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 107 16.00 P 1 15.00 O 5694 8.00 N 4967 7.00 C 18912 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A1246 " - pdb=" SG CYS A1327 " distance=2.15 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: 2.15 Conformation dependent library (CDL) restraints added in 1.3 seconds Enol-peptide restraints added in 715.3 nanoseconds 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7044 Finding SS restraints... Secondary structure from input PDB file: 166 helices and 34 sheets defined 50.7% alpha, 14.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.49 Creating SS restraints... Processing helix chain 'A' and resid 2 through 22 Processing helix chain 'A' and resid 27 through 32 Processing helix chain 'A' and resid 52 through 65 removed outlier: 3.527A pdb=" N MET A 56 " --> pdb=" O THR A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 70 removed outlier: 3.528A pdb=" N ALA A 70 " --> pdb=" O GLU A 66 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 90 removed outlier: 7.752A pdb=" N LYS A 86 " --> pdb=" O SER A 82 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N GLU A 87 " --> pdb=" O LYS A 83 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ILE A 88 " --> pdb=" O ASP A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 351 Processing helix chain 'A' and resid 355 through 383 removed outlier: 3.723A pdb=" N PHE A 361 " --> pdb=" O GLY A 357 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LYS A 365 " --> pdb=" O PHE A 361 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ALA A 373 " --> pdb=" O ALA A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 390 Processing helix chain 'A' and resid 395 through 399 Processing helix chain 'A' and resid 404 through 422 removed outlier: 4.008A pdb=" N LYS A 410 " --> pdb=" O TRP A 406 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU A 416 " --> pdb=" O SER A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 441 removed outlier: 3.952A pdb=" N VAL A 433 " --> pdb=" O ASP A 429 " (cutoff:3.500A) Processing helix chain 'A' and resid 444 through 457 Processing helix chain 'A' and resid 463 through 484 removed outlier: 3.789A pdb=" N GLN A 467 " --> pdb=" O GLY A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 521 through 532 Processing helix chain 'A' and resid 608 through 615 Processing helix chain 'A' and resid 652 through 669 Processing helix chain 'A' and resid 687 through 699 removed outlier: 3.758A pdb=" N GLU A 691 " --> pdb=" O SER A 687 " (cutoff:3.500A) Processing helix chain 'A' and resid 711 through 726 Processing helix chain 'A' and resid 741 through 754 removed outlier: 3.559A pdb=" N ALA A 747 " --> pdb=" O GLN A 743 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ILE A 749 " --> pdb=" O VAL A 745 " (cutoff:3.500A) Processing helix chain 'A' and resid 780 through 784 Processing helix chain 'A' and resid 785 through 796 Processing helix chain 'A' and resid 796 through 813 Processing helix chain 'A' and resid 838 through 846 Processing helix chain 'A' and resid 848 through 856 removed outlier: 4.153A pdb=" N HIS A 854 " --> pdb=" O PHE A 850 " (cutoff:3.500A) Processing helix chain 'A' and resid 857 through 860 removed outlier: 4.205A pdb=" N ASN A 860 " --> pdb=" O SER A 857 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 857 through 860' Processing helix chain 'A' and resid 881 through 883 No H-bonds generated for 'chain 'A' and resid 881 through 883' Processing helix chain 'A' and resid 884 through 890 Processing helix chain 'A' and resid 898 through 907 Processing helix chain 'A' and resid 910 through 920 Processing helix chain 'A' and resid 929 through 933 removed outlier: 3.736A pdb=" N PHE A 932 " --> pdb=" O GLY A 929 " (cutoff:3.500A) Processing helix chain 'A' and resid 935 through 969 removed outlier: 3.560A pdb=" N THR A 950 " --> pdb=" O GLU A 946 " (cutoff:3.500A) Processing helix chain 'A' and resid 971 through 976 removed outlier: 3.531A pdb=" N ALA A 976 " --> pdb=" O SER A 972 " (cutoff:3.500A) Processing helix chain 'A' and resid 997 through 1005 removed outlier: 3.728A pdb=" N VAL A1001 " --> pdb=" O PRO A 997 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLN A1003 " --> pdb=" O LYS A 999 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ILE A1004 " --> pdb=" O GLN A1000 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ALA A1005 " --> pdb=" O VAL A1001 " (cutoff:3.500A) Processing helix chain 'A' and resid 1006 through 1010 removed outlier: 3.751A pdb=" N GLU A1010 " --> pdb=" O ALA A1007 " (cutoff:3.500A) Processing helix chain 'A' and resid 1032 through 1042 Processing helix chain 'A' and resid 1046 through 1057 Processing helix chain 'A' and resid 1086 through 1100 removed outlier: 4.331A pdb=" N LYS A1090 " --> pdb=" O ASP A1086 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N ALA A1091 " --> pdb=" O LYS A1087 " (cutoff:3.500A) removed outlier: 5.163A pdb=" N THR A1095 " --> pdb=" O ALA A1091 " (cutoff:3.500A) removed outlier: 5.538A pdb=" N SER A1096 " --> pdb=" O LYS A1092 " (cutoff:3.500A) Processing helix chain 'A' and resid 1107 through 1112 removed outlier: 3.718A pdb=" N ASN A1112 " --> pdb=" O GLU A1109 " (cutoff:3.500A) Processing helix chain 'A' and resid 1137 through 1149 Processing helix chain 'A' and resid 1201 through 1208 Processing helix chain 'A' and resid 1209 through 1225 removed outlier: 3.596A pdb=" N LEU A1213 " --> pdb=" O ASP A1209 " (cutoff:3.500A) Processing helix chain 'A' and resid 1230 through 1237 Processing helix chain 'A' and resid 1239 through 1241 No H-bonds generated for 'chain 'A' and resid 1239 through 1241' Processing helix chain 'A' and resid 1253 through 1263 Processing helix chain 'A' and resid 1275 through 1280 removed outlier: 3.732A pdb=" N PHE A1279 " --> pdb=" O GLN A1276 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N ILE A1280 " --> pdb=" O GLU A1277 " (cutoff:3.500A) Processing helix chain 'A' and resid 1281 through 1291 Processing helix chain 'A' and resid 1306 through 1321 Processing helix chain 'A' and resid 1336 through 1346 Processing helix chain 'A' and resid 1351 through 1358 Processing helix chain 'A' and resid 1361 through 1366 removed outlier: 4.199A pdb=" N SER A1366 " --> pdb=" O ALA A1363 " (cutoff:3.500A) Processing helix chain 'A' and resid 1390 through 1397 Processing helix chain 'A' and resid 1424 through 1429 Processing helix chain 'A' and resid 1440 through 1443 Processing helix chain 'A' and resid 1444 through 1477 removed outlier: 3.542A pdb=" N GLN A1458 " --> pdb=" O THR A1454 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N GLU A1476 " --> pdb=" O LEU A1472 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ILE A1477 " --> pdb=" O GLU A1473 " (cutoff:3.500A) Processing helix chain 'A' and resid 1481 through 1509 Processing helix chain 'A' and resid 1520 through 1528 removed outlier: 3.523A pdb=" N LEU A1526 " --> pdb=" O LEU A1522 " (cutoff:3.500A) Processing helix chain 'A' and resid 1532 through 1536 removed outlier: 3.686A pdb=" N LEU A1536 " --> pdb=" O ILE A1533 " (cutoff:3.500A) Processing helix chain 'A' and resid 1546 through 1565 removed outlier: 4.153A pdb=" N LYS A1551 " --> pdb=" O LYS A1547 " (cutoff:3.500A) Processing helix chain 'A' and resid 1577 through 1582 removed outlier: 3.577A pdb=" N THR A1581 " --> pdb=" O GLN A1577 " (cutoff:3.500A) Processing helix chain 'A' and resid 1584 through 1586 No H-bonds generated for 'chain 'A' and resid 1584 through 1586' Processing helix chain 'A' and resid 1587 through 1603 Processing helix chain 'A' and resid 1615 through 1621 removed outlier: 3.607A pdb=" N GLN A1620 " --> pdb=" O ILE A1617 " (cutoff:3.500A) Processing helix chain 'A' and resid 1658 through 1663 removed outlier: 3.947A pdb=" N TYR A1662 " --> pdb=" O PRO A1658 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLY A1663 " --> pdb=" O ASP A1659 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1658 through 1663' Processing helix chain 'A' and resid 1666 through 1694 removed outlier: 3.672A pdb=" N TYR A1694 " --> pdb=" O ASN A1690 " (cutoff:3.500A) Processing helix chain 'A' and resid 1710 through 1717 Processing helix chain 'A' and resid 1734 through 1738 removed outlier: 3.795A pdb=" N ILE A1738 " --> pdb=" O SER A1735 " (cutoff:3.500A) Processing helix chain 'A' and resid 1740 through 1745 removed outlier: 3.954A pdb=" N TYR A1744 " --> pdb=" O SER A1740 " (cutoff:3.500A) Processing helix chain 'A' and resid 1746 through 1758 Processing helix chain 'A' and resid 1783 through 1791 removed outlier: 3.501A pdb=" N ILE A1787 " --> pdb=" O ASN A1783 " (cutoff:3.500A) Processing helix chain 'A' and resid 1792 through 1802 Processing helix chain 'A' and resid 1804 through 1824 removed outlier: 3.685A pdb=" N GLY A1824 " --> pdb=" O PHE A1820 " (cutoff:3.500A) Processing helix chain 'A' and resid 1853 through 1862 removed outlier: 3.628A pdb=" N LYS A1857 " --> pdb=" O GLY A1853 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ALA A1862 " --> pdb=" O ALA A1858 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 159 removed outlier: 4.354A pdb=" N HIS B 152 " --> pdb=" O SER B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 171 through 176 Processing helix chain 'B' and resid 179 through 195 removed outlier: 3.690A pdb=" N GLN B 183 " --> pdb=" O LYS B 179 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 215 removed outlier: 3.747A pdb=" N GLU B 211 " --> pdb=" O GLU B 207 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N THR B 212 " --> pdb=" O GLU B 208 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ASP B 215 " --> pdb=" O GLU B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 236 removed outlier: 4.357A pdb=" N SER B 225 " --> pdb=" O LEU B 221 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 254 removed outlier: 3.517A pdb=" N TRP B 254 " --> pdb=" O LEU B 250 " (cutoff:3.500A) Processing helix chain 'B' and resid 257 through 271 removed outlier: 4.126A pdb=" N GLY B 263 " --> pdb=" O GLY B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 279 through 299 removed outlier: 3.718A pdb=" N TYR B 294 " --> pdb=" O MET B 290 " (cutoff:3.500A) Processing helix chain 'G' and resid 26 through 41 removed outlier: 3.770A pdb=" N ALA G 30 " --> pdb=" O SER G 26 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLU G 35 " --> pdb=" O SER G 31 " (cutoff:3.500A) Processing helix chain 'G' and resid 45 through 49 removed outlier: 4.375A pdb=" N ALA G 49 " --> pdb=" O GLU G 46 " (cutoff:3.500A) Processing helix chain 'G' and resid 56 through 72 Processing helix chain 'G' and resid 80 through 96 Processing helix chain 'G' and resid 100 through 112 Processing helix chain 'G' and resid 115 through 133 Processing helix chain 'G' and resid 143 through 151 Processing helix chain 'G' and resid 169 through 202 removed outlier: 3.678A pdb=" N LEU G 173 " --> pdb=" O TYR G 169 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N VAL G 182 " --> pdb=" O GLN G 178 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N LEU G 183 " --> pdb=" O THR G 179 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N ASP G 186 " --> pdb=" O VAL G 182 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N LEU G 187 " --> pdb=" O LEU G 183 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LYS G 189 " --> pdb=" O GLY G 185 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ARG G 200 " --> pdb=" O SER G 196 " (cutoff:3.500A) Processing helix chain 'G' and resid 204 through 209 removed outlier: 3.795A pdb=" N VAL G 208 " --> pdb=" O ASP G 204 " (cutoff:3.500A) Processing helix chain 'G' and resid 214 through 221 Processing helix chain 'G' and resid 222 through 225 Processing helix chain 'G' and resid 227 through 232 Processing helix chain 'G' and resid 233 through 257 Proline residue: G 239 - end of helix Processing helix chain 'G' and resid 259 through 267 Processing helix chain 'G' and resid 275 through 286 removed outlier: 4.242A pdb=" N THR G 279 " --> pdb=" O GLN G 275 " (cutoff:3.500A) Processing helix chain 'G' and resid 289 through 291 No H-bonds generated for 'chain 'G' and resid 289 through 291' Processing helix chain 'G' and resid 292 through 314 Processing helix chain 'G' and resid 320 through 329 Processing helix chain 'G' and resid 345 through 360 removed outlier: 3.857A pdb=" N HIS G 359 " --> pdb=" O LYS G 355 " (cutoff:3.500A) Processing helix chain 'G' and resid 361 through 365 Processing helix chain 'G' and resid 382 through 397 removed outlier: 3.892A pdb=" N THR G 392 " --> pdb=" O GLY G 388 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ALA G 396 " --> pdb=" O THR G 392 " (cutoff:3.500A) Processing helix chain 'G' and resid 408 through 412 removed outlier: 3.577A pdb=" N ARG G 412 " --> pdb=" O PHE G 409 " (cutoff:3.500A) Processing helix chain 'G' and resid 429 through 433 Processing helix chain 'G' and resid 434 through 446 removed outlier: 4.207A pdb=" N LEU G 438 " --> pdb=" O PRO G 434 " (cutoff:3.500A) Processing helix chain 'G' and resid 474 through 485 Processing helix chain 'G' and resid 490 through 494 Processing helix chain 'G' and resid 511 through 520 removed outlier: 4.030A pdb=" N LEU G 515 " --> pdb=" O GLY G 511 " (cutoff:3.500A) Processing helix chain 'G' and resid 544 through 549 Processing helix chain 'G' and resid 560 through 565 Processing helix chain 'G' and resid 581 through 588 removed outlier: 3.591A pdb=" N LEU G 586 " --> pdb=" O LYS G 582 " (cutoff:3.500A) Processing helix chain 'G' and resid 603 through 612 Processing helix chain 'G' and resid 626 through 641 removed outlier: 3.877A pdb=" N GLN G 640 " --> pdb=" O SER G 636 " (cutoff:3.500A) Processing helix chain 'G' and resid 655 through 673 removed outlier: 3.789A pdb=" N TRP G 661 " --> pdb=" O PHE G 657 " (cutoff:3.500A) Proline residue: G 664 - end of helix Processing helix chain 'G' and resid 687 through 699 removed outlier: 3.708A pdb=" N GLY G 699 " --> pdb=" O ILE G 695 " (cutoff:3.500A) Processing helix chain 'G' and resid 709 through 723 Processing helix chain 'G' and resid 747 through 752 Processing helix chain 'G' and resid 753 through 759 Processing helix chain 'G' and resid 777 through 783 Processing helix chain 'G' and resid 784 through 790 removed outlier: 4.045A pdb=" N LYS G 788 " --> pdb=" O TRP G 785 " (cutoff:3.500A) Processing helix chain 'G' and resid 803 through 808 removed outlier: 3.821A pdb=" N ILE G 807 " --> pdb=" O ARG G 804 " (cutoff:3.500A) Processing helix chain 'G' and resid 814 through 823 Processing helix chain 'G' and resid 831 through 835 Processing helix chain 'G' and resid 859 through 872 Processing helix chain 'G' and resid 876 through 899 removed outlier: 4.706A pdb=" N VAL G 881 " --> pdb=" O LYS G 877 " (cutoff:3.500A) Proline residue: G 882 - end of helix removed outlier: 3.524A pdb=" N ALA G 886 " --> pdb=" O PRO G 882 " (cutoff:3.500A) removed outlier: 5.340A pdb=" N ASP G 889 " --> pdb=" O GLU G 885 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N TYR G 890 " --> pdb=" O ALA G 886 " (cutoff:3.500A) Processing helix chain 'G' and resid 918 through 930 Processing helix chain 'G' and resid 940 through 959 Processing helix chain 'G' and resid 969 through 974 Processing helix chain 'G' and resid 975 through 987 Processing helix chain 'G' and resid 988 through 992 Processing helix chain 'G' and resid 996 through 1007 Processing helix chain 'G' and resid 1024 through 1031 Processing helix chain 'G' and resid 1036 through 1043 removed outlier: 3.930A pdb=" N LEU G1040 " --> pdb=" O SER G1037 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N GLU G1041 " --> pdb=" O GLU G1038 " (cutoff:3.500A) Processing helix chain 'G' and resid 1047 through 1051 Processing helix chain 'G' and resid 1057 through 1062 removed outlier: 3.569A pdb=" N PHE G1062 " --> pdb=" O ALA G1059 " (cutoff:3.500A) Processing helix chain 'G' and resid 1069 through 1091 removed outlier: 3.764A pdb=" N LYS G1084 " --> pdb=" O GLY G1080 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLY G1091 " --> pdb=" O HIS G1087 " (cutoff:3.500A) Processing helix chain 'G' and resid 1093 through 1097 Processing helix chain 'G' and resid 1134 through 1144 Processing helix chain 'G' and resid 1148 through 1156 Processing helix chain 'G' and resid 1168 through 1174 Processing helix chain 'G' and resid 1189 through 1193 Processing helix chain 'G' and resid 1257 through 1270 Processing helix chain 'G' and resid 1293 through 1304 removed outlier: 3.921A pdb=" N VAL G1297 " --> pdb=" O THR G1293 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N HIS G1302 " --> pdb=" O TYR G1298 " (cutoff:3.500A) Processing helix chain 'G' and resid 1308 through 1312 removed outlier: 3.718A pdb=" N PHE G1311 " --> pdb=" O CYS G1308 " (cutoff:3.500A) Processing helix chain 'G' and resid 1322 through 1324 No H-bonds generated for 'chain 'G' and resid 1322 through 1324' Processing helix chain 'G' and resid 1325 through 1336 removed outlier: 3.685A pdb=" N VAL G1329 " --> pdb=" O PHE G1325 " (cutoff:3.500A) removed outlier: 5.250A pdb=" N ARG G1332 " --> pdb=" O VAL G1328 " (cutoff:3.500A) removed outlier: 5.334A pdb=" N ALA G1333 " --> pdb=" O VAL G1329 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LYS G1336 " --> pdb=" O ARG G1332 " (cutoff:3.500A) Processing helix chain 'G' and resid 1437 through 1447 removed outlier: 3.591A pdb=" N VAL G1443 " --> pdb=" O LYS G1439 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LYS G1447 " --> pdb=" O VAL G1443 " (cutoff:3.500A) Processing helix chain 'G' and resid 1514 through 1523 removed outlier: 3.652A pdb=" N ARG G1522 " --> pdb=" O ASP G1518 " (cutoff:3.500A) Processing helix chain 'G' and resid 1550 through 1558 removed outlier: 3.753A pdb=" N ALA G1554 " --> pdb=" O ASN G1550 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ARG G1555 " --> pdb=" O GLU G1551 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N VAL G1556 " --> pdb=" O PRO G1552 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLY G1558 " --> pdb=" O ALA G1554 " (cutoff:3.500A) Processing helix chain 'G' and resid 1561 through 1565 Processing helix chain 'G' and resid 1566 through 1573 Processing helix chain 'G' and resid 1581 through 1597 removed outlier: 3.647A pdb=" N LEU G1592 " --> pdb=" O SER G1588 " (cutoff:3.500A) Processing helix chain 'G' and resid 1684 through 1703 removed outlier: 3.656A pdb=" N VAL G1690 " --> pdb=" O ALA G1686 " (cutoff:3.500A) Processing helix chain 'G' and resid 1705 through 1713 Processing helix chain 'G' and resid 1722 through 1735 removed outlier: 3.954A pdb=" N GLY G1726 " --> pdb=" O GLY G1722 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ASN G1732 " --> pdb=" O ARG G1728 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ALA G1735 " --> pdb=" O GLU G1731 " (cutoff:3.500A) Processing helix chain 'G' and resid 1769 through 1772 Processing helix chain 'G' and resid 1773 through 1795 Proline residue: G1779 - end of helix Processing helix chain 'G' and resid 1809 through 1820 removed outlier: 3.859A pdb=" N ALA G1813 " --> pdb=" O LEU G1809 " (cutoff:3.500A) Processing helix chain 'G' and resid 1823 through 1840 Processing helix chain 'G' and resid 1858 through 1863 removed outlier: 3.843A pdb=" N VAL G1862 " --> pdb=" O ASN G1858 " (cutoff:3.500A) Processing helix chain 'G' and resid 1868 through 1882 removed outlier: 3.555A pdb=" N ARG G1881 " --> pdb=" O ARG G1877 " (cutoff:3.500A) Processing helix chain 'G' and resid 1904 through 1921 removed outlier: 4.069A pdb=" N VAL G1910 " --> pdb=" O ALA G1906 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N LYS G1918 " --> pdb=" O LEU G1914 " (cutoff:3.500A) Processing helix chain 'G' and resid 1923 through 1928 removed outlier: 4.069A pdb=" N LEU G1927 " --> pdb=" O ASP G1923 " (cutoff:3.500A) Processing helix chain 'G' and resid 1934 through 1948 removed outlier: 3.753A pdb=" N GLY G1938 " --> pdb=" O GLU G1934 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N GLU G1942 " --> pdb=" O GLY G1938 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N ILE G1943 " --> pdb=" O HIS G1939 " (cutoff:3.500A) Processing helix chain 'G' and resid 1984 through 1996 removed outlier: 3.726A pdb=" N PHE G1988 " --> pdb=" O GLY G1984 " (cutoff:3.500A) Processing helix chain 'G' and resid 2022 through 2033 removed outlier: 3.631A pdb=" N LEU G2032 " --> pdb=" O ASP G2028 " (cutoff:3.500A) Processing helix chain 'G' and resid 2035 through 2044 Processing sheet with id=AA1, first strand: chain 'A' and resid 77 through 80 removed outlier: 6.389A pdb=" N ARG A 43 " --> pdb=" O THR G1663 " (cutoff:3.500A) removed outlier: 7.796A pdb=" N VAL G1665 " --> pdb=" O ARG A 43 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N VAL A 45 " --> pdb=" O VAL G1665 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N THR G1662 " --> pdb=" O THR G1803 " (cutoff:3.500A) removed outlier: 9.090A pdb=" N ALA G1805 " --> pdb=" O THR G1662 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N PHE G1664 " --> pdb=" O ALA G1805 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 400 through 402 removed outlier: 6.713A pdb=" N VAL A 678 " --> pdb=" O VAL A 704 " (cutoff:3.500A) removed outlier: 7.887A pdb=" N THR A 706 " --> pdb=" O VAL A 678 " (cutoff:3.500A) removed outlier: 7.261A pdb=" N ILE A 680 " --> pdb=" O THR A 706 " (cutoff:3.500A) removed outlier: 9.586A pdb=" N VAL A 922 " --> pdb=" O LEU A 862 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N VAL A 864 " --> pdb=" O VAL A 922 " (cutoff:3.500A) removed outlier: 7.729A pdb=" N ALA A 924 " --> pdb=" O VAL A 864 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N GLY A 866 " --> pdb=" O ALA A 924 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N LEU A 926 " --> pdb=" O GLY A 866 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N ILE A 868 " --> pdb=" O LEU A 926 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N MET A 923 " --> pdb=" O ARG A 641 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 400 through 402 removed outlier: 6.713A pdb=" N VAL A 678 " --> pdb=" O VAL A 704 " (cutoff:3.500A) removed outlier: 7.887A pdb=" N THR A 706 " --> pdb=" O VAL A 678 " (cutoff:3.500A) removed outlier: 7.261A pdb=" N ILE A 680 " --> pdb=" O THR A 706 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N MET A 826 " --> pdb=" O ILE A 869 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 489 through 490 Processing sheet with id=AA5, first strand: chain 'A' and resid 497 through 499 Processing sheet with id=AA6, first strand: chain 'A' and resid 502 through 503 Processing sheet with id=AA7, first strand: chain 'A' and resid 872 through 873 Processing sheet with id=AA8, first strand: chain 'A' and resid 981 through 982 Processing sheet with id=AA9, first strand: chain 'A' and resid 1243 through 1245 removed outlier: 3.841A pdb=" N GLY A1023 " --> pdb=" O ILE A1386 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N MET A1388 " --> pdb=" O VAL A1021 " (cutoff:3.500A) removed outlier: 5.559A pdb=" N VAL A1021 " --> pdb=" O MET A1388 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N ILE A1019 " --> pdb=" O VAL A1404 " (cutoff:3.500A) removed outlier: 5.606A pdb=" N VAL A1404 " --> pdb=" O VAL A1656 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N VAL A1656 " --> pdb=" O VAL A1404 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL A1538 " --> pdb=" O ALA A1638 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N THR A1642 " --> pdb=" O SER A1540 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N VAL A1572 " --> pdb=" O LEU A1625 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 1060 through 1066 Processing sheet with id=AB2, first strand: chain 'A' and resid 1102 through 1105 removed outlier: 3.955A pdb=" N GLY A1102 " --> pdb=" O GLN A1188 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 1119 through 1126 removed outlier: 3.577A pdb=" N MET A1121 " --> pdb=" O LYS A1177 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 1134 through 1136 Processing sheet with id=AB5, first strand: chain 'A' and resid 1604 through 1605 Processing sheet with id=AB6, first strand: chain 'A' and resid 1723 through 1724 Processing sheet with id=AB7, first strand: chain 'A' and resid 1768 through 1775 Processing sheet with id=AB8, first strand: chain 'A' and resid 1837 through 1842 removed outlier: 5.545A pdb=" N VAL A1842 " --> pdb=" O ALA A1846 " (cutoff:3.500A) removed outlier: 5.004A pdb=" N ALA A1846 " --> pdb=" O VAL A1842 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'G' and resid 6 through 13 removed outlier: 3.688A pdb=" N LEU G 16 " --> pdb=" O HIS G 13 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'G' and resid 269 through 270 removed outlier: 3.718A pdb=" N GLY G 269 " --> pdb=" O LEU G 156 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N VAL G 157 " --> pdb=" O LEU G 502 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N ILE G 501 " --> pdb=" O ILE G 528 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 417 through 420 removed outlier: 6.122A pdb=" N SER G 380 " --> pdb=" O ILE G 368 " (cutoff:3.500A) removed outlier: 5.414A pdb=" N ILE G 368 " --> pdb=" O SER G 380 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 568 through 571 Processing sheet with id=AC4, first strand: chain 'G' and resid 592 through 594 removed outlier: 4.149A pdb=" N THR G 616 " --> pdb=" O LEU G 592 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N PHE G 647 " --> pdb=" O PHE G 678 " (cutoff:3.500A) removed outlier: 8.598A pdb=" N THR G 680 " --> pdb=" O PHE G 647 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N ILE G 649 " --> pdb=" O THR G 680 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N GLY G 682 " --> pdb=" O ILE G 649 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N LEU G 651 " --> pdb=" O GLY G 682 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N GLN G 677 " --> pdb=" O TYR G 702 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N GLY G 704 " --> pdb=" O GLN G 677 " (cutoff:3.500A) removed outlier: 5.975A pdb=" N LEU G 679 " --> pdb=" O GLY G 704 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N LEU G 703 " --> pdb=" O ALA G 729 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N GLN G 731 " --> pdb=" O LEU G 703 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N LEU G 705 " --> pdb=" O GLN G 731 " (cutoff:3.500A) removed outlier: 7.405A pdb=" N THR G 733 " --> pdb=" O LEU G 705 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N ILE G 728 " --> pdb=" O MET G 764 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N ILE G 766 " --> pdb=" O ILE G 728 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N LEU G 730 " --> pdb=" O ILE G 766 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N GLY G 768 " --> pdb=" O LEU G 730 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N TRP G 732 " --> pdb=" O GLY G 768 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLY G 798 " --> pdb=" O LEU G 765 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'G' and resid 739 through 740 removed outlier: 3.800A pdb=" N GLY G 739 " --> pdb=" O HIS G 855 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'G' and resid 906 through 907 Processing sheet with id=AC7, first strand: chain 'G' and resid 931 through 932 Processing sheet with id=AC8, first strand: chain 'G' and resid 1126 through 1128 removed outlier: 6.559A pdb=" N VAL G1195 " --> pdb=" O ILE G1210 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N ILE G1210 " --> pdb=" O VAL G1195 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N LEU G1197 " --> pdb=" O THR G1208 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLU G1204 " --> pdb=" O VAL G1201 " (cutoff:3.500A) removed outlier: 5.591A pdb=" N THR G1208 " --> pdb=" O ILE G1224 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N MET G1221 " --> pdb=" O LEU G1238 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N LEU G1238 " --> pdb=" O MET G1221 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 1158 through 1161 Processing sheet with id=AD1, first strand: chain 'G' and resid 1285 through 1291 removed outlier: 4.002A pdb=" N THR G1374 " --> pdb=" O GLY G1287 " (cutoff:3.500A) removed outlier: 5.268A pdb=" N ASP G1289 " --> pdb=" O VAL G1372 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N VAL G1372 " --> pdb=" O ASP G1289 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N ASP G1391 " --> pdb=" O GLU G1379 " (cutoff:3.500A) removed outlier: 4.940A pdb=" N VAL G1381 " --> pdb=" O ILE G1389 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N ILE G1389 " --> pdb=" O VAL G1381 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N MET G1404 " --> pdb=" O LEU G1396 " (cutoff:3.500A) removed outlier: 5.635A pdb=" N ARG G1398 " --> pdb=" O PRO G1402 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N THR G1642 " --> pdb=" O VAL G1650 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N THR G1652 " --> pdb=" O PHE G1640 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N PHE G1640 " --> pdb=" O THR G1652 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N ARG G1635 " --> pdb=" O MET G1631 " (cutoff:3.500A) removed outlier: 5.093A pdb=" N MET G1631 " --> pdb=" O ARG G1635 " (cutoff:3.500A) removed outlier: 7.281A pdb=" N LEU G1637 " --> pdb=" O VAL G1629 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL G1629 " --> pdb=" O LEU G1637 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N HIS G1628 " --> pdb=" O PRO G1538 " (cutoff:3.500A) removed outlier: 8.182A pdb=" N GLY G1630 " --> pdb=" O PRO G1536 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'G' and resid 1358 through 1359 removed outlier: 6.510A pdb=" N THR G1642 " --> pdb=" O VAL G1650 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N THR G1652 " --> pdb=" O PHE G1640 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N PHE G1640 " --> pdb=" O THR G1652 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'G' and resid 1424 through 1426 removed outlier: 3.768A pdb=" N PHE G1486 " --> pdb=" O GLU G1469 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ALA G1508 " --> pdb=" O VAL G1483 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N VAL G1491 " --> pdb=" O GLU G1500 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N GLU G1500 " --> pdb=" O VAL G1491 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'G' and resid 1424 through 1426 removed outlier: 3.768A pdb=" N PHE G1486 " --> pdb=" O GLU G1469 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N THR G1463 " --> pdb=" O GLU G1492 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU G1464 " --> pdb=" O MET G1433 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N TYR G1431 " --> pdb=" O PHE G1466 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'G' and resid 1716 through 1720 Processing sheet with id=AD6, first strand: chain 'G' and resid 1737 through 1741 removed outlier: 3.747A pdb=" N THR G1740 " --> pdb=" O LYS G1747 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'G' and resid 1886 through 1893 removed outlier: 6.810A pdb=" N VAL G1899 " --> pdb=" O VAL G1889 " (cutoff:3.500A) removed outlier: 5.262A pdb=" N TYR G1891 " --> pdb=" O GLN G1897 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N GLN G1897 " --> pdb=" O TYR G1891 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N GLY G1902 " --> pdb=" O GLY G1853 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLY G1853 " --> pdb=" O GLY G1902 " (cutoff:3.500A) 1461 hydrogen bonds defined for protein. 4089 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 8.07 Time building geometry restraints manager: 2.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.32: 5215 1.32 - 1.47: 7890 1.47 - 1.62: 17006 1.62 - 1.76: 0 1.76 - 1.91: 189 Bond restraints: 30300 Sorted by residual: bond pdb=" C PRO A1399 " pdb=" O PRO A1399 " ideal model delta sigma weight residual 1.233 1.173 0.060 1.10e-02 8.26e+03 2.97e+01 bond pdb=" N GLU G1199 " pdb=" CA GLU G1199 " ideal model delta sigma weight residual 1.453 1.496 -0.043 8.30e-03 1.45e+04 2.66e+01 bond pdb=" N ILE G1798 " pdb=" CA ILE G1798 " ideal model delta sigma weight residual 1.456 1.494 -0.038 8.60e-03 1.35e+04 1.97e+01 bond pdb=" C TYR A1174 " pdb=" O TYR A1174 " ideal model delta sigma weight residual 1.236 1.286 -0.050 1.14e-02 7.69e+03 1.92e+01 bond pdb=" CG MET A1121 " pdb=" SD MET A1121 " ideal model delta sigma weight residual 1.803 1.912 -0.109 2.50e-02 1.60e+03 1.89e+01 ... (remaining 30295 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.61: 33737 2.61 - 5.23: 6969 5.23 - 7.84: 326 7.84 - 10.46: 6 10.46 - 13.07: 3 Bond angle restraints: 41041 Sorted by residual: angle pdb=" CB GLU A 841 " pdb=" CG GLU A 841 " pdb=" CD GLU A 841 " ideal model delta sigma weight residual 112.60 125.67 -13.07 1.70e+00 3.46e-01 5.91e+01 angle pdb=" CB GLU A 780 " pdb=" CG GLU A 780 " pdb=" CD GLU A 780 " ideal model delta sigma weight residual 112.60 125.00 -12.40 1.70e+00 3.46e-01 5.32e+01 angle pdb=" CB GLU A 364 " pdb=" CG GLU A 364 " pdb=" CD GLU A 364 " ideal model delta sigma weight residual 112.60 124.41 -11.81 1.70e+00 3.46e-01 4.82e+01 angle pdb=" C SER A1417 " pdb=" N VAL A1418 " pdb=" CA VAL A1418 " ideal model delta sigma weight residual 120.33 125.87 -5.54 8.00e-01 1.56e+00 4.80e+01 angle pdb=" C SER G 233 " pdb=" N ILE G 234 " pdb=" CA ILE G 234 " ideal model delta sigma weight residual 120.24 124.54 -4.30 6.30e-01 2.52e+00 4.67e+01 ... (remaining 41036 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.84: 16357 17.84 - 35.67: 1522 35.67 - 53.51: 300 53.51 - 71.34: 81 71.34 - 89.18: 35 Dihedral angle restraints: 18295 sinusoidal: 7355 harmonic: 10940 Sorted by residual: dihedral pdb=" CA ALA G 897 " pdb=" C ALA G 897 " pdb=" N ASP G 898 " pdb=" CA ASP G 898 " ideal model delta harmonic sigma weight residual -180.00 -153.61 -26.39 0 5.00e+00 4.00e-02 2.79e+01 dihedral pdb=" CA PHE G1411 " pdb=" C PHE G1411 " pdb=" N TYR G1412 " pdb=" CA TYR G1412 " ideal model delta harmonic sigma weight residual 180.00 154.27 25.73 0 5.00e+00 4.00e-02 2.65e+01 dihedral pdb=" CB CYS A1246 " pdb=" SG CYS A1246 " pdb=" SG CYS A1327 " pdb=" CB CYS A1327 " ideal model delta sinusoidal sigma weight residual -86.00 -43.85 -42.15 1 1.00e+01 1.00e-02 2.48e+01 ... (remaining 18292 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 1932 0.055 - 0.110: 1649 0.110 - 0.165: 801 0.165 - 0.219: 206 0.219 - 0.274: 25 Chirality restraints: 4613 Sorted by residual: chirality pdb=" CA ILE G 652 " pdb=" N ILE G 652 " pdb=" C ILE G 652 " pdb=" CB ILE G 652 " both_signs ideal model delta sigma weight residual False 2.43 2.71 -0.27 2.00e-01 2.50e+01 1.88e+00 chirality pdb=" CA ILE A1384 " pdb=" N ILE A1384 " pdb=" C ILE A1384 " pdb=" CB ILE A1384 " both_signs ideal model delta sigma weight residual False 2.43 2.70 -0.27 2.00e-01 2.50e+01 1.84e+00 chirality pdb=" CA ILE A1326 " pdb=" N ILE A1326 " pdb=" C ILE A1326 " pdb=" CB ILE A1326 " both_signs ideal model delta sigma weight residual False 2.43 2.70 -0.27 2.00e-01 2.50e+01 1.77e+00 ... (remaining 4610 not shown) Planarity restraints: 5300 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A1660 " -0.045 2.00e-02 2.50e+03 2.59e-02 1.34e+01 pdb=" CG TYR A1660 " 0.053 2.00e-02 2.50e+03 pdb=" CD1 TYR A1660 " 0.009 2.00e-02 2.50e+03 pdb=" CD2 TYR A1660 " 0.013 2.00e-02 2.50e+03 pdb=" CE1 TYR A1660 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR A1660 " -0.008 2.00e-02 2.50e+03 pdb=" CZ TYR A1660 " -0.013 2.00e-02 2.50e+03 pdb=" OH TYR A1660 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR G 624 " -0.042 2.00e-02 2.50e+03 2.21e-02 9.74e+00 pdb=" CG TYR G 624 " 0.039 2.00e-02 2.50e+03 pdb=" CD1 TYR G 624 " 0.012 2.00e-02 2.50e+03 pdb=" CD2 TYR G 624 " 0.009 2.00e-02 2.50e+03 pdb=" CE1 TYR G 624 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR G 624 " 0.004 2.00e-02 2.50e+03 pdb=" CZ TYR G 624 " -0.005 2.00e-02 2.50e+03 pdb=" OH TYR G 624 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' FMN G2101 " 0.006 2.00e-02 2.50e+03 1.45e-02 9.49e+00 pdb=" C10 FMN G2101 " 0.016 2.00e-02 2.50e+03 pdb=" C2 FMN G2101 " -0.016 2.00e-02 2.50e+03 pdb=" C4 FMN G2101 " -0.001 2.00e-02 2.50e+03 pdb=" C4A FMN G2101 " 0.029 2.00e-02 2.50e+03 pdb=" C5A FMN G2101 " -0.000 2.00e-02 2.50e+03 pdb=" C6 FMN G2101 " -0.008 2.00e-02 2.50e+03 pdb=" C7 FMN G2101 " -0.009 2.00e-02 2.50e+03 pdb=" C7M FMN G2101 " -0.016 2.00e-02 2.50e+03 pdb=" C8 FMN G2101 " -0.001 2.00e-02 2.50e+03 pdb=" C8M FMN G2101 " -0.002 2.00e-02 2.50e+03 pdb=" C9 FMN G2101 " -0.005 2.00e-02 2.50e+03 pdb=" C9A FMN G2101 " -0.005 2.00e-02 2.50e+03 pdb=" N1 FMN G2101 " -0.003 2.00e-02 2.50e+03 pdb=" N10 FMN G2101 " 0.016 2.00e-02 2.50e+03 pdb=" N3 FMN G2101 " -0.019 2.00e-02 2.50e+03 pdb=" N5 FMN G2101 " 0.033 2.00e-02 2.50e+03 pdb=" O2 FMN G2101 " -0.016 2.00e-02 2.50e+03 ... (remaining 5297 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 1044 2.72 - 3.26: 30342 3.26 - 3.81: 46902 3.81 - 4.35: 64343 4.35 - 4.90: 104227 Nonbonded interactions: 246858 Sorted by model distance: nonbonded pdb=" OH TYR A 89 " pdb=" OD2 ASP G1791 " model vdw 2.170 3.040 nonbonded pdb=" OG1 THR G1470 " pdb=" ND2 ASN G1514 " model vdw 2.215 3.120 nonbonded pdb=" OH TYR G1266 " pdb=" OD1 ASN G1561 " model vdw 2.235 3.040 nonbonded pdb=" O GLY A 389 " pdb=" ND2 ASN A 738 " model vdw 2.245 3.120 nonbonded pdb=" O VAL G1381 " pdb=" OG1 THR G1422 " model vdw 2.268 3.040 ... (remaining 246853 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.380 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: 0.050 Extract box with map and model: 0.490 Check model and map are aligned: 0.110 Set scattering table: 0.060 Process input model: 28.140 Find NCS groups from input model: 0.120 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: 0.010 Load rotamer database and sin/cos tables:0.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 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 : 0.014 0.115 30301 Z= 1.047 Angle : 1.912 13.073 41043 Z= 1.395 Chirality : 0.088 0.274 4613 Planarity : 0.006 0.028 5300 Dihedral : 15.238 89.176 11248 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.58 % Allowed : 7.87 % Favored : 91.55 % Rotamer: Outliers : 0.74 % Allowed : 5.14 % Favored : 94.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.56 % 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 aren not related in a simple way. whole: -3.68 (0.11), residues: 3774 helix: -2.80 (0.09), residues: 1658 sheet: -2.25 (0.22), residues: 415 loop : -1.92 (0.14), residues: 1701 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A1036 TYR 0.053 0.005 TYR A1660 PHE 0.042 0.005 PHE G 939 TRP 0.035 0.006 TRP G 865 HIS 0.014 0.003 HIS A1689 Details of bonding type rmsd covalent geometry : bond 0.01387 (30300) covalent geometry : angle 1.91065 (41041) SS BOND : bond 0.11535 ( 1) SS BOND : angle 10.53320 ( 2) hydrogen bonds : bond 0.21818 ( 1428) hydrogen bonds : angle 9.54546 ( 4089) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 3253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 337 time to evaluate : 1.083 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 340 ARG cc_start: 0.9108 (mtm-85) cc_final: 0.8278 (mmt180) REVERT: A 431 GLU cc_start: 0.9151 (tp30) cc_final: 0.8852 (tp30) REVERT: A 708 SER cc_start: 0.8708 (OUTLIER) cc_final: 0.8462 (m) REVERT: A 713 GLN cc_start: 0.8958 (tm-30) cc_final: 0.8617 (tm-30) REVERT: A 754 ASP cc_start: 0.9451 (t0) cc_final: 0.9182 (t0) REVERT: A 925 ASP cc_start: 0.9264 (t0) cc_final: 0.8946 (t70) REVERT: A 1124 GLU cc_start: 0.8766 (pp20) cc_final: 0.8353 (pp20) REVERT: A 1267 ASP cc_start: 0.8864 (t0) cc_final: 0.8649 (t70) REVERT: A 1268 GLU cc_start: 0.8916 (mm-30) cc_final: 0.8669 (mm-30) REVERT: A 1332 TYR cc_start: 0.8924 (p90) cc_final: 0.8705 (p90) REVERT: B 185 GLU cc_start: 0.8727 (mt-10) cc_final: 0.8333 (mt-10) REVERT: B 277 LEU cc_start: 0.7769 (OUTLIER) cc_final: 0.7452 (mm) REVERT: G 229 ASP cc_start: 0.9056 (m-30) cc_final: 0.8586 (t0) REVERT: G 268 LYS cc_start: 0.8800 (mmmt) cc_final: 0.8550 (mmmm) REVERT: G 425 SER cc_start: 0.9385 (t) cc_final: 0.9100 (p) REVERT: G 564 GLU cc_start: 0.8737 (mt-10) cc_final: 0.8392 (tp30) REVERT: G 630 MET cc_start: 0.8812 (tpp) cc_final: 0.8307 (tpp) REVERT: G 750 MET cc_start: 0.8975 (mmt) cc_final: 0.8590 (mmt) REVERT: G 1011 MET cc_start: 0.9308 (mtt) cc_final: 0.8633 (tmm) REVERT: G 1067 ASP cc_start: 0.8912 (OUTLIER) cc_final: 0.8530 (t70) REVERT: G 1136 GLU cc_start: 0.9107 (tp30) cc_final: 0.8860 (pp20) REVERT: G 1299 ASP cc_start: 0.9216 (t0) cc_final: 0.9008 (t0) REVERT: G 1405 GLU cc_start: 0.7370 (pt0) cc_final: 0.6925 (tm-30) REVERT: G 1631 MET cc_start: 0.5418 (tpt) cc_final: 0.4720 (tpp) REVERT: G 1676 MET cc_start: 0.7813 (ptm) cc_final: 0.7076 (ptm) REVERT: G 1784 MET cc_start: 0.8100 (tmm) cc_final: 0.7669 (tmm) outliers start: 24 outliers final: 10 residues processed: 354 average time/residue: 0.1546 time to fit residues: 90.6013 Evaluate side-chains 265 residues out of total 3253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 252 time to evaluate : 0.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 708 SER Chi-restraints excluded: chain A residue 1061 SER Chi-restraints excluded: chain A residue 1308 SER Chi-restraints excluded: chain A residue 1496 GLU Chi-restraints excluded: chain B residue 241 PHE Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain G residue 81 ASP Chi-restraints excluded: chain G residue 167 ASP Chi-restraints excluded: chain G residue 191 SER Chi-restraints excluded: chain G residue 482 CYS Chi-restraints excluded: chain G residue 855 HIS Chi-restraints excluded: chain G residue 1067 ASP Chi-restraints excluded: chain G residue 1511 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 197 optimal weight: 6.9990 chunk 215 optimal weight: 8.9990 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 7.9990 chunk 207 optimal weight: 7.9990 chunk 155 optimal weight: 20.0000 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 4.9990 chunk 298 optimal weight: 7.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 342 GLN A 422 HIS A 438 ASN A 524 GLN A 758 ASN ** A 821 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 829 ASN A 881 ASN A 882 ASN A 987 ASN A 989 GLN A1000 GLN A1063 HIS A1239 HIS A1385 GLN A1432 HIS A1482 GLN A1549 ASN A1563 HIS A1570 ASN A1610 ASN A1689 HIS A1703 HIS A1766 ASN A1783 ASN A1845 ASN B 271 ASN G 36 GLN G 85 ASN G 181 HIS ** G 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 248 HIS G 440 ASN G 500 HIS G 640 GLN G 715 GLN G 747 HIS G 910 GLN G 993 GLN G1055 HIS G1241 ASN G1302 HIS ** G1355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G1383 ASN G1451 GLN G1476 ASN G1514 ASN ** G1581 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G1627 GLN G1628 HIS G1890 ASN G1995 ASN G2044 ASN Total number of N/Q/H flips: 49 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.085650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.065010 restraints weight = 110132.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.066535 restraints weight = 51973.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.067060 restraints weight = 27125.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.067062 restraints weight = 23013.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.067119 restraints weight = 22187.935| |-----------------------------------------------------------------------------| r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.1642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 30301 Z= 0.186 Angle : 0.614 8.207 41043 Z= 0.326 Chirality : 0.044 0.276 4613 Planarity : 0.004 0.056 5300 Dihedral : 5.745 58.802 4063 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.97 % Favored : 96.98 % Rotamer: Outliers : 1.35 % Allowed : 9.56 % Favored : 89.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.56 % 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 aren not related in a simple way. whole: -1.14 (0.13), residues: 3774 helix: -0.22 (0.12), residues: 1679 sheet: -1.67 (0.21), residues: 481 loop : -0.88 (0.15), residues: 1614 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG G1881 TYR 0.020 0.002 TYR A 81 PHE 0.022 0.002 PHE A 450 TRP 0.021 0.002 TRP G1449 HIS 0.008 0.001 HIS G1352 Details of bonding type rmsd covalent geometry : bond 0.00423 (30300) covalent geometry : angle 0.61292 (41041) SS BOND : bond 0.01700 ( 1) SS BOND : angle 4.76087 ( 2) hydrogen bonds : bond 0.04504 ( 1428) hydrogen bonds : angle 5.54591 ( 4089) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 3253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 285 time to evaluate : 1.224 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 340 ARG cc_start: 0.8740 (mtm-85) cc_final: 0.7995 (mmt180) REVERT: A 1124 GLU cc_start: 0.8342 (pp20) cc_final: 0.8135 (pp20) REVERT: A 1308 SER cc_start: 0.9073 (OUTLIER) cc_final: 0.8826 (t) REVERT: A 1496 GLU cc_start: 0.8453 (OUTLIER) cc_final: 0.8089 (mp0) REVERT: B 185 GLU cc_start: 0.7994 (mt-10) cc_final: 0.7555 (mt-10) REVERT: B 277 LEU cc_start: 0.8477 (OUTLIER) cc_final: 0.8055 (mm) REVERT: G 546 GLU cc_start: 0.7491 (mt-10) cc_final: 0.6725 (mm-30) REVERT: G 630 MET cc_start: 0.7724 (tpp) cc_final: 0.7382 (tpp) REVERT: G 1645 GLU cc_start: 0.3021 (OUTLIER) cc_final: 0.2784 (pm20) REVERT: G 1676 MET cc_start: 0.7698 (ptm) cc_final: 0.7175 (ptm) REVERT: G 1693 ARG cc_start: 0.8396 (mtp85) cc_final: 0.8161 (ttm110) REVERT: G 1784 MET cc_start: 0.7902 (tmm) cc_final: 0.7664 (tmm) REVERT: G 1822 MET cc_start: 0.5827 (mpp) cc_final: 0.5195 (mpp) outliers start: 44 outliers final: 22 residues processed: 317 average time/residue: 0.1623 time to fit residues: 85.8593 Evaluate side-chains 265 residues out of total 3253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 239 time to evaluate : 1.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1061 SER Chi-restraints excluded: chain A residue 1085 ASP Chi-restraints excluded: chain A residue 1131 LEU Chi-restraints excluded: chain A residue 1308 SER Chi-restraints excluded: chain A residue 1496 GLU Chi-restraints excluded: chain A residue 1777 THR Chi-restraints excluded: chain A residue 1866 ASP Chi-restraints excluded: chain B residue 171 THR Chi-restraints excluded: chain B residue 241 PHE Chi-restraints excluded: chain B residue 243 ILE Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain G residue 81 ASP Chi-restraints excluded: chain G residue 243 VAL Chi-restraints excluded: chain G residue 318 SER Chi-restraints excluded: chain G residue 448 VAL Chi-restraints excluded: chain G residue 482 CYS Chi-restraints excluded: chain G residue 1209 VAL Chi-restraints excluded: chain G residue 1409 SER Chi-restraints excluded: chain G residue 1511 SER Chi-restraints excluded: chain G residue 1543 ASP Chi-restraints excluded: chain G residue 1645 GLU Chi-restraints excluded: chain G residue 1718 THR Chi-restraints excluded: chain G residue 1821 VAL Chi-restraints excluded: chain G residue 1871 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 225 optimal weight: 6.9990 chunk 94 optimal weight: 0.9980 chunk 166 optimal weight: 8.9990 chunk 360 optimal weight: 8.9990 chunk 33 optimal weight: 9.9990 chunk 228 optimal weight: 8.9990 chunk 173 optimal weight: 20.0000 chunk 89 optimal weight: 5.9990 chunk 202 optimal weight: 3.9990 chunk 163 optimal weight: 0.0980 chunk 119 optimal weight: 0.8980 overall best weight: 2.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 342 GLN A 475 GLN ** A 821 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1444 ASN B 271 ASN B 292 GLN ** G 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G1088 GLN ** G1355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1581 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1628 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.086762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.066117 restraints weight = 110048.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.067784 restraints weight = 54164.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.068017 restraints weight = 29419.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.068414 restraints weight = 24000.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.068457 restraints weight = 21425.654| |-----------------------------------------------------------------------------| r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.1923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 30301 Z= 0.131 Angle : 0.558 8.683 41043 Z= 0.289 Chirality : 0.043 0.285 4613 Planarity : 0.004 0.064 5300 Dihedral : 5.265 59.706 4055 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.21 % Favored : 96.74 % Rotamer: Outliers : 1.20 % Allowed : 11.38 % Favored : 87.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.56 % 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 aren not related in a simple way. whole: -0.18 (0.14), residues: 3774 helix: 0.75 (0.12), residues: 1670 sheet: -1.38 (0.22), residues: 499 loop : -0.49 (0.16), residues: 1605 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G1881 TYR 0.023 0.001 TYR G1608 PHE 0.016 0.001 PHE A 450 TRP 0.012 0.001 TRP G1449 HIS 0.006 0.001 HIS G1352 Details of bonding type rmsd covalent geometry : bond 0.00298 (30300) covalent geometry : angle 0.55709 (41041) SS BOND : bond 0.01940 ( 1) SS BOND : angle 4.71653 ( 2) hydrogen bonds : bond 0.03845 ( 1428) hydrogen bonds : angle 5.07336 ( 4089) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 3253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 276 time to evaluate : 1.018 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 841 GLU cc_start: 0.5717 (tp30) cc_final: 0.4916 (tp30) REVERT: A 1496 GLU cc_start: 0.8285 (OUTLIER) cc_final: 0.7913 (mp0) REVERT: B 185 GLU cc_start: 0.8068 (mt-10) cc_final: 0.7682 (mt-10) REVERT: G 630 MET cc_start: 0.7659 (tpp) cc_final: 0.7323 (tpp) REVERT: G 1412 TYR cc_start: 0.7090 (m-10) cc_final: 0.6438 (m-10) REVERT: G 1604 ARG cc_start: 0.6038 (ptp90) cc_final: 0.5806 (mtm110) REVERT: G 1676 MET cc_start: 0.7744 (ptm) cc_final: 0.7335 (ptm) REVERT: G 1693 ARG cc_start: 0.8342 (mtp85) cc_final: 0.8128 (ttm110) outliers start: 39 outliers final: 24 residues processed: 302 average time/residue: 0.1569 time to fit residues: 79.4047 Evaluate side-chains 268 residues out of total 3253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 243 time to evaluate : 0.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1085 ASP Chi-restraints excluded: chain A residue 1131 LEU Chi-restraints excluded: chain A residue 1234 MET Chi-restraints excluded: chain A residue 1260 MET Chi-restraints excluded: chain A residue 1308 SER Chi-restraints excluded: chain A residue 1496 GLU Chi-restraints excluded: chain A residue 1708 ASP Chi-restraints excluded: chain A residue 1777 THR Chi-restraints excluded: chain A residue 1866 ASP Chi-restraints excluded: chain B residue 243 ILE Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain G residue 215 ILE Chi-restraints excluded: chain G residue 318 SER Chi-restraints excluded: chain G residue 439 ILE Chi-restraints excluded: chain G residue 1209 VAL Chi-restraints excluded: chain G residue 1343 VAL Chi-restraints excluded: chain G residue 1409 SER Chi-restraints excluded: chain G residue 1489 ILE Chi-restraints excluded: chain G residue 1511 SER Chi-restraints excluded: chain G residue 1543 ASP Chi-restraints excluded: chain G residue 1718 THR Chi-restraints excluded: chain G residue 1821 VAL Chi-restraints excluded: chain G residue 1845 ASP Chi-restraints excluded: chain G residue 1871 LEU Chi-restraints excluded: chain G residue 1881 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 370 optimal weight: 50.0000 chunk 192 optimal weight: 6.9990 chunk 154 optimal weight: 30.0000 chunk 292 optimal weight: 20.0000 chunk 13 optimal weight: 8.9990 chunk 79 optimal weight: 0.5980 chunk 106 optimal weight: 4.9990 chunk 31 optimal weight: 6.9990 chunk 197 optimal weight: 0.0070 chunk 142 optimal weight: 0.0770 chunk 272 optimal weight: 5.9990 overall best weight: 2.3360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 GLN A 342 GLN A 798 ASN A1552 ASN A1758 ASN B 271 ASN B 292 GLN ** G 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 350 GLN ** G1581 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.087347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.066789 restraints weight = 109963.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.068580 restraints weight = 51097.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.068830 restraints weight = 26611.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.069055 restraints weight = 21946.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.069081 restraints weight = 20362.442| |-----------------------------------------------------------------------------| r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.2166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 30301 Z= 0.127 Angle : 0.533 9.058 41043 Z= 0.276 Chirality : 0.042 0.294 4613 Planarity : 0.004 0.065 5300 Dihedral : 4.924 59.926 4047 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.99 % Favored : 96.95 % Rotamer: Outliers : 1.63 % Allowed : 12.05 % Favored : 86.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.56 % 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 aren not related in a simple way. whole: 0.19 (0.14), residues: 3774 helix: 1.06 (0.13), residues: 1677 sheet: -1.24 (0.22), residues: 515 loop : -0.27 (0.16), residues: 1582 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 200 TYR 0.021 0.001 TYR A 81 PHE 0.015 0.001 PHE A 450 TRP 0.011 0.001 TRP G1449 HIS 0.007 0.001 HIS G1568 Details of bonding type rmsd covalent geometry : bond 0.00287 (30300) covalent geometry : angle 0.53201 (41041) SS BOND : bond 0.01890 ( 1) SS BOND : angle 5.02144 ( 2) hydrogen bonds : bond 0.03564 ( 1428) hydrogen bonds : angle 4.84788 ( 4089) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 3253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 277 time to evaluate : 0.951 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 841 GLU cc_start: 0.5683 (tp30) cc_final: 0.4916 (tp30) REVERT: A 1496 GLU cc_start: 0.8236 (OUTLIER) cc_final: 0.7867 (mp0) REVERT: B 179 LYS cc_start: 0.6941 (OUTLIER) cc_final: 0.6132 (mmtt) REVERT: B 185 GLU cc_start: 0.8039 (mt-10) cc_final: 0.7630 (mt-10) REVERT: B 241 PHE cc_start: 0.7624 (OUTLIER) cc_final: 0.6442 (m-80) REVERT: B 247 ARG cc_start: 0.8066 (mmm160) cc_final: 0.7817 (mmt180) REVERT: G 630 MET cc_start: 0.7593 (tpp) cc_final: 0.7270 (tpp) REVERT: G 1223 MET cc_start: 0.5865 (tpt) cc_final: 0.5628 (tpt) REVERT: G 1404 MET cc_start: 0.6379 (tmm) cc_final: 0.4164 (ptp) REVERT: G 1405 GLU cc_start: 0.7118 (tm-30) cc_final: 0.6441 (tm-30) REVERT: G 1645 GLU cc_start: 0.2683 (OUTLIER) cc_final: 0.2393 (pm20) REVERT: G 1676 MET cc_start: 0.7734 (ptm) cc_final: 0.7324 (ptm) REVERT: G 1763 THR cc_start: 0.9154 (m) cc_final: 0.8708 (p) REVERT: G 1822 MET cc_start: 0.5701 (mpp) cc_final: 0.4974 (mpp) outliers start: 53 outliers final: 33 residues processed: 314 average time/residue: 0.1592 time to fit residues: 83.0223 Evaluate side-chains 283 residues out of total 3253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 246 time to evaluate : 1.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 910 THR Chi-restraints excluded: chain A residue 1085 ASP Chi-restraints excluded: chain A residue 1124 GLU Chi-restraints excluded: chain A residue 1131 LEU Chi-restraints excluded: chain A residue 1150 ASP Chi-restraints excluded: chain A residue 1260 MET Chi-restraints excluded: chain A residue 1308 SER Chi-restraints excluded: chain A residue 1496 GLU Chi-restraints excluded: chain A residue 1540 SER Chi-restraints excluded: chain A residue 1633 THR Chi-restraints excluded: chain A residue 1708 ASP Chi-restraints excluded: chain A residue 1777 THR Chi-restraints excluded: chain A residue 1866 ASP Chi-restraints excluded: chain B residue 171 THR Chi-restraints excluded: chain B residue 179 LYS Chi-restraints excluded: chain B residue 241 PHE Chi-restraints excluded: chain B residue 243 ILE Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain G residue 115 THR Chi-restraints excluded: chain G residue 318 SER Chi-restraints excluded: chain G residue 439 ILE Chi-restraints excluded: chain G residue 448 VAL Chi-restraints excluded: chain G residue 840 THR Chi-restraints excluded: chain G residue 1343 VAL Chi-restraints excluded: chain G residue 1489 ILE Chi-restraints excluded: chain G residue 1511 SER Chi-restraints excluded: chain G residue 1543 ASP Chi-restraints excluded: chain G residue 1645 GLU Chi-restraints excluded: chain G residue 1648 VAL Chi-restraints excluded: chain G residue 1708 ASP Chi-restraints excluded: chain G residue 1718 THR Chi-restraints excluded: chain G residue 1821 VAL Chi-restraints excluded: chain G residue 1845 ASP Chi-restraints excluded: chain G residue 1871 LEU Chi-restraints excluded: chain G residue 1881 ARG Chi-restraints excluded: chain G residue 1885 LEU Chi-restraints excluded: chain G residue 1966 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 42 optimal weight: 2.9990 chunk 265 optimal weight: 7.9990 chunk 297 optimal weight: 10.0000 chunk 162 optimal weight: 0.7980 chunk 22 optimal weight: 0.0670 chunk 262 optimal weight: 10.0000 chunk 331 optimal weight: 20.0000 chunk 89 optimal weight: 6.9990 chunk 338 optimal weight: 4.9990 chunk 339 optimal weight: 5.9990 chunk 182 optimal weight: 3.9990 overall best weight: 2.5724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 342 GLN A 527 GLN B 271 ASN ** G 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 350 GLN ** G1352 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1581 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.087465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.066882 restraints weight = 110518.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.068618 restraints weight = 52072.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.068977 restraints weight = 26753.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.069197 restraints weight = 21324.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.069236 restraints weight = 20530.567| |-----------------------------------------------------------------------------| r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.2310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 30301 Z= 0.131 Angle : 0.538 12.383 41043 Z= 0.275 Chirality : 0.042 0.334 4613 Planarity : 0.004 0.065 5300 Dihedral : 4.851 59.804 4047 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.18 % Favored : 96.77 % Rotamer: Outliers : 1.75 % Allowed : 12.85 % Favored : 85.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.56 % 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 aren not related in a simple way. whole: 0.33 (0.14), residues: 3774 helix: 1.15 (0.13), residues: 1686 sheet: -1.13 (0.22), residues: 524 loop : -0.19 (0.16), residues: 1564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG G1604 TYR 0.023 0.001 TYR A 81 PHE 0.024 0.001 PHE A 22 TRP 0.011 0.001 TRP G1449 HIS 0.006 0.001 HIS G1568 Details of bonding type rmsd covalent geometry : bond 0.00298 (30300) covalent geometry : angle 0.53687 (41041) SS BOND : bond 0.01097 ( 1) SS BOND : angle 4.40064 ( 2) hydrogen bonds : bond 0.03505 ( 1428) hydrogen bonds : angle 4.76300 ( 4089) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 3253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 270 time to evaluate : 0.787 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 607 LYS cc_start: 0.8585 (OUTLIER) cc_final: 0.8078 (mttt) REVERT: A 841 GLU cc_start: 0.5882 (tp30) cc_final: 0.5193 (tp30) REVERT: A 1317 GLU cc_start: 0.8273 (mm-30) cc_final: 0.8061 (mm-30) REVERT: A 1496 GLU cc_start: 0.8230 (OUTLIER) cc_final: 0.7894 (mp0) REVERT: B 179 LYS cc_start: 0.7040 (OUTLIER) cc_final: 0.6182 (mmtt) REVERT: B 185 GLU cc_start: 0.8034 (mt-10) cc_final: 0.7626 (mt-10) REVERT: B 241 PHE cc_start: 0.7651 (OUTLIER) cc_final: 0.6317 (m-80) REVERT: B 247 ARG cc_start: 0.8050 (mmm160) cc_final: 0.7773 (mmt180) REVERT: G 630 MET cc_start: 0.7593 (tpp) cc_final: 0.7359 (tpp) REVERT: G 1323 MET cc_start: 0.4153 (tpt) cc_final: 0.3450 (mmm) REVERT: G 1404 MET cc_start: 0.6428 (tmm) cc_final: 0.4087 (ptp) REVERT: G 1405 GLU cc_start: 0.7062 (tm-30) cc_final: 0.6280 (tm-30) REVERT: G 1652 THR cc_start: 0.7101 (p) cc_final: 0.6878 (p) REVERT: G 1676 MET cc_start: 0.7702 (ptm) cc_final: 0.7031 (ptm) REVERT: G 1763 THR cc_start: 0.9150 (m) cc_final: 0.8534 (p) outliers start: 57 outliers final: 35 residues processed: 312 average time/residue: 0.1634 time to fit residues: 84.3749 Evaluate side-chains 280 residues out of total 3253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 241 time to evaluate : 0.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 607 LYS Chi-restraints excluded: chain A residue 788 SER Chi-restraints excluded: chain A residue 910 THR Chi-restraints excluded: chain A residue 1085 ASP Chi-restraints excluded: chain A residue 1124 GLU Chi-restraints excluded: chain A residue 1131 LEU Chi-restraints excluded: chain A residue 1150 ASP Chi-restraints excluded: chain A residue 1260 MET Chi-restraints excluded: chain A residue 1496 GLU Chi-restraints excluded: chain A residue 1540 SER Chi-restraints excluded: chain A residue 1633 THR Chi-restraints excluded: chain A residue 1708 ASP Chi-restraints excluded: chain A residue 1777 THR Chi-restraints excluded: chain A residue 1866 ASP Chi-restraints excluded: chain B residue 171 THR Chi-restraints excluded: chain B residue 179 LYS Chi-restraints excluded: chain B residue 241 PHE Chi-restraints excluded: chain B residue 243 ILE Chi-restraints excluded: chain B residue 248 LYS Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain G residue 115 THR Chi-restraints excluded: chain G residue 215 ILE Chi-restraints excluded: chain G residue 318 SER Chi-restraints excluded: chain G residue 439 ILE Chi-restraints excluded: chain G residue 840 THR Chi-restraints excluded: chain G residue 1133 THR Chi-restraints excluded: chain G residue 1343 VAL Chi-restraints excluded: chain G residue 1489 ILE Chi-restraints excluded: chain G residue 1511 SER Chi-restraints excluded: chain G residue 1543 ASP Chi-restraints excluded: chain G residue 1648 VAL Chi-restraints excluded: chain G residue 1718 THR Chi-restraints excluded: chain G residue 1821 VAL Chi-restraints excluded: chain G residue 1845 ASP Chi-restraints excluded: chain G residue 1871 LEU Chi-restraints excluded: chain G residue 1881 ARG Chi-restraints excluded: chain G residue 1885 LEU Chi-restraints excluded: chain G residue 1966 CYS Chi-restraints excluded: chain G residue 2035 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 271 optimal weight: 4.9990 chunk 149 optimal weight: 7.9990 chunk 274 optimal weight: 5.9990 chunk 341 optimal weight: 10.0000 chunk 159 optimal weight: 9.9990 chunk 188 optimal weight: 6.9990 chunk 83 optimal weight: 9.9990 chunk 371 optimal weight: 10.0000 chunk 179 optimal weight: 20.0000 chunk 332 optimal weight: 1.9990 chunk 257 optimal weight: 0.0870 overall best weight: 4.0166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 342 GLN ** A 821 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 292 GLN ** G 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 350 GLN G1523 ASN ** G1581 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.086682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.066223 restraints weight = 110065.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.068031 restraints weight = 49915.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.068315 restraints weight = 24784.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.068472 restraints weight = 22407.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.068542 restraints weight = 20860.410| |-----------------------------------------------------------------------------| r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.2401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 30301 Z= 0.175 Angle : 0.568 10.304 41043 Z= 0.292 Chirality : 0.043 0.323 4613 Planarity : 0.004 0.066 5300 Dihedral : 4.872 59.432 4046 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.66 % Favored : 96.29 % Rotamer: Outliers : 1.81 % Allowed : 13.62 % Favored : 84.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.56 % 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 aren not related in a simple way. whole: 0.26 (0.14), residues: 3774 helix: 1.06 (0.13), residues: 1702 sheet: -1.10 (0.22), residues: 514 loop : -0.23 (0.16), residues: 1558 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G1604 TYR 0.023 0.002 TYR A 81 PHE 0.021 0.001 PHE A 450 TRP 0.020 0.001 TRP G2045 HIS 0.006 0.001 HIS G1568 Details of bonding type rmsd covalent geometry : bond 0.00396 (30300) covalent geometry : angle 0.56622 (41041) SS BOND : bond 0.01871 ( 1) SS BOND : angle 6.60925 ( 2) hydrogen bonds : bond 0.03696 ( 1428) hydrogen bonds : angle 4.83270 ( 4089) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 3253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 246 time to evaluate : 0.739 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 GLU cc_start: 0.7503 (OUTLIER) cc_final: 0.7158 (mt-10) REVERT: A 607 LYS cc_start: 0.8606 (OUTLIER) cc_final: 0.8116 (mttt) REVERT: A 841 GLU cc_start: 0.5780 (tp30) cc_final: 0.5091 (tp30) REVERT: A 1317 GLU cc_start: 0.8263 (mm-30) cc_final: 0.8057 (mm-30) REVERT: A 1496 GLU cc_start: 0.8327 (OUTLIER) cc_final: 0.7952 (mp0) REVERT: B 168 MET cc_start: 0.6756 (tpp) cc_final: 0.6386 (tpp) REVERT: B 179 LYS cc_start: 0.7069 (OUTLIER) cc_final: 0.6179 (mmtt) REVERT: B 185 GLU cc_start: 0.8143 (mt-10) cc_final: 0.7746 (mt-10) REVERT: B 241 PHE cc_start: 0.7772 (OUTLIER) cc_final: 0.6404 (m-80) REVERT: G 630 MET cc_start: 0.7704 (tpp) cc_final: 0.7400 (tpp) REVERT: G 1323 MET cc_start: 0.4147 (tpt) cc_final: 0.3376 (mmm) REVERT: G 1404 MET cc_start: 0.6342 (tmm) cc_final: 0.3953 (ptp) REVERT: G 1405 GLU cc_start: 0.7017 (tm-30) cc_final: 0.6150 (tm-30) REVERT: G 1676 MET cc_start: 0.7617 (ptm) cc_final: 0.6705 (ptm) REVERT: G 1763 THR cc_start: 0.9125 (m) cc_final: 0.8707 (p) outliers start: 59 outliers final: 40 residues processed: 293 average time/residue: 0.1589 time to fit residues: 77.2576 Evaluate side-chains 278 residues out of total 3253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 233 time to evaluate : 0.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 GLU Chi-restraints excluded: chain A residue 607 LYS Chi-restraints excluded: chain A residue 788 SER Chi-restraints excluded: chain A residue 910 THR Chi-restraints excluded: chain A residue 1085 ASP Chi-restraints excluded: chain A residue 1124 GLU Chi-restraints excluded: chain A residue 1131 LEU Chi-restraints excluded: chain A residue 1150 ASP Chi-restraints excluded: chain A residue 1260 MET Chi-restraints excluded: chain A residue 1496 GLU Chi-restraints excluded: chain A residue 1540 SER Chi-restraints excluded: chain A residue 1633 THR Chi-restraints excluded: chain A residue 1708 ASP Chi-restraints excluded: chain A residue 1726 LYS Chi-restraints excluded: chain A residue 1777 THR Chi-restraints excluded: chain A residue 1866 ASP Chi-restraints excluded: chain B residue 171 THR Chi-restraints excluded: chain B residue 179 LYS Chi-restraints excluded: chain B residue 236 LYS Chi-restraints excluded: chain B residue 241 PHE Chi-restraints excluded: chain B residue 243 ILE Chi-restraints excluded: chain B residue 248 LYS Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain G residue 115 THR Chi-restraints excluded: chain G residue 215 ILE Chi-restraints excluded: chain G residue 318 SER Chi-restraints excluded: chain G residue 334 VAL Chi-restraints excluded: chain G residue 439 ILE Chi-restraints excluded: chain G residue 528 ILE Chi-restraints excluded: chain G residue 840 THR Chi-restraints excluded: chain G residue 1133 THR Chi-restraints excluded: chain G residue 1343 VAL Chi-restraints excluded: chain G residue 1489 ILE Chi-restraints excluded: chain G residue 1511 SER Chi-restraints excluded: chain G residue 1543 ASP Chi-restraints excluded: chain G residue 1611 GLN Chi-restraints excluded: chain G residue 1629 VAL Chi-restraints excluded: chain G residue 1648 VAL Chi-restraints excluded: chain G residue 1718 THR Chi-restraints excluded: chain G residue 1821 VAL Chi-restraints excluded: chain G residue 1845 ASP Chi-restraints excluded: chain G residue 1871 LEU Chi-restraints excluded: chain G residue 1881 ARG Chi-restraints excluded: chain G residue 1966 CYS Chi-restraints excluded: chain G residue 2035 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 345 optimal weight: 5.9990 chunk 65 optimal weight: 3.9990 chunk 298 optimal weight: 10.0000 chunk 338 optimal weight: 0.6980 chunk 101 optimal weight: 1.9990 chunk 372 optimal weight: 20.0000 chunk 184 optimal weight: 5.9990 chunk 231 optimal weight: 0.7980 chunk 153 optimal weight: 6.9990 chunk 341 optimal weight: 10.0000 chunk 125 optimal weight: 6.9990 overall best weight: 2.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 342 GLN A1442 ASN A1652 GLN B 292 GLN ** G 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 350 GLN ** G1581 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.087476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.066978 restraints weight = 110367.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.068721 restraints weight = 52254.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.069039 restraints weight = 27127.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.069282 restraints weight = 21596.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.069325 restraints weight = 20527.832| |-----------------------------------------------------------------------------| r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.2515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 30301 Z= 0.135 Angle : 0.547 11.581 41043 Z= 0.279 Chirality : 0.043 0.342 4613 Planarity : 0.004 0.067 5300 Dihedral : 4.754 61.885 4046 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.13 % Favored : 96.82 % Rotamer: Outliers : 1.81 % Allowed : 14.21 % Favored : 83.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.56 % 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 aren not related in a simple way. whole: 0.42 (0.14), residues: 3774 helix: 1.23 (0.13), residues: 1683 sheet: -1.07 (0.22), residues: 533 loop : -0.13 (0.16), residues: 1558 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 200 TYR 0.024 0.001 TYR A 81 PHE 0.018 0.001 PHE A 450 TRP 0.015 0.001 TRP A1813 HIS 0.005 0.001 HIS A 454 Details of bonding type rmsd covalent geometry : bond 0.00307 (30300) covalent geometry : angle 0.54578 (41041) SS BOND : bond 0.01367 ( 1) SS BOND : angle 5.07001 ( 2) hydrogen bonds : bond 0.03493 ( 1428) hydrogen bonds : angle 4.72375 ( 4089) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 3253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 253 time to evaluate : 1.271 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 GLU cc_start: 0.7298 (OUTLIER) cc_final: 0.7062 (mt-10) REVERT: A 451 MET cc_start: 0.8377 (mtm) cc_final: 0.8124 (mtp) REVERT: A 841 GLU cc_start: 0.5928 (tp30) cc_final: 0.5408 (tp30) REVERT: A 1406 MET cc_start: 0.8902 (ttp) cc_final: 0.8662 (ppp) REVERT: A 1496 GLU cc_start: 0.8347 (OUTLIER) cc_final: 0.7946 (mp0) REVERT: B 179 LYS cc_start: 0.7074 (OUTLIER) cc_final: 0.6143 (mmtm) REVERT: B 185 GLU cc_start: 0.8115 (mt-10) cc_final: 0.7723 (mt-10) REVERT: B 241 PHE cc_start: 0.7677 (OUTLIER) cc_final: 0.6383 (m-80) REVERT: B 247 ARG cc_start: 0.8031 (mmm160) cc_final: 0.7525 (mtp85) REVERT: G 630 MET cc_start: 0.7647 (tpp) cc_final: 0.7392 (tpp) REVERT: G 1323 MET cc_start: 0.4460 (tpt) cc_final: 0.3563 (mmm) REVERT: G 1359 MET cc_start: 0.1298 (mmm) cc_final: 0.0566 (mtt) REVERT: G 1404 MET cc_start: 0.6310 (tmm) cc_final: 0.3812 (ptp) REVERT: G 1405 GLU cc_start: 0.7025 (tm-30) cc_final: 0.6031 (tm-30) REVERT: G 1412 TYR cc_start: 0.7145 (m-10) cc_final: 0.6549 (m-10) REVERT: G 1676 MET cc_start: 0.7515 (ptm) cc_final: 0.7037 (ptm) REVERT: G 1763 THR cc_start: 0.9146 (m) cc_final: 0.8693 (p) outliers start: 59 outliers final: 41 residues processed: 298 average time/residue: 0.1969 time to fit residues: 97.0701 Evaluate side-chains 283 residues out of total 3253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 238 time to evaluate : 2.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 GLU Chi-restraints excluded: chain A residue 788 SER Chi-restraints excluded: chain A residue 910 THR Chi-restraints excluded: chain A residue 1085 ASP Chi-restraints excluded: chain A residue 1124 GLU Chi-restraints excluded: chain A residue 1131 LEU Chi-restraints excluded: chain A residue 1150 ASP Chi-restraints excluded: chain A residue 1260 MET Chi-restraints excluded: chain A residue 1496 GLU Chi-restraints excluded: chain A residue 1540 SER Chi-restraints excluded: chain A residue 1633 THR Chi-restraints excluded: chain A residue 1666 THR Chi-restraints excluded: chain A residue 1708 ASP Chi-restraints excluded: chain A residue 1726 LYS Chi-restraints excluded: chain A residue 1777 THR Chi-restraints excluded: chain A residue 1779 ILE Chi-restraints excluded: chain A residue 1866 ASP Chi-restraints excluded: chain B residue 171 THR Chi-restraints excluded: chain B residue 179 LYS Chi-restraints excluded: chain B residue 236 LYS Chi-restraints excluded: chain B residue 241 PHE Chi-restraints excluded: chain B residue 243 ILE Chi-restraints excluded: chain B residue 248 LYS Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain G residue 115 THR Chi-restraints excluded: chain G residue 215 ILE Chi-restraints excluded: chain G residue 318 SER Chi-restraints excluded: chain G residue 334 VAL Chi-restraints excluded: chain G residue 439 ILE Chi-restraints excluded: chain G residue 528 ILE Chi-restraints excluded: chain G residue 755 SER Chi-restraints excluded: chain G residue 840 THR Chi-restraints excluded: chain G residue 1133 THR Chi-restraints excluded: chain G residue 1285 ILE Chi-restraints excluded: chain G residue 1343 VAL Chi-restraints excluded: chain G residue 1489 ILE Chi-restraints excluded: chain G residue 1629 VAL Chi-restraints excluded: chain G residue 1648 VAL Chi-restraints excluded: chain G residue 1718 THR Chi-restraints excluded: chain G residue 1821 VAL Chi-restraints excluded: chain G residue 1845 ASP Chi-restraints excluded: chain G residue 1871 LEU Chi-restraints excluded: chain G residue 1881 ARG Chi-restraints excluded: chain G residue 1966 CYS Chi-restraints excluded: chain G residue 2035 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 344 optimal weight: 20.0000 chunk 246 optimal weight: 0.1980 chunk 202 optimal weight: 1.9990 chunk 111 optimal weight: 3.9990 chunk 366 optimal weight: 7.9990 chunk 126 optimal weight: 2.9990 chunk 40 optimal weight: 5.9990 chunk 238 optimal weight: 8.9990 chunk 244 optimal weight: 0.9980 chunk 322 optimal weight: 20.0000 chunk 253 optimal weight: 1.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 GLN A 342 GLN A 821 GLN B 292 GLN ** G 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 350 GLN G1355 ASN ** G1581 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.088283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.067774 restraints weight = 110402.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.069601 restraints weight = 49603.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.070057 restraints weight = 24453.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.070064 restraints weight = 21227.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.070223 restraints weight = 20408.853| |-----------------------------------------------------------------------------| r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.2676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 30301 Z= 0.108 Angle : 0.533 12.120 41043 Z= 0.270 Chirality : 0.042 0.337 4613 Planarity : 0.004 0.069 5300 Dihedral : 4.611 62.664 4045 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.94 % Favored : 97.01 % Rotamer: Outliers : 1.60 % Allowed : 14.76 % Favored : 83.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.56 % 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 aren not related in a simple way. whole: 0.59 (0.14), residues: 3774 helix: 1.36 (0.13), residues: 1684 sheet: -0.92 (0.22), residues: 520 loop : -0.08 (0.16), residues: 1570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 200 TYR 0.025 0.001 TYR G1506 PHE 0.017 0.001 PHE B 194 TRP 0.017 0.001 TRP A1813 HIS 0.006 0.001 HIS G1568 Details of bonding type rmsd covalent geometry : bond 0.00245 (30300) covalent geometry : angle 0.53193 (41041) SS BOND : bond 0.01096 ( 1) SS BOND : angle 4.09896 ( 2) hydrogen bonds : bond 0.03291 ( 1428) hydrogen bonds : angle 4.59491 ( 4089) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 3253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 275 time to evaluate : 1.284 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.4160 (ttt) cc_final: 0.2837 (tpt) REVERT: A 87 GLU cc_start: 0.7309 (OUTLIER) cc_final: 0.7059 (mt-10) REVERT: A 451 MET cc_start: 0.8320 (mtm) cc_final: 0.8050 (mtp) REVERT: A 841 GLU cc_start: 0.6073 (tp30) cc_final: 0.5554 (tp30) REVERT: A 917 CYS cc_start: 0.7593 (p) cc_final: 0.7293 (p) REVERT: A 923 MET cc_start: 0.8248 (tpt) cc_final: 0.8040 (tpt) REVERT: A 1406 MET cc_start: 0.8901 (ttp) cc_final: 0.8600 (ppp) REVERT: A 1496 GLU cc_start: 0.8318 (OUTLIER) cc_final: 0.7950 (mp0) REVERT: A 1681 GLU cc_start: 0.8344 (tm-30) cc_final: 0.7815 (tm-30) REVERT: B 168 MET cc_start: 0.6709 (tpp) cc_final: 0.6433 (tpp) REVERT: B 179 LYS cc_start: 0.7055 (OUTLIER) cc_final: 0.6119 (mmtm) REVERT: B 185 GLU cc_start: 0.8091 (mt-10) cc_final: 0.7766 (mt-10) REVERT: B 241 PHE cc_start: 0.7676 (OUTLIER) cc_final: 0.6393 (m-80) REVERT: B 247 ARG cc_start: 0.8022 (mmm160) cc_final: 0.7465 (mtp85) REVERT: B 251 GLN cc_start: 0.8438 (tp40) cc_final: 0.8039 (mm-40) REVERT: G 55 THR cc_start: 0.7585 (OUTLIER) cc_final: 0.7137 (t) REVERT: G 527 VAL cc_start: 0.8586 (t) cc_final: 0.8321 (p) REVERT: G 1323 MET cc_start: 0.4570 (tpt) cc_final: 0.3804 (mmm) REVERT: G 1359 MET cc_start: 0.1229 (mmm) cc_final: 0.0501 (mtt) REVERT: G 1404 MET cc_start: 0.6235 (tmm) cc_final: 0.3776 (ptp) REVERT: G 1405 GLU cc_start: 0.6983 (tm-30) cc_final: 0.5998 (tm-30) REVERT: G 1412 TYR cc_start: 0.7123 (m-10) cc_final: 0.6602 (m-10) REVERT: G 1676 MET cc_start: 0.7490 (ptm) cc_final: 0.6919 (ptm) REVERT: G 1736 MET cc_start: 0.6834 (mmp) cc_final: 0.6528 (mtt) REVERT: G 1763 THR cc_start: 0.9165 (m) cc_final: 0.8650 (p) REVERT: G 1784 MET cc_start: 0.7582 (tmm) cc_final: 0.7331 (tmm) outliers start: 52 outliers final: 35 residues processed: 315 average time/residue: 0.1963 time to fit residues: 102.6454 Evaluate side-chains 286 residues out of total 3253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 246 time to evaluate : 1.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 GLU Chi-restraints excluded: chain A residue 788 SER Chi-restraints excluded: chain A residue 910 THR Chi-restraints excluded: chain A residue 1124 GLU Chi-restraints excluded: chain A residue 1131 LEU Chi-restraints excluded: chain A residue 1150 ASP Chi-restraints excluded: chain A residue 1260 MET Chi-restraints excluded: chain A residue 1496 GLU Chi-restraints excluded: chain A residue 1540 SER Chi-restraints excluded: chain A residue 1666 THR Chi-restraints excluded: chain A residue 1708 ASP Chi-restraints excluded: chain A residue 1726 LYS Chi-restraints excluded: chain A residue 1777 THR Chi-restraints excluded: chain A residue 1842 VAL Chi-restraints excluded: chain A residue 1866 ASP Chi-restraints excluded: chain B residue 171 THR Chi-restraints excluded: chain B residue 179 LYS Chi-restraints excluded: chain B residue 236 LYS Chi-restraints excluded: chain B residue 241 PHE Chi-restraints excluded: chain B residue 243 ILE Chi-restraints excluded: chain B residue 248 LYS Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain G residue 55 THR Chi-restraints excluded: chain G residue 115 THR Chi-restraints excluded: chain G residue 318 SER Chi-restraints excluded: chain G residue 334 VAL Chi-restraints excluded: chain G residue 755 SER Chi-restraints excluded: chain G residue 840 THR Chi-restraints excluded: chain G residue 1133 THR Chi-restraints excluded: chain G residue 1285 ILE Chi-restraints excluded: chain G residue 1343 VAL Chi-restraints excluded: chain G residue 1355 ASN Chi-restraints excluded: chain G residue 1489 ILE Chi-restraints excluded: chain G residue 1629 VAL Chi-restraints excluded: chain G residue 1648 VAL Chi-restraints excluded: chain G residue 1708 ASP Chi-restraints excluded: chain G residue 1821 VAL Chi-restraints excluded: chain G residue 1845 ASP Chi-restraints excluded: chain G residue 1881 ARG Chi-restraints excluded: chain G residue 1966 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 241 optimal weight: 1.9990 chunk 177 optimal weight: 0.9990 chunk 224 optimal weight: 0.5980 chunk 292 optimal weight: 20.0000 chunk 321 optimal weight: 9.9990 chunk 225 optimal weight: 5.9990 chunk 99 optimal weight: 0.8980 chunk 80 optimal weight: 6.9990 chunk 39 optimal weight: 10.0000 chunk 358 optimal weight: 6.9990 chunk 0 optimal weight: 30.0000 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 342 GLN A 821 GLN B 271 ASN ** G 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G1355 ASN ** G1581 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.088225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.067812 restraints weight = 109598.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.069539 restraints weight = 48814.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.069845 restraints weight = 24700.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.070020 restraints weight = 22068.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.070046 restraints weight = 20151.372| |-----------------------------------------------------------------------------| r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.2738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 30301 Z= 0.120 Angle : 0.542 12.417 41043 Z= 0.274 Chirality : 0.042 0.331 4613 Planarity : 0.004 0.066 5300 Dihedral : 4.585 62.740 4045 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.94 % Favored : 97.01 % Rotamer: Outliers : 1.48 % Allowed : 15.16 % Favored : 83.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.56 % 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 aren not related in a simple way. whole: 0.60 (0.14), residues: 3774 helix: 1.34 (0.13), residues: 1700 sheet: -0.84 (0.23), residues: 508 loop : -0.10 (0.16), residues: 1566 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG G 200 TYR 0.024 0.001 TYR A 81 PHE 0.019 0.001 PHE B 286 TRP 0.018 0.001 TRP A1813 HIS 0.006 0.001 HIS G1568 Details of bonding type rmsd covalent geometry : bond 0.00274 (30300) covalent geometry : angle 0.53991 (41041) SS BOND : bond 0.01190 ( 1) SS BOND : angle 6.37079 ( 2) hydrogen bonds : bond 0.03346 ( 1428) hydrogen bonds : angle 4.59468 ( 4089) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 3253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 253 time to evaluate : 1.273 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 GLU cc_start: 0.7341 (OUTLIER) cc_final: 0.7104 (mt-10) REVERT: A 841 GLU cc_start: 0.6330 (tp30) cc_final: 0.5921 (tp30) REVERT: A 1406 MET cc_start: 0.8922 (ttp) cc_final: 0.8610 (ppp) REVERT: A 1681 GLU cc_start: 0.8388 (tm-30) cc_final: 0.7899 (tm-30) REVERT: B 179 LYS cc_start: 0.7003 (OUTLIER) cc_final: 0.6051 (mmtm) REVERT: B 185 GLU cc_start: 0.8160 (mt-10) cc_final: 0.7870 (mt-10) REVERT: B 241 PHE cc_start: 0.7669 (OUTLIER) cc_final: 0.6362 (m-80) REVERT: B 247 ARG cc_start: 0.8027 (mmm160) cc_final: 0.7704 (mmt180) REVERT: G 55 THR cc_start: 0.7595 (OUTLIER) cc_final: 0.7145 (t) REVERT: G 199 ILE cc_start: 0.8966 (mt) cc_final: 0.8755 (mt) REVERT: G 527 VAL cc_start: 0.8592 (t) cc_final: 0.8336 (p) REVERT: G 1323 MET cc_start: 0.4551 (tpt) cc_final: 0.3786 (mmm) REVERT: G 1359 MET cc_start: 0.1292 (mmm) cc_final: 0.0600 (mtt) REVERT: G 1404 MET cc_start: 0.6304 (tmm) cc_final: 0.3854 (ptp) REVERT: G 1405 GLU cc_start: 0.6991 (tm-30) cc_final: 0.6004 (tm-30) REVERT: G 1676 MET cc_start: 0.7482 (ptm) cc_final: 0.6918 (ptm) REVERT: G 1707 LEU cc_start: 0.8166 (OUTLIER) cc_final: 0.7874 (mp) REVERT: G 1784 MET cc_start: 0.7533 (tmm) cc_final: 0.7268 (tmm) REVERT: G 2006 LEU cc_start: 0.7027 (OUTLIER) cc_final: 0.6645 (mt) outliers start: 48 outliers final: 35 residues processed: 294 average time/residue: 0.1927 time to fit residues: 94.3815 Evaluate side-chains 283 residues out of total 3253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 242 time to evaluate : 1.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 GLU Chi-restraints excluded: chain A residue 788 SER Chi-restraints excluded: chain A residue 910 THR Chi-restraints excluded: chain A residue 1124 GLU Chi-restraints excluded: chain A residue 1131 LEU Chi-restraints excluded: chain A residue 1150 ASP Chi-restraints excluded: chain A residue 1260 MET Chi-restraints excluded: chain A residue 1540 SER Chi-restraints excluded: chain A residue 1666 THR Chi-restraints excluded: chain A residue 1708 ASP Chi-restraints excluded: chain A residue 1726 LYS Chi-restraints excluded: chain A residue 1777 THR Chi-restraints excluded: chain A residue 1842 VAL Chi-restraints excluded: chain A residue 1850 GLU Chi-restraints excluded: chain B residue 171 THR Chi-restraints excluded: chain B residue 179 LYS Chi-restraints excluded: chain B residue 241 PHE Chi-restraints excluded: chain B residue 243 ILE Chi-restraints excluded: chain B residue 248 LYS Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain G residue 55 THR Chi-restraints excluded: chain G residue 115 THR Chi-restraints excluded: chain G residue 318 SER Chi-restraints excluded: chain G residue 334 VAL Chi-restraints excluded: chain G residue 528 ILE Chi-restraints excluded: chain G residue 755 SER Chi-restraints excluded: chain G residue 840 THR Chi-restraints excluded: chain G residue 1133 THR Chi-restraints excluded: chain G residue 1285 ILE Chi-restraints excluded: chain G residue 1343 VAL Chi-restraints excluded: chain G residue 1355 ASN Chi-restraints excluded: chain G residue 1611 GLN Chi-restraints excluded: chain G residue 1629 VAL Chi-restraints excluded: chain G residue 1648 VAL Chi-restraints excluded: chain G residue 1707 LEU Chi-restraints excluded: chain G residue 1821 VAL Chi-restraints excluded: chain G residue 1845 ASP Chi-restraints excluded: chain G residue 1881 ARG Chi-restraints excluded: chain G residue 1966 CYS Chi-restraints excluded: chain G residue 2006 LEU Chi-restraints excluded: chain G residue 2035 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 175 optimal weight: 4.9990 chunk 106 optimal weight: 0.0170 chunk 368 optimal weight: 30.0000 chunk 29 optimal weight: 1.9990 chunk 51 optimal weight: 0.8980 chunk 323 optimal weight: 8.9990 chunk 93 optimal weight: 0.9990 chunk 297 optimal weight: 0.9990 chunk 201 optimal weight: 3.9990 chunk 194 optimal weight: 9.9990 chunk 128 optimal weight: 4.9990 overall best weight: 0.9824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 342 GLN A1780 ASN B 271 ASN ** G 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 517 HIS ** G1564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1581 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.089378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.068861 restraints weight = 109985.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.070786 restraints weight = 50176.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.071127 restraints weight = 24816.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.071249 restraints weight = 20730.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.071292 restraints weight = 19916.349| |-----------------------------------------------------------------------------| r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.2890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 30301 Z= 0.102 Angle : 0.544 11.854 41043 Z= 0.273 Chirality : 0.042 0.312 4613 Planarity : 0.004 0.066 5300 Dihedral : 4.295 59.086 4042 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.97 % Favored : 96.98 % Rotamer: Outliers : 1.23 % Allowed : 15.62 % Favored : 83.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.56 % 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 aren not related in a simple way. whole: 0.70 (0.14), residues: 3774 helix: 1.40 (0.13), residues: 1698 sheet: -0.70 (0.23), residues: 510 loop : -0.04 (0.16), residues: 1566 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 200 TYR 0.025 0.001 TYR G1506 PHE 0.019 0.001 PHE B 286 TRP 0.038 0.001 TRP G2045 HIS 0.007 0.001 HIS A 454 Details of bonding type rmsd covalent geometry : bond 0.00227 (30300) covalent geometry : angle 0.54305 (41041) SS BOND : bond 0.01292 ( 1) SS BOND : angle 4.90613 ( 2) hydrogen bonds : bond 0.03196 ( 1428) hydrogen bonds : angle 4.52247 ( 4089) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 3253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 282 time to evaluate : 1.194 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 GLU cc_start: 0.7415 (OUTLIER) cc_final: 0.7182 (mt-10) REVERT: A 841 GLU cc_start: 0.6281 (tp30) cc_final: 0.5997 (tp30) REVERT: A 1406 MET cc_start: 0.8894 (ttp) cc_final: 0.8592 (ppp) REVERT: A 1681 GLU cc_start: 0.8271 (tm-30) cc_final: 0.7766 (tm-30) REVERT: B 179 LYS cc_start: 0.7108 (OUTLIER) cc_final: 0.6104 (mmtm) REVERT: B 185 GLU cc_start: 0.8082 (mt-10) cc_final: 0.7671 (mt-10) REVERT: B 241 PHE cc_start: 0.7710 (OUTLIER) cc_final: 0.6443 (m-80) REVERT: B 247 ARG cc_start: 0.7979 (mmm160) cc_final: 0.7428 (mtp85) REVERT: B 272 GLU cc_start: 0.8448 (mt-10) cc_final: 0.8235 (mp0) REVERT: G 527 VAL cc_start: 0.8464 (t) cc_final: 0.8210 (p) REVERT: G 630 MET cc_start: 0.7501 (tpp) cc_final: 0.7089 (mmt) REVERT: G 631 THR cc_start: 0.9277 (m) cc_final: 0.9033 (p) REVERT: G 1319 MET cc_start: 0.4023 (ttp) cc_final: 0.3217 (ttp) REVERT: G 1323 MET cc_start: 0.4475 (tpt) cc_final: 0.3748 (mmm) REVERT: G 1359 MET cc_start: 0.1205 (mmm) cc_final: 0.0382 (mtt) REVERT: G 1404 MET cc_start: 0.6273 (tmm) cc_final: 0.3824 (ptp) REVERT: G 1405 GLU cc_start: 0.7011 (tm-30) cc_final: 0.6031 (tm-30) REVERT: G 1412 TYR cc_start: 0.7106 (m-10) cc_final: 0.6450 (m-80) REVERT: G 1676 MET cc_start: 0.7489 (ptm) cc_final: 0.7239 (ptm) REVERT: G 1784 MET cc_start: 0.7473 (tmm) cc_final: 0.7238 (tmm) REVERT: G 1822 MET cc_start: 0.5197 (mpp) cc_final: 0.4446 (mpp) REVERT: G 2006 LEU cc_start: 0.7051 (OUTLIER) cc_final: 0.6665 (mt) outliers start: 40 outliers final: 28 residues processed: 315 average time/residue: 0.1924 time to fit residues: 99.7192 Evaluate side-chains 284 residues out of total 3253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 252 time to evaluate : 1.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 GLU Chi-restraints excluded: chain A residue 788 SER Chi-restraints excluded: chain A residue 838 MET Chi-restraints excluded: chain A residue 910 THR Chi-restraints excluded: chain A residue 1150 ASP Chi-restraints excluded: chain A residue 1260 MET Chi-restraints excluded: chain A residue 1540 SER Chi-restraints excluded: chain A residue 1666 THR Chi-restraints excluded: chain A residue 1708 ASP Chi-restraints excluded: chain A residue 1726 LYS Chi-restraints excluded: chain A residue 1842 VAL Chi-restraints excluded: chain A residue 1850 GLU Chi-restraints excluded: chain B residue 179 LYS Chi-restraints excluded: chain B residue 241 PHE Chi-restraints excluded: chain B residue 243 ILE Chi-restraints excluded: chain B residue 248 LYS Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain G residue 115 THR Chi-restraints excluded: chain G residue 334 VAL Chi-restraints excluded: chain G residue 528 ILE Chi-restraints excluded: chain G residue 840 THR Chi-restraints excluded: chain G residue 1133 THR Chi-restraints excluded: chain G residue 1285 ILE Chi-restraints excluded: chain G residue 1343 VAL Chi-restraints excluded: chain G residue 1434 HIS Chi-restraints excluded: chain G residue 1821 VAL Chi-restraints excluded: chain G residue 1845 ASP Chi-restraints excluded: chain G residue 1881 ARG Chi-restraints excluded: chain G residue 1966 CYS Chi-restraints excluded: chain G residue 2006 LEU Chi-restraints excluded: chain G residue 2035 SER Chi-restraints excluded: chain G residue 2045 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 119 optimal weight: 5.9990 chunk 353 optimal weight: 7.9990 chunk 94 optimal weight: 0.8980 chunk 46 optimal weight: 4.9990 chunk 222 optimal weight: 10.0000 chunk 316 optimal weight: 6.9990 chunk 252 optimal weight: 0.9990 chunk 283 optimal weight: 0.4980 chunk 309 optimal weight: 1.9990 chunk 293 optimal weight: 9.9990 chunk 39 optimal weight: 9.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 342 GLN B 271 ASN ** G 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G1355 ASN ** G1564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1581 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.088863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.068374 restraints weight = 110978.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.070374 restraints weight = 50226.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.070588 restraints weight = 25201.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.070712 restraints weight = 21160.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.070752 restraints weight = 19842.871| |-----------------------------------------------------------------------------| r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.2952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 30301 Z= 0.118 Angle : 0.556 10.976 41043 Z= 0.281 Chirality : 0.042 0.297 4613 Planarity : 0.004 0.070 5300 Dihedral : 4.327 59.507 4042 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.13 % Favored : 96.82 % Rotamer: Outliers : 1.29 % Allowed : 16.08 % Favored : 82.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.56 % 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 aren not related in a simple way. whole: 0.72 (0.14), residues: 3774 helix: 1.40 (0.13), residues: 1698 sheet: -0.63 (0.23), residues: 506 loop : -0.03 (0.16), residues: 1570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG G 200 TYR 0.036 0.001 TYR G1762 PHE 0.019 0.001 PHE G1466 TRP 0.032 0.001 TRP G2045 HIS 0.006 0.001 HIS A 454 Details of bonding type rmsd covalent geometry : bond 0.00271 (30300) covalent geometry : angle 0.55490 (41041) SS BOND : bond 0.01534 ( 1) SS BOND : angle 5.67704 ( 2) hydrogen bonds : bond 0.03292 ( 1428) hydrogen bonds : angle 4.54660 ( 4089) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4616.47 seconds wall clock time: 81 minutes 3.73 seconds (4863.73 seconds total)