Starting phenix.real_space_refine on Mon Aug 25 19:44:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ps1_17842/08_2025/8ps1_17842.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ps1_17842/08_2025/8ps1_17842.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ps1_17842/08_2025/8ps1_17842.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ps1_17842/08_2025/8ps1_17842.map" model { file = "/net/cci-nas-00/data/ceres_data/8ps1_17842/08_2025/8ps1_17842.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ps1_17842/08_2025/8ps1_17842.cif" } resolution = 2.8 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= -0.001 sd= 0.017 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 10 5.49 5 S 108 5.16 5 C 18953 2.51 5 N 4980 2.21 5 O 5736 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 38 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: 29787 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 12379 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1584, 12379 Classifications: {'peptide': 1584} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 61, 'TRANS': 1522} 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: 16010 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2034, 16010 Classifications: {'peptide': 2034} Link IDs: {'PCIS': 1, 'PTRANS': 108, 'TRANS': 1924} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'J8W:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'NAP': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 127 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 127 Unusual residues: {'COA': 1, 'FMN': 1, 'NAP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 6.91, per 1000 atoms: 0.23 Number of scatterers: 29787 At special positions: 0 Unit cell: (185.68, 182.515, 178.295, 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 108 16.00 P 10 15.00 O 5736 8.00 N 4980 7.00 C 18953 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.45 Conformation dependent library (CDL) restraints added in 1.4 seconds Enol-peptide restraints added in 715.3 nanoseconds 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7034 Finding SS restraints... Secondary structure from input PDB file: 173 helices and 27 sheets defined 51.4% alpha, 10.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.59 Creating SS restraints... Processing helix chain 'A' and resid 2 through 22 removed outlier: 3.574A pdb=" N PHE A 22 " --> pdb=" O LEU A 18 " (cutoff:3.500A) Processing helix chain 'A' and resid 28 through 38 Processing helix chain 'A' and resid 51 through 65 Processing helix chain 'A' and resid 65 through 72 Processing helix chain 'A' and resid 84 through 89 Processing helix chain 'A' and resid 329 through 351 Processing helix chain 'A' and resid 355 through 382 removed outlier: 3.576A pdb=" N ASP A 366 " --> pdb=" O LEU A 362 " (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: 4.547A pdb=" N LYS A 410 " --> pdb=" O TRP A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 441 Processing helix chain 'A' and resid 444 through 457 Processing helix chain 'A' and resid 459 through 462 Processing helix chain 'A' and resid 463 through 483 Processing helix chain 'A' and resid 521 through 532 removed outlier: 3.502A pdb=" N TYR A 525 " --> pdb=" O LYS A 521 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLY A 532 " --> pdb=" O GLU A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 608 through 615 removed outlier: 3.602A pdb=" N SER A 615 " --> pdb=" O LYS A 611 " (cutoff:3.500A) Processing helix chain 'A' and resid 652 through 670 Processing helix chain 'A' and resid 687 through 699 removed outlier: 3.914A 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 Processing helix chain 'A' and resid 780 through 784 removed outlier: 3.556A pdb=" N ILE A 784 " --> pdb=" O LEU A 781 " (cutoff:3.500A) Processing helix chain 'A' and resid 785 through 796 Processing helix chain 'A' and resid 796 through 813 removed outlier: 3.536A pdb=" N ARG A 813 " --> pdb=" O GLN A 809 " (cutoff:3.500A) Processing helix chain 'A' and resid 838 through 846 Processing helix chain 'A' and resid 848 through 856 removed outlier: 4.618A pdb=" N HIS A 854 " --> pdb=" O PHE A 850 " (cutoff:3.500A) Processing helix chain 'A' and resid 884 through 889 Processing helix chain 'A' and resid 890 through 892 No H-bonds generated for 'chain 'A' and resid 890 through 892' Processing helix chain 'A' and resid 897 through 907 Processing helix chain 'A' and resid 910 through 918 removed outlier: 3.572A pdb=" N GLN A 918 " --> pdb=" O VAL A 914 " (cutoff:3.500A) Processing helix chain 'A' and resid 935 through 970 removed outlier: 3.626A pdb=" N LEU A 947 " --> pdb=" O LEU A 943 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N THR A 950 " --> pdb=" O GLU A 946 " (cutoff:3.500A) Processing helix chain 'A' and resid 997 through 1002 Processing helix chain 'A' and resid 1006 through 1010 removed outlier: 3.705A 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 1085 through 1100 removed outlier: 4.418A pdb=" N LYS A1090 " --> pdb=" O ASP A1086 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N ALA A1091 " --> pdb=" O LYS A1087 " (cutoff:3.500A) removed outlier: 5.423A pdb=" N THR A1095 " --> pdb=" O ALA A1091 " (cutoff:3.500A) removed outlier: 5.827A pdb=" N SER A1096 " --> pdb=" O LYS A1092 " (cutoff:3.500A) Processing helix chain 'A' and resid 1107 through 1111 Processing helix chain 'A' and resid 1137 through 1149 Processing helix chain 'A' and resid 1194 through 1199 Processing helix chain 'A' and resid 1201 through 1208 Processing helix chain 'A' and resid 1209 through 1225 removed outlier: 3.849A 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 1262 Processing helix chain 'A' and resid 1281 through 1291 Processing helix chain 'A' and resid 1303 through 1305 No H-bonds generated for 'chain 'A' and resid 1303 through 1305' 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 1365 Processing helix chain 'A' and resid 1390 through 1397 Processing helix chain 'A' and resid 1423 through 1430 Processing helix chain 'A' and resid 1440 through 1443 Processing helix chain 'A' and resid 1444 through 1477 removed outlier: 4.262A pdb=" N GLU A1476 " --> pdb=" O LEU A1472 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ILE A1477 " --> pdb=" O GLU A1473 " (cutoff:3.500A) Processing helix chain 'A' and resid 1481 through 1510 removed outlier: 3.566A pdb=" N GLN A1500 " --> pdb=" O GLU A1496 " (cutoff:3.500A) Processing helix chain 'A' and resid 1520 through 1528 removed outlier: 3.617A pdb=" N LEU A1526 " --> pdb=" O LEU A1522 " (cutoff:3.500A) Processing helix chain 'A' and resid 1532 through 1536 Processing helix chain 'A' and resid 1546 through 1564 removed outlier: 3.813A pdb=" N LYS A1551 " --> pdb=" O LYS A1547 " (cutoff:3.500A) Processing helix chain 'A' and resid 1577 through 1582 removed outlier: 3.656A 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: 3.532A pdb=" N GLN A1620 " --> pdb=" O ILE A1617 " (cutoff:3.500A) Processing helix chain 'A' and resid 1658 through 1665 removed outlier: 3.613A pdb=" N TYR A1662 " --> pdb=" O ASP A1659 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N GLY A1663 " --> pdb=" O TYR A1660 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ILE A1665 " --> pdb=" O TYR A1662 " (cutoff:3.500A) Processing helix chain 'A' and resid 1666 through 1694 Processing helix chain 'A' and resid 1710 through 1717 Processing helix chain 'A' and resid 1734 through 1738 Processing helix chain 'A' and resid 1740 through 1745 removed outlier: 4.057A 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 1777 through 1779 No H-bonds generated for 'chain 'A' and resid 1777 through 1779' Processing helix chain 'A' and resid 1783 through 1791 removed outlier: 3.644A pdb=" N ILE A1787 " --> pdb=" O ASN A1783 " (cutoff:3.500A) Processing helix chain 'A' and resid 1792 through 1800 Processing helix chain 'A' and resid 1804 through 1824 Processing helix chain 'A' and resid 1853 through 1863 Processing helix chain 'B' and resid 146 through 159 removed outlier: 3.629A pdb=" N HIS B 152 " --> pdb=" O SER B 148 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LYS B 158 " --> pdb=" O LEU B 154 " (cutoff:3.500A) Processing helix chain 'B' and resid 171 through 176 removed outlier: 3.760A pdb=" N LEU B 175 " --> pdb=" O THR B 171 " (cutoff:3.500A) Processing helix chain 'B' and resid 179 through 194 removed outlier: 3.574A pdb=" N GLN B 183 " --> pdb=" O LYS B 179 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ASN B 184 " --> pdb=" O SER B 180 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LYS B 192 " --> pdb=" O GLY B 188 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 215 removed outlier: 3.611A pdb=" N GLU B 211 " --> pdb=" O GLU B 207 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ASP B 215 " --> pdb=" O GLU B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 236 Processing helix chain 'B' and resid 242 through 253 Processing helix chain 'B' and resid 257 through 271 removed outlier: 3.733A pdb=" N GLY B 263 " --> pdb=" O GLY B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 279 through 299 removed outlier: 3.644A pdb=" N ILE B 297 " --> pdb=" O LYS B 293 " (cutoff:3.500A) Processing helix chain 'G' and resid 23 through 25 No H-bonds generated for 'chain 'G' and resid 23 through 25' Processing helix chain 'G' and resid 26 through 41 removed outlier: 3.721A pdb=" N ALA G 30 " --> pdb=" O SER G 26 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ILE G 40 " --> pdb=" O GLN G 36 " (cutoff:3.500A) Processing helix chain 'G' and resid 56 through 72 removed outlier: 3.619A pdb=" N LEU G 71 " --> pdb=" O TYR G 67 " (cutoff:3.500A) Processing helix chain 'G' and resid 80 through 95 removed outlier: 3.823A pdb=" N LEU G 86 " --> pdb=" O GLN G 82 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N THR G 89 " --> pdb=" O ASN G 85 " (cutoff:3.500A) Processing helix chain 'G' and resid 100 through 111 removed outlier: 3.655A pdb=" N LEU G 104 " --> pdb=" O ASP G 100 " (cutoff:3.500A) Processing helix chain 'G' and resid 115 through 133 Processing helix chain 'G' and resid 143 through 152 Processing helix chain 'G' and resid 169 through 180 removed outlier: 3.754A pdb=" N LEU G 173 " --> pdb=" O TYR G 169 " (cutoff:3.500A) Processing helix chain 'G' and resid 180 through 202 removed outlier: 5.424A pdb=" N ASP G 186 " --> pdb=" O VAL G 182 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N LEU G 187 " --> pdb=" O LEU G 183 " (cutoff:3.500A) Processing helix chain 'G' and resid 214 through 221 Processing helix chain 'G' and resid 227 through 232 Processing helix chain 'G' and resid 233 through 255 Proline residue: G 239 - end of helix Processing helix chain 'G' and resid 259 through 266 Processing helix chain 'G' and resid 275 through 284 removed outlier: 3.871A pdb=" N THR G 279 " --> pdb=" O GLN G 275 " (cutoff:3.500A) Processing helix chain 'G' and resid 291 through 314 removed outlier: 3.952A pdb=" N SER G 295 " --> pdb=" O SER G 291 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N TYR G 311 " --> pdb=" O GLY G 307 " (cutoff:3.500A) Processing helix chain 'G' and resid 320 through 329 Processing helix chain 'G' and resid 345 through 360 removed outlier: 3.503A pdb=" N TYR G 352 " --> pdb=" O GLN G 348 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N SER G 358 " --> pdb=" O ASN G 354 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N HIS G 359 " --> pdb=" O LYS G 355 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LEU G 360 " --> pdb=" O THR G 356 " (cutoff:3.500A) Processing helix chain 'G' and resid 361 through 365 removed outlier: 3.691A pdb=" N LYS G 364 " --> pdb=" O PRO G 361 " (cutoff:3.500A) Processing helix chain 'G' and resid 382 through 395 removed outlier: 3.862A pdb=" N LYS G 395 " --> pdb=" O LEU G 391 " (cutoff:3.500A) Processing helix chain 'G' and resid 408 through 412 Processing helix chain 'G' and resid 429 through 431 No H-bonds generated for 'chain 'G' and resid 429 through 431' Processing helix chain 'G' and resid 432 through 446 removed outlier: 3.776A pdb=" N SER G 436 " --> pdb=" O LEU G 432 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N ASP G 437 " --> pdb=" O VAL G 433 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N LEU G 438 " --> pdb=" O PRO G 434 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N VAL G 444 " --> pdb=" O ASN G 440 " (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 507 through 510 Processing helix chain 'G' and resid 511 through 520 removed outlier: 3.654A pdb=" N LEU G 515 " --> pdb=" O GLY G 511 " (cutoff:3.500A) Processing helix chain 'G' and resid 544 through 549 removed outlier: 4.018A pdb=" N PHE G 548 " --> pdb=" O LYS G 544 " (cutoff:3.500A) Processing helix chain 'G' and resid 560 through 565 Processing helix chain 'G' and resid 581 through 588 removed outlier: 3.575A pdb=" N LEU G 586 " --> pdb=" O LYS G 582 " (cutoff:3.500A) Processing helix chain 'G' and resid 603 through 614 Processing helix chain 'G' and resid 622 through 624 No H-bonds generated for 'chain 'G' and resid 622 through 624' Processing helix chain 'G' and resid 626 through 641 removed outlier: 3.670A pdb=" N GLN G 640 " --> pdb=" O SER G 636 " (cutoff:3.500A) Processing helix chain 'G' and resid 655 through 672 removed outlier: 3.745A 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 698 Processing helix chain 'G' and resid 709 through 723 removed outlier: 3.580A pdb=" N HIS G 723 " --> pdb=" O ILE G 719 " (cutoff:3.500A) Processing helix chain 'G' and resid 747 through 759 removed outlier: 5.215A pdb=" N SER G 755 " --> pdb=" O LEU G 751 " (cutoff:3.500A) removed outlier: 5.119A pdb=" N LYS G 756 " --> pdb=" O GLN G 752 " (cutoff:3.500A) Processing helix chain 'G' and resid 773 through 782 Proline residue: G 779 - end of helix Processing helix chain 'G' and resid 783 through 788 removed outlier: 3.661A pdb=" N SER G 786 " --> pdb=" O GLY G 783 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N LYS G 788 " --> pdb=" O TRP G 785 " (cutoff:3.500A) Processing helix chain 'G' and resid 802 through 806 Processing helix chain 'G' and resid 814 through 823 Processing helix chain 'G' and resid 831 through 837 Processing helix chain 'G' and resid 859 through 872 Processing helix chain 'G' and resid 876 through 899 removed outlier: 4.500A pdb=" N VAL G 881 " --> pdb=" O LYS G 877 " (cutoff:3.500A) Proline residue: G 882 - end of helix removed outlier: 5.769A pdb=" N ASP G 889 " --> pdb=" O GLU G 885 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N TYR G 890 " --> pdb=" O ALA G 886 " (cutoff:3.500A) Processing helix chain 'G' and resid 913 through 917 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 removed outlier: 3.502A pdb=" N ASP G 974 " --> pdb=" O SER G 971 " (cutoff:3.500A) Processing helix chain 'G' and resid 975 through 987 removed outlier: 3.508A pdb=" N ALA G 979 " --> pdb=" O LYS G 975 " (cutoff:3.500A) 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 1034 through 1043 removed outlier: 3.977A pdb=" N SER G1037 " --> pdb=" O LEU G1034 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N LEU G1040 " --> pdb=" O SER G1037 " (cutoff:3.500A) removed outlier: 6.561A 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 1058 through 1062 Processing helix chain 'G' and resid 1069 through 1090 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 1169 through 1174 Processing helix chain 'G' and resid 1189 through 1192 Processing helix chain 'G' and resid 1257 through 1271 Processing helix chain 'G' and resid 1293 through 1305 Processing helix chain 'G' and resid 1308 through 1312 Processing helix chain 'G' and resid 1324 through 1335 removed outlier: 4.082A pdb=" N VAL G1328 " --> pdb=" O ASP G1324 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N ARG G1332 " --> pdb=" O VAL G1328 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N ALA G1333 " --> pdb=" O VAL G1329 " (cutoff:3.500A) Processing helix chain 'G' and resid 1336 through 1339 removed outlier: 3.594A pdb=" N PHE G1339 " --> pdb=" O LYS G1336 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 1336 through 1339' Processing helix chain 'G' and resid 1418 through 1421 Processing helix chain 'G' and resid 1437 through 1447 removed outlier: 3.609A pdb=" N ILE G1441 " --> pdb=" O THR G1437 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LYS G1447 " --> pdb=" O VAL G1443 " (cutoff:3.500A) Processing helix chain 'G' and resid 1514 through 1524 Processing helix chain 'G' and resid 1550 through 1558 removed outlier: 3.667A pdb=" N VAL G1556 " --> pdb=" O PRO G1552 " (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 Processing helix chain 'G' and resid 1601 through 1603 No H-bonds generated for 'chain 'G' and resid 1601 through 1603' Processing helix chain 'G' and resid 1677 through 1684 removed outlier: 3.586A pdb=" N THR G1683 " --> pdb=" O ASP G1679 " (cutoff:3.500A) Processing helix chain 'G' and resid 1684 through 1703 Processing helix chain 'G' and resid 1705 through 1713 Processing helix chain 'G' and resid 1722 through 1733 removed outlier: 3.558A pdb=" N LYS G1727 " --> pdb=" O GLY G1723 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ARG G1728 " --> pdb=" O GLU G1724 " (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 1819 removed outlier: 4.044A 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: 3.685A pdb=" N VAL G1862 " --> pdb=" O ASN G1858 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ALA G1863 " --> pdb=" O PRO G1859 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 1858 through 1863' Processing helix chain 'G' and resid 1867 through 1882 removed outlier: 3.525A pdb=" N LYS G1880 " --> pdb=" O GLU G1876 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N THR G1882 " --> pdb=" O VAL G1878 " (cutoff:3.500A) Processing helix chain 'G' and resid 1903 through 1921 removed outlier: 3.712A pdb=" N LEU G1919 " --> pdb=" O ASN G1915 " (cutoff:3.500A) Processing helix chain 'G' and resid 1926 through 1931 removed outlier: 3.580A pdb=" N LEU G1931 " --> pdb=" O LEU G1927 " (cutoff:3.500A) Processing helix chain 'G' and resid 1934 through 1953 removed outlier: 3.901A pdb=" N GLY G1938 " --> pdb=" O GLU G1934 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N GLU G1942 " --> pdb=" O GLY G1938 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ILE G1943 " --> pdb=" O HIS G1939 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LYS G1950 " --> pdb=" O GLU G1946 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N VAL G1953 " --> pdb=" O LYS G1949 " (cutoff:3.500A) Processing helix chain 'G' and resid 1979 through 1983 removed outlier: 4.389A pdb=" N ASN G1983 " --> pdb=" O TYR G1980 " (cutoff:3.500A) Processing helix chain 'G' and resid 1984 through 1996 removed outlier: 3.583A pdb=" N LYS G1994 " --> pdb=" O SER G1990 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ASN G1995 " --> pdb=" O PHE G1991 " (cutoff:3.500A) Processing helix chain 'G' and resid 1997 through 2001 Processing helix chain 'G' and resid 2002 through 2006 Processing helix chain 'G' and resid 2022 through 2031 Processing helix chain 'G' and resid 2035 through 2044 Processing helix chain 'G' and resid 2044 through 2050 removed outlier: 3.520A pdb=" N TYR G2048 " --> pdb=" O ASN G2044 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 26 through 27 removed outlier: 6.663A pdb=" N VAL G1899 " --> pdb=" O VAL G1889 " (cutoff:3.500A) removed outlier: 5.547A pdb=" N TYR G1891 " --> pdb=" O GLN G1897 " (cutoff:3.500A) removed outlier: 8.127A pdb=" N GLN G1897 " --> pdb=" O TYR G1891 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 77 through 80 removed outlier: 6.718A pdb=" N THR G1662 " --> pdb=" O THR G1803 " (cutoff:3.500A) removed outlier: 8.572A pdb=" N ALA G1805 " --> pdb=" O THR G1662 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N PHE G1664 " --> pdb=" O ALA G1805 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 400 through 402 removed outlier: 6.631A pdb=" N TYR A 677 " --> pdb=" O ALA A 767 " (cutoff:3.500A) removed outlier: 8.149A pdb=" N ILE A 769 " --> pdb=" O TYR A 677 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N LEU A 679 " --> pdb=" O ILE A 769 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N ILE A 768 " --> pdb=" O ILE A 823 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N MET A 923 " --> pdb=" O ARG A 641 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 497 through 503 Processing sheet with id=AA5, first strand: chain 'A' and resid 981 through 982 Processing sheet with id=AA6, first strand: chain 'A' and resid 1019 through 1027 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 1019 through 1027 current: chain 'A' and resid 1326 through 1333 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 1381 through 1389 current: chain 'A' and resid 1572 through 1575 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 1624 through 1625 current: chain 'A' and resid 1650 through 1656 Processing sheet with id=AA7, first strand: chain 'A' and resid 1060 through 1067 removed outlier: 3.781A pdb=" N ARG A1070 " --> pdb=" O LEU A1067 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 1103 through 1105 Processing sheet with id=AA9, first strand: chain 'A' and resid 1119 through 1126 Processing sheet with id=AB1, first strand: chain 'A' and resid 1134 through 1136 Processing sheet with id=AB2, first strand: chain 'A' and resid 1604 through 1605 Processing sheet with id=AB3, first strand: chain 'A' and resid 1723 through 1724 Processing sheet with id=AB4, first strand: chain 'A' and resid 1768 through 1775 Processing sheet with id=AB5, first strand: chain 'A' and resid 1838 through 1840 Processing sheet with id=AB6, first strand: chain 'G' and resid 7 through 13 removed outlier: 3.808A pdb=" N LEU G 16 " --> pdb=" O HIS G 13 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'G' and resid 459 through 460 removed outlier: 8.580A pdb=" N TYR G 460 " --> pdb=" O LYS G 268 " (cutoff:3.500A) removed outlier: 7.563A pdb=" N ALA G 270 " --> pdb=" O TYR G 460 " (cutoff:3.500A) removed outlier: 7.504A pdb=" N LEU G 156 " --> pdb=" O LYS G 268 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N ALA G 270 " --> pdb=" O LEU G 156 " (cutoff:3.500A) removed outlier: 5.935A pdb=" N ALA G 158 " --> pdb=" O ALA G 270 " (cutoff:3.500A) removed outlier: 5.504A pdb=" N GLY G 272 " --> pdb=" O ALA G 158 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N PHE G 160 " --> pdb=" O GLY G 272 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N ILE G 501 " --> pdb=" O ILE G 528 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N VAL G 527 " --> pdb=" O GLY G 542 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'G' and resid 417 through 420 removed outlier: 7.295A pdb=" N ASN G 376 " --> pdb=" O VAL G 371 " (cutoff:3.500A) removed outlier: 5.182A pdb=" N VAL G 371 " --> pdb=" O ASN G 376 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N VAL G 378 " --> pdb=" O SER G 369 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'G' and resid 568 through 571 Processing sheet with id=AC1, first strand: chain 'G' and resid 592 through 594 removed outlier: 3.923A pdb=" N THR G 616 " --> pdb=" O LEU G 592 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N ILE G 617 " --> pdb=" O GLY G 648 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N ASN G 650 " --> pdb=" O ILE G 617 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N LEU G 619 " --> pdb=" O ASN G 650 " (cutoff:3.500A) removed outlier: 8.447A pdb=" N ILE G 652 " --> pdb=" O LEU G 619 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N PHE G 647 " --> pdb=" O PHE G 678 " (cutoff:3.500A) removed outlier: 8.410A pdb=" N THR G 680 " --> pdb=" O PHE G 647 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N ILE G 649 " --> pdb=" O THR G 680 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N GLY G 682 " --> pdb=" O ILE G 649 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N LEU G 651 " --> pdb=" O GLY G 682 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N GLN G 677 " --> pdb=" O TYR G 702 " (cutoff:3.500A) removed outlier: 8.095A pdb=" N GLY G 704 " --> pdb=" O GLN G 677 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N LEU G 679 " --> pdb=" O GLY G 704 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N LEU G 703 " --> pdb=" O ALA G 729 " (cutoff:3.500A) removed outlier: 7.220A pdb=" N GLN G 731 " --> pdb=" O LEU G 703 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N LEU G 705 " --> pdb=" O GLN G 731 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N ILE G 728 " --> pdb=" O MET G 764 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N ILE G 766 " --> pdb=" O ILE G 728 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N LEU G 730 " --> pdb=" O ILE G 766 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLY G 798 " --> pdb=" O LEU G 765 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 739 through 740 removed outlier: 3.539A pdb=" N GLY G 739 " --> pdb=" O HIS G 855 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 906 through 907 Processing sheet with id=AC4, first strand: chain 'G' and resid 931 through 932 Processing sheet with id=AC5, first strand: chain 'G' and resid 1125 through 1128 removed outlier: 6.541A pdb=" N GLU G1199 " --> pdb=" O PRO G1207 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N VAL G1201 " --> pdb=" O LEU G1205 " (cutoff:3.500A) removed outlier: 5.288A pdb=" N LEU G1205 " --> pdb=" O VAL G1201 " (cutoff:3.500A) removed outlier: 5.476A pdb=" N THR G1208 " --> pdb=" O ILE G1224 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N ILE G1218 " --> pdb=" O LEU G1214 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'G' and resid 1158 through 1161 Processing sheet with id=AC7, first strand: chain 'G' and resid 1285 through 1291 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 1285 through 1291 current: chain 'G' and resid 1387 through 1398 removed outlier: 3.821A pdb=" N MET G1404 " --> pdb=" O LEU G1396 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N ARG G1398 " --> pdb=" O PRO G1402 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 1401 through 1406 current: chain 'G' and resid 1482 through 1492 removed outlier: 3.551A pdb=" N VAL G1483 " --> pdb=" O ALA G1508 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N VAL G1491 " --> pdb=" O GLU G1500 " (cutoff:3.500A) removed outlier: 5.775A pdb=" N GLU G1500 " --> pdb=" O VAL G1491 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 1498 through 1508 current: chain 'G' and resid 1635 through 1643 removed outlier: 6.059A pdb=" N LYS G1636 " --> pdb=" O GLU G1656 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N GLU G1656 " --> pdb=" O LYS G1636 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N ILE G1638 " --> pdb=" O GLU G1654 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N GLU G1654 " --> pdb=" O ILE G1638 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N PHE G1640 " --> pdb=" O THR G1652 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N THR G1652 " --> pdb=" O PHE G1640 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N THR G1642 " --> pdb=" O VAL G1650 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 1716 through 1720 Processing sheet with id=AC9, first strand: chain 'G' and resid 1737 through 1741 1386 hydrogen bonds defined for protein. 3861 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: 8.46 Time building geometry restraints manager: 3.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.30: 5068 1.30 - 1.44: 7721 1.44 - 1.58: 17421 1.58 - 1.73: 16 1.73 - 1.87: 190 Bond restraints: 30416 Sorted by residual: bond pdb=" OG J8W G1808 " pdb=" C2 J8W G1808 " ideal model delta sigma weight residual 1.331 1.470 -0.139 2.00e-02 2.50e+03 4.86e+01 bond pdb=" C ILE A 733 " pdb=" O ILE A 733 " ideal model delta sigma weight residual 1.237 1.158 0.079 1.20e-02 6.94e+03 4.29e+01 bond pdb=" C ASN A1690 " pdb=" O ASN A1690 " ideal model delta sigma weight residual 1.236 1.162 0.074 1.15e-02 7.56e+03 4.12e+01 bond pdb=" C ILE A1386 " pdb=" O ILE A1386 " ideal model delta sigma weight residual 1.237 1.168 0.070 1.10e-02 8.26e+03 3.99e+01 bond pdb=" C PRO A1029 " pdb=" O PRO A1029 " ideal model delta sigma weight residual 1.235 1.155 0.080 1.30e-02 5.92e+03 3.79e+01 ... (remaining 30411 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.24: 31109 2.24 - 4.48: 9134 4.48 - 6.72: 925 6.72 - 8.96: 49 8.96 - 11.20: 9 Bond angle restraints: 41226 Sorted by residual: angle pdb=" C SER A1417 " pdb=" N VAL A1418 " pdb=" CA VAL A1418 " ideal model delta sigma weight residual 120.24 125.57 -5.33 6.30e-01 2.52e+00 7.15e+01 angle pdb=" CA ASN A1288 " pdb=" CB ASN A1288 " pdb=" CG ASN A1288 " ideal model delta sigma weight residual 112.60 104.80 7.80 1.00e+00 1.00e+00 6.08e+01 angle pdb=" C ARG G1150 " pdb=" CA ARG G1150 " pdb=" CB ARG G1150 " ideal model delta sigma weight residual 110.79 99.77 11.02 1.66e+00 3.63e-01 4.41e+01 angle pdb=" C THR A1370 " pdb=" CA THR A1370 " pdb=" CB THR A1370 " ideal model delta sigma weight residual 109.80 120.28 -10.48 1.65e+00 3.67e-01 4.04e+01 angle pdb=" C LYS B 179 " pdb=" N SER B 180 " pdb=" CA SER B 180 " ideal model delta sigma weight residual 120.28 129.34 -9.06 1.44e+00 4.82e-01 3.96e+01 ... (remaining 41221 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.74: 16440 17.74 - 35.48: 1550 35.48 - 53.23: 326 53.23 - 70.97: 94 70.97 - 88.71: 52 Dihedral angle restraints: 18462 sinusoidal: 7539 harmonic: 10923 Sorted by residual: dihedral pdb=" CA GLY B 178 " pdb=" C GLY B 178 " pdb=" N LYS B 179 " pdb=" CA LYS B 179 " ideal model delta harmonic sigma weight residual -180.00 -153.10 -26.90 0 5.00e+00 4.00e-02 2.90e+01 dihedral pdb=" CA ASP G 974 " pdb=" C ASP G 974 " pdb=" N LYS G 975 " pdb=" CA LYS G 975 " ideal model delta harmonic sigma weight residual 180.00 155.80 24.20 0 5.00e+00 4.00e-02 2.34e+01 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 -156.12 -23.88 0 5.00e+00 4.00e-02 2.28e+01 ... (remaining 18459 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.085: 2871 0.085 - 0.170: 1497 0.170 - 0.255: 244 0.255 - 0.341: 16 0.341 - 0.426: 1 Chirality restraints: 4629 Sorted by residual: chirality pdb=" CA MET B 237 " pdb=" N MET B 237 " pdb=" C MET B 237 " pdb=" CB MET B 237 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.43 2.00e-01 2.50e+01 4.53e+00 chirality pdb=" CA ILE G1751 " pdb=" N ILE G1751 " pdb=" C ILE G1751 " pdb=" CB ILE G1751 " both_signs ideal model delta sigma weight residual False 2.43 2.74 -0.31 2.00e-01 2.50e+01 2.43e+00 chirality pdb=" CA ILE G1053 " pdb=" N ILE G1053 " pdb=" C ILE G1053 " pdb=" CB ILE G1053 " both_signs ideal model delta sigma weight residual False 2.43 2.72 -0.29 2.00e-01 2.50e+01 2.09e+00 ... (remaining 4626 not shown) Planarity restraints: 5302 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' FMN G2101 " 0.028 2.00e-02 2.50e+03 3.92e-02 6.93e+01 pdb=" C10 FMN G2101 " 0.010 2.00e-02 2.50e+03 pdb=" C2 FMN G2101 " -0.044 2.00e-02 2.50e+03 pdb=" C4 FMN G2101 " -0.007 2.00e-02 2.50e+03 pdb=" C4A FMN G2101 " 0.025 2.00e-02 2.50e+03 pdb=" C5A FMN G2101 " 0.062 2.00e-02 2.50e+03 pdb=" C6 FMN G2101 " 0.021 2.00e-02 2.50e+03 pdb=" C7 FMN G2101 " -0.020 2.00e-02 2.50e+03 pdb=" C7M FMN G2101 " -0.067 2.00e-02 2.50e+03 pdb=" C8 FMN G2101 " -0.014 2.00e-02 2.50e+03 pdb=" C8M FMN G2101 " -0.059 2.00e-02 2.50e+03 pdb=" C9 FMN G2101 " 0.018 2.00e-02 2.50e+03 pdb=" C9A FMN G2101 " 0.057 2.00e-02 2.50e+03 pdb=" N1 FMN G2101 " -0.013 2.00e-02 2.50e+03 pdb=" N10 FMN G2101 " 0.036 2.00e-02 2.50e+03 pdb=" N3 FMN G2101 " -0.051 2.00e-02 2.50e+03 pdb=" N5 FMN G2101 " 0.051 2.00e-02 2.50e+03 pdb=" O2 FMN G2101 " -0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 753 " 0.062 2.00e-02 2.50e+03 3.57e-02 2.55e+01 pdb=" CG TYR A 753 " -0.045 2.00e-02 2.50e+03 pdb=" CD1 TYR A 753 " -0.018 2.00e-02 2.50e+03 pdb=" CD2 TYR A 753 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR A 753 " -0.016 2.00e-02 2.50e+03 pdb=" CE2 TYR A 753 " -0.036 2.00e-02 2.50e+03 pdb=" CZ TYR A 753 " 0.005 2.00e-02 2.50e+03 pdb=" OH TYR A 753 " 0.049 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A1286 " 0.062 2.00e-02 2.50e+03 3.08e-02 2.37e+01 pdb=" CG TRP A1286 " -0.016 2.00e-02 2.50e+03 pdb=" CD1 TRP A1286 " -0.015 2.00e-02 2.50e+03 pdb=" CD2 TRP A1286 " -0.030 2.00e-02 2.50e+03 pdb=" NE1 TRP A1286 " -0.013 2.00e-02 2.50e+03 pdb=" CE2 TRP A1286 " 0.005 2.00e-02 2.50e+03 pdb=" CE3 TRP A1286 " -0.046 2.00e-02 2.50e+03 pdb=" CZ2 TRP A1286 " 0.023 2.00e-02 2.50e+03 pdb=" CZ3 TRP A1286 " -0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP A1286 " 0.037 2.00e-02 2.50e+03 ... (remaining 5299 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 4461 2.80 - 3.33: 29676 3.33 - 3.85: 46745 3.85 - 4.38: 62783 4.38 - 4.90: 100573 Nonbonded interactions: 244238 Sorted by model distance: nonbonded pdb=" O SER A1293 " pdb=" OG SER A1293 " model vdw 2.279 3.040 nonbonded pdb=" O VAL G1048 " pdb=" OG1 THR G1051 " model vdw 2.281 3.040 nonbonded pdb=" OH TYR G 615 " pdb=" OD1 ASP G1075 " model vdw 2.329 3.040 nonbonded pdb=" OH TYR G 754 " pdb=" O PRO G 795 " model vdw 2.338 3.040 nonbonded pdb=" OH TYR A1694 " pdb=" OD2 ASP G1001 " model vdw 2.338 3.040 ... (remaining 244233 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.500 Check model and map are aligned: 0.080 Set scattering table: 0.080 Process input model: 30.650 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.050 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:6.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8679 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 0.139 30416 Z= 1.043 Angle : 1.923 11.196 41226 Z= 1.388 Chirality : 0.092 0.426 4629 Planarity : 0.007 0.047 5302 Dihedral : 15.626 88.711 11428 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 1.98 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.74 % Favored : 94.02 % Rotamer: Outliers : 1.08 % Allowed : 5.42 % Favored : 93.50 % Cbeta Deviations : 0.09 % 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: -3.45 (0.11), residues: 3764 helix: -2.98 (0.09), residues: 1653 sheet: -1.60 (0.20), residues: 508 loop : -1.49 (0.14), residues: 1603 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.002 ARG A1036 TYR 0.062 0.008 TYR A 753 PHE 0.067 0.008 PHE G 799 TRP 0.062 0.011 TRP A1286 HIS 0.015 0.004 HIS A1358 Details of bonding type rmsd covalent geometry : bond 0.01423 (30416) covalent geometry : angle 1.92308 (41226) hydrogen bonds : bond 0.23276 ( 1386) hydrogen bonds : angle 9.16976 ( 3861) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 3248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 170 time to evaluate : 1.214 Fit side-chains REVERT: A 59 ARG cc_start: 0.8437 (mtp180) cc_final: 0.8161 (mtp-110) REVERT: A 413 LEU cc_start: 0.9271 (OUTLIER) cc_final: 0.9055 (tm) REVERT: A 431 GLU cc_start: 0.8757 (tp30) cc_final: 0.8490 (tp30) REVERT: A 518 LYS cc_start: 0.8139 (pttt) cc_final: 0.7486 (tptp) REVERT: A 1066 ASN cc_start: 0.7206 (t0) cc_final: 0.6883 (t0) REVERT: A 1160 THR cc_start: 0.7844 (p) cc_final: 0.7218 (t) REVERT: A 1234 MET cc_start: 0.8862 (mtm) cc_final: 0.8583 (mtm) REVERT: A 1332 TYR cc_start: 0.9199 (OUTLIER) cc_final: 0.8176 (p90) REVERT: A 1365 MET cc_start: 0.8805 (mtt) cc_final: 0.8604 (mtt) REVERT: A 1561 MET cc_start: 0.9009 (mmp) cc_final: 0.8729 (mmp) REVERT: A 1838 GLU cc_start: 0.7958 (tt0) cc_final: 0.7271 (tm-30) REVERT: A 1850 GLU cc_start: 0.6499 (OUTLIER) cc_final: 0.5954 (tm-30) REVERT: A 1868 LYS cc_start: 0.7425 (tptm) cc_final: 0.6977 (pttt) REVERT: G 91 PHE cc_start: 0.8502 (t80) cc_final: 0.8093 (t80) REVERT: G 138 ASP cc_start: 0.7761 (p0) cc_final: 0.7264 (t0) REVERT: G 442 ASP cc_start: 0.8336 (m-30) cc_final: 0.8084 (m-30) REVERT: G 597 MET cc_start: 0.8998 (mtm) cc_final: 0.8593 (mtm) REVERT: G 630 MET cc_start: 0.8842 (tpp) cc_final: 0.8400 (ttm) REVERT: G 764 MET cc_start: 0.9054 (mtm) cc_final: 0.8831 (mtm) REVERT: G 850 MET cc_start: 0.8078 (mmt) cc_final: 0.7771 (mmm) REVERT: G 877 LYS cc_start: 0.8071 (mmpt) cc_final: 0.7714 (tmmt) REVERT: G 1255 MET cc_start: 0.8869 (mmm) cc_final: 0.8635 (mmm) outliers start: 35 outliers final: 13 residues processed: 205 average time/residue: 0.8053 time to fit residues: 190.8710 Evaluate side-chains 128 residues out of total 3248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 112 time to evaluate : 1.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 855 SER Chi-restraints excluded: chain A residue 940 THR Chi-restraints excluded: chain A residue 967 VAL Chi-restraints excluded: chain A residue 1164 SER Chi-restraints excluded: chain A residue 1284 SER Chi-restraints excluded: chain A residue 1332 TYR Chi-restraints excluded: chain A residue 1850 GLU Chi-restraints excluded: chain B residue 230 SER Chi-restraints excluded: chain G residue 318 SER Chi-restraints excluded: chain G residue 340 SER Chi-restraints excluded: chain G residue 599 PRO Chi-restraints excluded: chain G residue 1373 SER Chi-restraints excluded: chain G residue 1381 VAL Chi-restraints excluded: chain G residue 1586 SER Chi-restraints excluded: chain G residue 1650 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 197 optimal weight: 5.9990 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 10.0000 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 7.9990 chunk 244 optimal weight: 7.9990 chunk 183 optimal weight: 10.0000 chunk 298 optimal weight: 5.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 GLN A 32 GLN A 344 GLN A 356 ASN A 618 ASN A 743 GLN A1380 GLN A1444 ASN B 292 GLN G 38 ASN G 85 ASN G 102 HIS G 155 GLN G 221 ASN G 245 GLN G 365 GLN G 440 ASN G 718 ASN G 747 HIS G1217 ASN G1241 ASN G1341 ASN G1355 ASN G1424 GLN G1451 GLN G1523 ASN G1697 HIS G1890 ASN G1895 ASN G1912 ASN G1983 ASN G2013 ASN G2020 GLN Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.064191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.048046 restraints weight = 90241.459| |-----------------------------------------------------------------------------| r_work (start): 0.2863 rms_B_bonded: 1.87 r_work: 0.2752 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2643 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2643 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8575 moved from start: 0.1555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 30416 Z= 0.164 Angle : 0.576 8.869 41226 Z= 0.306 Chirality : 0.044 0.187 4629 Planarity : 0.004 0.041 5302 Dihedral : 8.060 79.148 4254 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 1.11 % Allowed : 8.38 % Favored : 90.51 % 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: -0.52 (0.13), residues: 3764 helix: 0.09 (0.12), residues: 1677 sheet: -1.01 (0.21), residues: 522 loop : -0.39 (0.16), residues: 1565 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG G1849 TYR 0.022 0.002 TYR A 417 PHE 0.024 0.002 PHE A 35 TRP 0.018 0.002 TRP G 832 HIS 0.008 0.001 HIS A1689 Details of bonding type rmsd covalent geometry : bond 0.00375 (30416) covalent geometry : angle 0.57575 (41226) hydrogen bonds : bond 0.04662 ( 1386) hydrogen bonds : angle 5.07549 ( 3861) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 3248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 119 time to evaluate : 1.315 Fit side-chains REVERT: A 75 HIS cc_start: 0.7911 (OUTLIER) cc_final: 0.7243 (p90) REVERT: A 431 GLU cc_start: 0.8364 (tp30) cc_final: 0.8151 (mm-30) REVERT: A 518 LYS cc_start: 0.7876 (pttt) cc_final: 0.7566 (tptp) REVERT: A 1066 ASN cc_start: 0.6819 (t0) cc_final: 0.6363 (t0) REVERT: A 1127 VAL cc_start: 0.8304 (t) cc_final: 0.7968 (p) REVERT: A 1160 THR cc_start: 0.7892 (p) cc_final: 0.7349 (t) REVERT: A 1234 MET cc_start: 0.9040 (mtm) cc_final: 0.8689 (mtm) REVERT: A 1289 MET cc_start: 0.9201 (mtp) cc_final: 0.8981 (mtp) REVERT: A 1786 PHE cc_start: 0.7661 (t80) cc_final: 0.7343 (t80) REVERT: A 1835 LYS cc_start: 0.7168 (OUTLIER) cc_final: 0.6630 (tmtt) REVERT: A 1838 GLU cc_start: 0.7676 (tt0) cc_final: 0.7015 (tm-30) REVERT: A 1850 GLU cc_start: 0.6432 (OUTLIER) cc_final: 0.5979 (tm-30) REVERT: G 38 ASN cc_start: 0.7703 (OUTLIER) cc_final: 0.7454 (m110) REVERT: G 442 ASP cc_start: 0.7545 (m-30) cc_final: 0.7265 (m-30) REVERT: G 597 MET cc_start: 0.9164 (mtm) cc_final: 0.8731 (mtm) REVERT: G 850 MET cc_start: 0.7928 (mmt) cc_final: 0.7681 (mmm) REVERT: G 1631 MET cc_start: 0.9046 (OUTLIER) cc_final: 0.8738 (mmm) REVERT: G 2036 GLU cc_start: 0.8032 (OUTLIER) cc_final: 0.7817 (mp0) outliers start: 36 outliers final: 16 residues processed: 150 average time/residue: 0.8136 time to fit residues: 142.5548 Evaluate side-chains 132 residues out of total 3248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 110 time to evaluate : 1.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 HIS Chi-restraints excluded: chain A residue 940 THR Chi-restraints excluded: chain A residue 1164 SER Chi-restraints excluded: chain A residue 1333 ASP Chi-restraints excluded: chain A residue 1773 VAL Chi-restraints excluded: chain A residue 1808 SER Chi-restraints excluded: chain A residue 1835 LYS Chi-restraints excluded: chain A residue 1850 GLU Chi-restraints excluded: chain G residue 38 ASN Chi-restraints excluded: chain G residue 86 LEU Chi-restraints excluded: chain G residue 318 SER Chi-restraints excluded: chain G residue 784 GLU Chi-restraints excluded: chain G residue 1380 SER Chi-restraints excluded: chain G residue 1381 VAL Chi-restraints excluded: chain G residue 1417 THR Chi-restraints excluded: chain G residue 1472 VAL Chi-restraints excluded: chain G residue 1631 MET Chi-restraints excluded: chain G residue 1650 VAL Chi-restraints excluded: chain G residue 1772 SER Chi-restraints excluded: chain G residue 1925 ILE Chi-restraints excluded: chain G residue 1939 HIS Chi-restraints excluded: chain G residue 2036 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 168 optimal weight: 4.9990 chunk 351 optimal weight: 4.9990 chunk 345 optimal weight: 6.9990 chunk 46 optimal weight: 7.9990 chunk 78 optimal weight: 9.9990 chunk 182 optimal weight: 6.9990 chunk 314 optimal weight: 5.9990 chunk 328 optimal weight: 1.9990 chunk 96 optimal weight: 10.0000 chunk 205 optimal weight: 9.9990 chunk 212 optimal weight: 8.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 527 GLN A1794 GLN G 500 HIS G1564 HIS G2013 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.064685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.048663 restraints weight = 90298.216| |-----------------------------------------------------------------------------| r_work (start): 0.2873 rms_B_bonded: 1.87 r_work: 0.2753 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2643 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2643 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8576 moved from start: 0.1861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 30416 Z= 0.192 Angle : 0.562 10.743 41226 Z= 0.294 Chirality : 0.045 0.174 4629 Planarity : 0.004 0.051 5302 Dihedral : 7.707 77.848 4240 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 1.20 % Allowed : 9.92 % Favored : 88.88 % 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: 0.30 (0.14), residues: 3764 helix: 0.99 (0.13), residues: 1678 sheet: -0.83 (0.22), residues: 516 loop : -0.15 (0.16), residues: 1570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 632 TYR 0.022 0.002 TYR G 624 PHE 0.025 0.002 PHE A 35 TRP 0.013 0.002 TRP G 832 HIS 0.007 0.001 HIS A1689 Details of bonding type rmsd covalent geometry : bond 0.00444 (30416) covalent geometry : angle 0.56197 (41226) hydrogen bonds : bond 0.04549 ( 1386) hydrogen bonds : angle 4.81495 ( 3861) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 3248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 113 time to evaluate : 1.236 Fit side-chains REVERT: A 75 HIS cc_start: 0.7945 (OUTLIER) cc_final: 0.7299 (p90) REVERT: A 518 LYS cc_start: 0.7875 (pttt) cc_final: 0.7536 (tptp) REVERT: A 1066 ASN cc_start: 0.6892 (t0) cc_final: 0.6411 (t0) REVERT: A 1127 VAL cc_start: 0.8333 (t) cc_final: 0.8084 (p) REVERT: A 1160 THR cc_start: 0.7838 (p) cc_final: 0.7386 (t) REVERT: A 1234 MET cc_start: 0.9045 (mtm) cc_final: 0.8739 (mtm) REVERT: A 1850 GLU cc_start: 0.6303 (OUTLIER) cc_final: 0.6103 (tm-30) REVERT: G 442 ASP cc_start: 0.7373 (m-30) cc_final: 0.7054 (m-30) REVERT: G 597 MET cc_start: 0.9127 (mtm) cc_final: 0.8756 (mtm) REVERT: G 2036 GLU cc_start: 0.8136 (OUTLIER) cc_final: 0.7915 (mp0) outliers start: 39 outliers final: 21 residues processed: 147 average time/residue: 0.7927 time to fit residues: 137.0455 Evaluate side-chains 129 residues out of total 3248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 105 time to evaluate : 1.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 HIS Chi-restraints excluded: chain A residue 412 SER Chi-restraints excluded: chain A residue 940 THR Chi-restraints excluded: chain A residue 1001 VAL Chi-restraints excluded: chain A residue 1164 SER Chi-restraints excluded: chain A residue 1260 MET Chi-restraints excluded: chain A residue 1333 ASP Chi-restraints excluded: chain A residue 1773 VAL Chi-restraints excluded: chain A residue 1808 SER Chi-restraints excluded: chain A residue 1836 ASP Chi-restraints excluded: chain A residue 1850 GLU Chi-restraints excluded: chain G residue 86 LEU Chi-restraints excluded: chain G residue 318 SER Chi-restraints excluded: chain G residue 784 GLU Chi-restraints excluded: chain G residue 981 GLU Chi-restraints excluded: chain G residue 1380 SER Chi-restraints excluded: chain G residue 1381 VAL Chi-restraints excluded: chain G residue 1417 THR Chi-restraints excluded: chain G residue 1472 VAL Chi-restraints excluded: chain G residue 1650 VAL Chi-restraints excluded: chain G residue 1772 SER Chi-restraints excluded: chain G residue 1925 ILE Chi-restraints excluded: chain G residue 1939 HIS Chi-restraints excluded: chain G residue 2036 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 274 optimal weight: 7.9990 chunk 85 optimal weight: 3.9990 chunk 99 optimal weight: 8.9990 chunk 261 optimal weight: 2.9990 chunk 336 optimal weight: 8.9990 chunk 301 optimal weight: 0.4980 chunk 218 optimal weight: 10.0000 chunk 294 optimal weight: 6.9990 chunk 58 optimal weight: 5.9990 chunk 65 optimal weight: 9.9990 chunk 182 optimal weight: 9.9990 overall best weight: 4.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 341 GLN A1063 HIS A1794 GLN G 752 GLN ** G2013 ASN ** 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 = 0.3340 r_free = 0.3340 target = 0.065225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.049437 restraints weight = 89634.108| |-----------------------------------------------------------------------------| r_work (start): 0.2897 rms_B_bonded: 1.83 r_work: 0.2778 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2666 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2666 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.2049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 30416 Z= 0.163 Angle : 0.524 10.254 41226 Z= 0.274 Chirality : 0.043 0.160 4629 Planarity : 0.004 0.039 5302 Dihedral : 7.422 74.177 4240 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.42 % Allowed : 10.44 % Favored : 88.14 % 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: 0.64 (0.14), residues: 3764 helix: 1.34 (0.13), residues: 1680 sheet: -0.73 (0.22), residues: 528 loop : -0.03 (0.16), residues: 1556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G1849 TYR 0.019 0.002 TYR G 624 PHE 0.023 0.002 PHE A 35 TRP 0.011 0.001 TRP G 832 HIS 0.007 0.001 HIS A1689 Details of bonding type rmsd covalent geometry : bond 0.00380 (30416) covalent geometry : angle 0.52419 (41226) hydrogen bonds : bond 0.04187 ( 1386) hydrogen bonds : angle 4.66999 ( 3861) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 3248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 108 time to evaluate : 1.353 Fit side-chains REVERT: A 75 HIS cc_start: 0.7914 (OUTLIER) cc_final: 0.7227 (p90) REVERT: A 518 LYS cc_start: 0.7895 (pttt) cc_final: 0.7536 (tptp) REVERT: A 1066 ASN cc_start: 0.6973 (t0) cc_final: 0.6511 (t0) REVERT: A 1127 VAL cc_start: 0.8337 (t) cc_final: 0.8056 (p) REVERT: A 1160 THR cc_start: 0.7790 (p) cc_final: 0.7248 (t) REVERT: A 1234 MET cc_start: 0.9015 (mtm) cc_final: 0.8747 (mtm) REVERT: G 442 ASP cc_start: 0.7323 (m-30) cc_final: 0.6992 (m-30) REVERT: G 597 MET cc_start: 0.9107 (mtm) cc_final: 0.8816 (mtm) REVERT: G 2036 GLU cc_start: 0.8106 (OUTLIER) cc_final: 0.7887 (mp0) outliers start: 46 outliers final: 26 residues processed: 145 average time/residue: 0.8388 time to fit residues: 142.1642 Evaluate side-chains 135 residues out of total 3248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 107 time to evaluate : 1.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 HIS Chi-restraints excluded: chain A residue 412 SER Chi-restraints excluded: chain A residue 509 ILE Chi-restraints excluded: chain A residue 940 THR Chi-restraints excluded: chain A residue 1001 VAL Chi-restraints excluded: chain A residue 1164 SER Chi-restraints excluded: chain A residue 1333 ASP Chi-restraints excluded: chain A residue 1773 VAL Chi-restraints excluded: chain A residue 1808 SER Chi-restraints excluded: chain A residue 1836 ASP Chi-restraints excluded: chain G residue 86 LEU Chi-restraints excluded: chain G residue 115 THR Chi-restraints excluded: chain G residue 201 THR Chi-restraints excluded: chain G residue 340 SER Chi-restraints excluded: chain G residue 777 THR Chi-restraints excluded: chain G residue 784 GLU Chi-restraints excluded: chain G residue 981 GLU Chi-restraints excluded: chain G residue 1380 SER Chi-restraints excluded: chain G residue 1381 VAL Chi-restraints excluded: chain G residue 1417 THR Chi-restraints excluded: chain G residue 1472 VAL Chi-restraints excluded: chain G residue 1650 VAL Chi-restraints excluded: chain G residue 1736 MET Chi-restraints excluded: chain G residue 1772 SER Chi-restraints excluded: chain G residue 1925 ILE Chi-restraints excluded: chain G residue 1939 HIS Chi-restraints excluded: chain G residue 1959 LYS Chi-restraints excluded: chain G residue 2036 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 238 optimal weight: 10.0000 chunk 304 optimal weight: 9.9990 chunk 255 optimal weight: 0.4980 chunk 262 optimal weight: 0.9980 chunk 136 optimal weight: 0.9980 chunk 263 optimal weight: 6.9990 chunk 157 optimal weight: 10.0000 chunk 148 optimal weight: 5.9990 chunk 223 optimal weight: 9.9990 chunk 298 optimal weight: 5.9990 chunk 45 optimal weight: 10.0000 overall best weight: 2.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1794 GLN ** B 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G2013 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.065615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.049855 restraints weight = 90157.799| |-----------------------------------------------------------------------------| r_work (start): 0.2910 rms_B_bonded: 1.85 r_work: 0.2790 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2677 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 moved from start: 0.2141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 30416 Z= 0.130 Angle : 0.493 9.458 41226 Z= 0.257 Chirality : 0.042 0.159 4629 Planarity : 0.004 0.061 5302 Dihedral : 7.074 71.891 4236 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 1.54 % Allowed : 10.90 % Favored : 87.56 % 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: 0.89 (0.14), residues: 3764 helix: 1.59 (0.13), residues: 1678 sheet: -0.64 (0.22), residues: 532 loop : 0.06 (0.16), residues: 1554 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG A 632 TYR 0.016 0.001 TYR G 624 PHE 0.024 0.001 PHE A 35 TRP 0.011 0.001 TRP G 865 HIS 0.006 0.001 HIS A1689 Details of bonding type rmsd covalent geometry : bond 0.00297 (30416) covalent geometry : angle 0.49285 (41226) hydrogen bonds : bond 0.03885 ( 1386) hydrogen bonds : angle 4.53447 ( 3861) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 3248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 111 time to evaluate : 0.874 Fit side-chains REVERT: A 74 LEU cc_start: 0.8849 (OUTLIER) cc_final: 0.8613 (pp) REVERT: A 75 HIS cc_start: 0.7935 (OUTLIER) cc_final: 0.7221 (p90) REVERT: A 518 LYS cc_start: 0.7979 (pttt) cc_final: 0.7572 (tptp) REVERT: A 1066 ASN cc_start: 0.7032 (t0) cc_final: 0.6634 (t0) REVERT: A 1127 VAL cc_start: 0.8340 (t) cc_final: 0.8063 (p) REVERT: A 1160 THR cc_start: 0.7692 (p) cc_final: 0.7212 (t) REVERT: G 11 LEU cc_start: 0.7494 (OUTLIER) cc_final: 0.7210 (pt) REVERT: G 442 ASP cc_start: 0.7276 (m-30) cc_final: 0.6978 (m-30) REVERT: G 481 ASP cc_start: 0.8595 (OUTLIER) cc_final: 0.8292 (t70) REVERT: G 1064 LYS cc_start: 0.8172 (OUTLIER) cc_final: 0.7455 (mmmm) REVERT: G 1881 ARG cc_start: 0.7839 (OUTLIER) cc_final: 0.7094 (tpm170) REVERT: G 2036 GLU cc_start: 0.8110 (OUTLIER) cc_final: 0.7887 (mp0) outliers start: 50 outliers final: 25 residues processed: 154 average time/residue: 0.6912 time to fit residues: 125.7293 Evaluate side-chains 140 residues out of total 3248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 108 time to evaluate : 1.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 THR Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 75 HIS Chi-restraints excluded: chain A residue 412 SER Chi-restraints excluded: chain A residue 940 THR Chi-restraints excluded: chain A residue 1001 VAL Chi-restraints excluded: chain A residue 1164 SER Chi-restraints excluded: chain A residue 1254 VAL Chi-restraints excluded: chain A residue 1333 ASP Chi-restraints excluded: chain A residue 1773 VAL Chi-restraints excluded: chain A residue 1808 SER Chi-restraints excluded: chain A residue 1836 ASP Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 86 LEU Chi-restraints excluded: chain G residue 115 THR Chi-restraints excluded: chain G residue 340 SER Chi-restraints excluded: chain G residue 481 ASP Chi-restraints excluded: chain G residue 777 THR Chi-restraints excluded: chain G residue 784 GLU Chi-restraints excluded: chain G residue 981 GLU Chi-restraints excluded: chain G residue 1064 LYS Chi-restraints excluded: chain G residue 1380 SER Chi-restraints excluded: chain G residue 1381 VAL Chi-restraints excluded: chain G residue 1392 VAL Chi-restraints excluded: chain G residue 1417 THR Chi-restraints excluded: chain G residue 1650 VAL Chi-restraints excluded: chain G residue 1708 ASP Chi-restraints excluded: chain G residue 1736 MET Chi-restraints excluded: chain G residue 1881 ARG Chi-restraints excluded: chain G residue 1925 ILE Chi-restraints excluded: chain G residue 1939 HIS Chi-restraints excluded: chain G residue 2036 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 66 optimal weight: 5.9990 chunk 189 optimal weight: 6.9990 chunk 207 optimal weight: 8.9990 chunk 333 optimal weight: 7.9990 chunk 180 optimal weight: 4.9990 chunk 94 optimal weight: 0.9990 chunk 16 optimal weight: 10.0000 chunk 34 optimal weight: 8.9990 chunk 261 optimal weight: 8.9990 chunk 89 optimal weight: 0.7980 chunk 262 optimal weight: 7.9990 overall best weight: 3.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1794 GLN ** B 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G1421 ASN G1995 ASN ** G2013 ASN ** 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 = 0.3344 r_free = 0.3344 target = 0.065419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.049578 restraints weight = 89828.123| |-----------------------------------------------------------------------------| r_work (start): 0.2902 rms_B_bonded: 1.83 r_work: 0.2785 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2673 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.2673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 moved from start: 0.2200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 30416 Z= 0.160 Angle : 0.512 10.011 41226 Z= 0.266 Chirality : 0.043 0.168 4629 Planarity : 0.004 0.043 5302 Dihedral : 7.013 70.453 4236 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.66 % Allowed : 11.43 % Favored : 86.91 % 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: 0.90 (0.14), residues: 3764 helix: 1.58 (0.13), residues: 1677 sheet: -0.60 (0.22), residues: 529 loop : 0.08 (0.16), residues: 1558 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1070 TYR 0.017 0.001 TYR G 624 PHE 0.022 0.002 PHE A 35 TRP 0.011 0.001 TRP G 865 HIS 0.006 0.001 HIS A1689 Details of bonding type rmsd covalent geometry : bond 0.00370 (30416) covalent geometry : angle 0.51206 (41226) hydrogen bonds : bond 0.04078 ( 1386) hydrogen bonds : angle 4.57094 ( 3861) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 3248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 108 time to evaluate : 1.197 Fit side-chains REVERT: A 75 HIS cc_start: 0.7912 (OUTLIER) cc_final: 0.7157 (p90) REVERT: A 518 LYS cc_start: 0.7970 (pttt) cc_final: 0.7559 (tptp) REVERT: A 1066 ASN cc_start: 0.7037 (t0) cc_final: 0.6642 (t0) REVERT: A 1070 ARG cc_start: 0.6904 (ttm110) cc_final: 0.6629 (mtp85) REVERT: A 1127 VAL cc_start: 0.8352 (t) cc_final: 0.8074 (p) REVERT: A 1160 THR cc_start: 0.7678 (p) cc_final: 0.7270 (t) REVERT: G 11 LEU cc_start: 0.7523 (OUTLIER) cc_final: 0.7249 (pt) REVERT: G 481 ASP cc_start: 0.8587 (OUTLIER) cc_final: 0.8268 (t70) REVERT: G 1064 LYS cc_start: 0.8163 (OUTLIER) cc_final: 0.7441 (mmmm) REVERT: G 1881 ARG cc_start: 0.7861 (OUTLIER) cc_final: 0.7131 (tpm170) REVERT: G 2036 GLU cc_start: 0.8127 (OUTLIER) cc_final: 0.7923 (mp0) REVERT: G 2047 LYS cc_start: 0.8282 (mttm) cc_final: 0.7763 (tmmm) outliers start: 54 outliers final: 34 residues processed: 157 average time/residue: 0.7291 time to fit residues: 135.4689 Evaluate side-chains 146 residues out of total 3248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 106 time to evaluate : 1.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 THR Chi-restraints excluded: chain A residue 75 HIS Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 412 SER Chi-restraints excluded: chain A residue 509 ILE Chi-restraints excluded: chain A residue 744 ASP Chi-restraints excluded: chain A residue 940 THR Chi-restraints excluded: chain A residue 1001 VAL Chi-restraints excluded: chain A residue 1254 VAL Chi-restraints excluded: chain A residue 1284 SER Chi-restraints excluded: chain A residue 1333 ASP Chi-restraints excluded: chain A residue 1435 SER Chi-restraints excluded: chain A residue 1773 VAL Chi-restraints excluded: chain A residue 1808 SER Chi-restraints excluded: chain A residue 1836 ASP Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 86 LEU Chi-restraints excluded: chain G residue 115 THR Chi-restraints excluded: chain G residue 201 THR Chi-restraints excluded: chain G residue 340 SER Chi-restraints excluded: chain G residue 481 ASP Chi-restraints excluded: chain G residue 777 THR Chi-restraints excluded: chain G residue 981 GLU Chi-restraints excluded: chain G residue 1064 LYS Chi-restraints excluded: chain G residue 1380 SER Chi-restraints excluded: chain G residue 1381 VAL Chi-restraints excluded: chain G residue 1392 VAL Chi-restraints excluded: chain G residue 1417 THR Chi-restraints excluded: chain G residue 1472 VAL Chi-restraints excluded: chain G residue 1479 ILE Chi-restraints excluded: chain G residue 1565 VAL Chi-restraints excluded: chain G residue 1650 VAL Chi-restraints excluded: chain G residue 1708 ASP Chi-restraints excluded: chain G residue 1736 MET Chi-restraints excluded: chain G residue 1772 SER Chi-restraints excluded: chain G residue 1881 ARG Chi-restraints excluded: chain G residue 1925 ILE Chi-restraints excluded: chain G residue 1939 HIS Chi-restraints excluded: chain G residue 1959 LYS Chi-restraints excluded: chain G residue 2036 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 252 optimal weight: 6.9990 chunk 21 optimal weight: 6.9990 chunk 175 optimal weight: 10.0000 chunk 310 optimal weight: 6.9990 chunk 90 optimal weight: 4.9990 chunk 57 optimal weight: 20.0000 chunk 84 optimal weight: 0.9990 chunk 189 optimal weight: 8.9990 chunk 42 optimal weight: 8.9990 chunk 362 optimal weight: 20.0000 chunk 118 optimal weight: 4.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 63 ASN A1794 GLN ** B 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G1055 HIS ** G2013 ASN ** 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 = 0.3338 r_free = 0.3338 target = 0.065173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.049308 restraints weight = 89664.603| |-----------------------------------------------------------------------------| r_work (start): 0.2895 rms_B_bonded: 1.83 r_work: 0.2777 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2666 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.2666 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 moved from start: 0.2257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 30416 Z= 0.189 Angle : 0.538 10.295 41226 Z= 0.280 Chirality : 0.044 0.168 4629 Planarity : 0.004 0.069 5302 Dihedral : 7.055 68.955 4235 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.69 % Allowed : 11.86 % Favored : 86.45 % 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: 0.84 (0.14), residues: 3764 helix: 1.53 (0.13), residues: 1672 sheet: -0.63 (0.22), residues: 530 loop : 0.05 (0.16), residues: 1562 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG A 632 TYR 0.019 0.002 TYR G 624 PHE 0.024 0.002 PHE A1376 TRP 0.011 0.002 TRP G1596 HIS 0.006 0.001 HIS A1689 Details of bonding type rmsd covalent geometry : bond 0.00440 (30416) covalent geometry : angle 0.53829 (41226) hydrogen bonds : bond 0.04297 ( 1386) hydrogen bonds : angle 4.63679 ( 3861) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 3248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 109 time to evaluate : 1.255 Fit side-chains REVERT: A 52 THR cc_start: 0.8829 (OUTLIER) cc_final: 0.8363 (m) REVERT: A 75 HIS cc_start: 0.7921 (OUTLIER) cc_final: 0.7161 (p90) REVERT: A 518 LYS cc_start: 0.7967 (pttt) cc_final: 0.7517 (tptp) REVERT: A 1066 ASN cc_start: 0.7089 (t0) cc_final: 0.6676 (t0) REVERT: A 1127 VAL cc_start: 0.8361 (t) cc_final: 0.8108 (p) REVERT: A 1160 THR cc_start: 0.7708 (p) cc_final: 0.7298 (t) REVERT: B 167 PRO cc_start: 0.7496 (Cg_endo) cc_final: 0.7263 (Cg_exo) REVERT: G 11 LEU cc_start: 0.7525 (OUTLIER) cc_final: 0.7218 (pp) REVERT: G 481 ASP cc_start: 0.8556 (OUTLIER) cc_final: 0.8220 (t70) REVERT: G 1064 LYS cc_start: 0.8175 (OUTLIER) cc_final: 0.7440 (mmmm) REVERT: G 1074 MET cc_start: 0.8875 (mmp) cc_final: 0.8610 (mmm) REVERT: G 1881 ARG cc_start: 0.7862 (OUTLIER) cc_final: 0.7162 (tpm170) REVERT: G 1959 LYS cc_start: 0.7609 (OUTLIER) cc_final: 0.7285 (mmmm) REVERT: G 2036 GLU cc_start: 0.8131 (OUTLIER) cc_final: 0.7929 (mp0) REVERT: G 2047 LYS cc_start: 0.8302 (mttm) cc_final: 0.7860 (tmmm) outliers start: 55 outliers final: 38 residues processed: 158 average time/residue: 0.6382 time to fit residues: 120.0320 Evaluate side-chains 153 residues out of total 3248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 107 time to evaluate : 0.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 THR Chi-restraints excluded: chain A residue 75 HIS Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 412 SER Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 509 ILE Chi-restraints excluded: chain A residue 744 ASP Chi-restraints excluded: chain A residue 940 THR Chi-restraints excluded: chain A residue 1001 VAL Chi-restraints excluded: chain A residue 1209 ASP Chi-restraints excluded: chain A residue 1254 VAL Chi-restraints excluded: chain A residue 1284 SER Chi-restraints excluded: chain A residue 1333 ASP Chi-restraints excluded: chain A residue 1380 GLN Chi-restraints excluded: chain A residue 1435 SER Chi-restraints excluded: chain A residue 1773 VAL Chi-restraints excluded: chain A residue 1808 SER Chi-restraints excluded: chain A residue 1836 ASP Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 86 LEU Chi-restraints excluded: chain G residue 113 ASP Chi-restraints excluded: chain G residue 115 THR Chi-restraints excluded: chain G residue 201 THR Chi-restraints excluded: chain G residue 281 VAL Chi-restraints excluded: chain G residue 340 SER Chi-restraints excluded: chain G residue 481 ASP Chi-restraints excluded: chain G residue 845 THR Chi-restraints excluded: chain G residue 981 GLU Chi-restraints excluded: chain G residue 1064 LYS Chi-restraints excluded: chain G residue 1190 SER Chi-restraints excluded: chain G residue 1380 SER Chi-restraints excluded: chain G residue 1381 VAL Chi-restraints excluded: chain G residue 1392 VAL Chi-restraints excluded: chain G residue 1417 THR Chi-restraints excluded: chain G residue 1472 VAL Chi-restraints excluded: chain G residue 1479 ILE Chi-restraints excluded: chain G residue 1565 VAL Chi-restraints excluded: chain G residue 1650 VAL Chi-restraints excluded: chain G residue 1708 ASP Chi-restraints excluded: chain G residue 1736 MET Chi-restraints excluded: chain G residue 1772 SER Chi-restraints excluded: chain G residue 1881 ARG Chi-restraints excluded: chain G residue 1925 ILE Chi-restraints excluded: chain G residue 1939 HIS Chi-restraints excluded: chain G residue 1959 LYS Chi-restraints excluded: chain G residue 2036 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 24 optimal weight: 5.9990 chunk 116 optimal weight: 7.9990 chunk 296 optimal weight: 5.9990 chunk 251 optimal weight: 5.9990 chunk 265 optimal weight: 7.9990 chunk 204 optimal weight: 5.9990 chunk 284 optimal weight: 3.9990 chunk 329 optimal weight: 5.9990 chunk 112 optimal weight: 9.9990 chunk 84 optimal weight: 1.9990 chunk 154 optimal weight: 6.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1794 GLN ** B 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G2013 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.065280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.049432 restraints weight = 89878.309| |-----------------------------------------------------------------------------| r_work (start): 0.2898 rms_B_bonded: 1.82 r_work: 0.2780 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2669 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.2669 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.2300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 30416 Z= 0.185 Angle : 0.534 10.311 41226 Z= 0.278 Chirality : 0.044 0.168 4629 Planarity : 0.004 0.045 5302 Dihedral : 7.023 67.788 4235 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 1.63 % Allowed : 12.07 % Favored : 86.30 % 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: 0.84 (0.14), residues: 3764 helix: 1.55 (0.13), residues: 1672 sheet: -0.65 (0.22), residues: 529 loop : 0.04 (0.16), residues: 1563 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G1413 TYR 0.019 0.002 TYR G 624 PHE 0.022 0.002 PHE A1376 TRP 0.011 0.001 TRP G 865 HIS 0.006 0.001 HIS A1689 Details of bonding type rmsd covalent geometry : bond 0.00429 (30416) covalent geometry : angle 0.53429 (41226) hydrogen bonds : bond 0.04254 ( 1386) hydrogen bonds : angle 4.62487 ( 3861) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 3248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 107 time to evaluate : 0.819 Fit side-chains REVERT: A 52 THR cc_start: 0.8808 (OUTLIER) cc_final: 0.8408 (m) REVERT: A 74 LEU cc_start: 0.8825 (OUTLIER) cc_final: 0.8583 (pp) REVERT: A 75 HIS cc_start: 0.7901 (OUTLIER) cc_final: 0.7132 (p90) REVERT: A 518 LYS cc_start: 0.7999 (pttt) cc_final: 0.7522 (tptp) REVERT: A 1066 ASN cc_start: 0.7018 (t0) cc_final: 0.6619 (t0) REVERT: A 1127 VAL cc_start: 0.8356 (t) cc_final: 0.8106 (p) REVERT: A 1160 THR cc_start: 0.7720 (p) cc_final: 0.7306 (t) REVERT: B 167 PRO cc_start: 0.7486 (Cg_endo) cc_final: 0.7260 (Cg_exo) REVERT: G 11 LEU cc_start: 0.7479 (OUTLIER) cc_final: 0.7173 (pp) REVERT: G 481 ASP cc_start: 0.8556 (OUTLIER) cc_final: 0.8218 (t70) REVERT: G 1064 LYS cc_start: 0.8177 (OUTLIER) cc_final: 0.7441 (mmmm) REVERT: G 1881 ARG cc_start: 0.7856 (OUTLIER) cc_final: 0.7173 (tpm170) REVERT: G 1959 LYS cc_start: 0.7648 (OUTLIER) cc_final: 0.7273 (mmmm) REVERT: G 2036 GLU cc_start: 0.8146 (OUTLIER) cc_final: 0.7944 (mp0) outliers start: 53 outliers final: 37 residues processed: 156 average time/residue: 0.6018 time to fit residues: 111.7657 Evaluate side-chains 152 residues out of total 3248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 106 time to evaluate : 1.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 THR Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 75 HIS Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 412 SER Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 509 ILE Chi-restraints excluded: chain A residue 744 ASP Chi-restraints excluded: chain A residue 940 THR Chi-restraints excluded: chain A residue 1001 VAL Chi-restraints excluded: chain A residue 1209 ASP Chi-restraints excluded: chain A residue 1254 VAL Chi-restraints excluded: chain A residue 1284 SER Chi-restraints excluded: chain A residue 1333 ASP Chi-restraints excluded: chain A residue 1380 GLN Chi-restraints excluded: chain A residue 1435 SER Chi-restraints excluded: chain A residue 1773 VAL Chi-restraints excluded: chain A residue 1808 SER Chi-restraints excluded: chain A residue 1836 ASP Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 86 LEU Chi-restraints excluded: chain G residue 201 THR Chi-restraints excluded: chain G residue 281 VAL Chi-restraints excluded: chain G residue 340 SER Chi-restraints excluded: chain G residue 481 ASP Chi-restraints excluded: chain G residue 845 THR Chi-restraints excluded: chain G residue 981 GLU Chi-restraints excluded: chain G residue 1064 LYS Chi-restraints excluded: chain G residue 1190 SER Chi-restraints excluded: chain G residue 1380 SER Chi-restraints excluded: chain G residue 1381 VAL Chi-restraints excluded: chain G residue 1392 VAL Chi-restraints excluded: chain G residue 1417 THR Chi-restraints excluded: chain G residue 1472 VAL Chi-restraints excluded: chain G residue 1479 ILE Chi-restraints excluded: chain G residue 1565 VAL Chi-restraints excluded: chain G residue 1650 VAL Chi-restraints excluded: chain G residue 1708 ASP Chi-restraints excluded: chain G residue 1736 MET Chi-restraints excluded: chain G residue 1772 SER Chi-restraints excluded: chain G residue 1881 ARG Chi-restraints excluded: chain G residue 1925 ILE Chi-restraints excluded: chain G residue 1939 HIS Chi-restraints excluded: chain G residue 1948 SER Chi-restraints excluded: chain G residue 1959 LYS Chi-restraints excluded: chain G residue 2036 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 324 optimal weight: 8.9990 chunk 118 optimal weight: 0.0040 chunk 47 optimal weight: 6.9990 chunk 372 optimal weight: 7.9990 chunk 344 optimal weight: 10.0000 chunk 220 optimal weight: 0.0050 chunk 268 optimal weight: 9.9990 chunk 112 optimal weight: 0.0870 chunk 279 optimal weight: 6.9990 chunk 1 optimal weight: 5.9990 chunk 173 optimal weight: 10.0000 overall best weight: 2.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1794 GLN ** B 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G2013 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.065854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.049659 restraints weight = 89599.978| |-----------------------------------------------------------------------------| r_work (start): 0.2909 rms_B_bonded: 1.87 r_work: 0.2800 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2689 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.2689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.2344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 30416 Z= 0.125 Angle : 0.491 9.439 41226 Z= 0.255 Chirality : 0.042 0.156 4629 Planarity : 0.004 0.075 5302 Dihedral : 6.772 65.654 4235 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.48 % Allowed : 12.13 % Favored : 86.39 % 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: 1.06 (0.14), residues: 3764 helix: 1.76 (0.13), residues: 1670 sheet: -0.58 (0.22), residues: 532 loop : 0.14 (0.16), residues: 1562 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.000 ARG A 632 TYR 0.016 0.001 TYR A 417 PHE 0.024 0.001 PHE A 35 TRP 0.011 0.001 TRP G 865 HIS 0.007 0.001 HIS A1689 Details of bonding type rmsd covalent geometry : bond 0.00285 (30416) covalent geometry : angle 0.49074 (41226) hydrogen bonds : bond 0.03810 ( 1386) hydrogen bonds : angle 4.48841 ( 3861) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 3248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 108 time to evaluate : 1.158 Fit side-chains REVERT: A 52 THR cc_start: 0.8850 (OUTLIER) cc_final: 0.8340 (m) REVERT: A 74 LEU cc_start: 0.8841 (OUTLIER) cc_final: 0.8597 (pp) REVERT: A 75 HIS cc_start: 0.7882 (OUTLIER) cc_final: 0.7112 (p90) REVERT: A 518 LYS cc_start: 0.8007 (pttt) cc_final: 0.7533 (tptp) REVERT: A 1066 ASN cc_start: 0.7058 (t0) cc_final: 0.6649 (t0) REVERT: A 1127 VAL cc_start: 0.8343 (t) cc_final: 0.8060 (p) REVERT: A 1160 THR cc_start: 0.7679 (p) cc_final: 0.7269 (t) REVERT: A 1180 ARG cc_start: 0.6558 (mmt180) cc_final: 0.5993 (mmt180) REVERT: B 167 PRO cc_start: 0.7439 (Cg_endo) cc_final: 0.7213 (Cg_exo) REVERT: B 168 MET cc_start: 0.6958 (tpp) cc_final: 0.6581 (tmt) REVERT: G 11 LEU cc_start: 0.7485 (OUTLIER) cc_final: 0.7223 (pt) REVERT: G 481 ASP cc_start: 0.8576 (OUTLIER) cc_final: 0.8251 (t70) REVERT: G 1881 ARG cc_start: 0.7844 (OUTLIER) cc_final: 0.7152 (tpm170) REVERT: G 1959 LYS cc_start: 0.7610 (OUTLIER) cc_final: 0.7282 (mmmm) REVERT: G 2036 GLU cc_start: 0.8120 (OUTLIER) cc_final: 0.7893 (mp0) outliers start: 48 outliers final: 36 residues processed: 152 average time/residue: 0.6168 time to fit residues: 112.0800 Evaluate side-chains 150 residues out of total 3248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 106 time to evaluate : 0.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 THR Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 75 HIS Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 412 SER Chi-restraints excluded: chain A residue 428 VAL Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 744 ASP Chi-restraints excluded: chain A residue 888 ILE Chi-restraints excluded: chain A residue 940 THR Chi-restraints excluded: chain A residue 1001 VAL Chi-restraints excluded: chain A residue 1189 ILE Chi-restraints excluded: chain A residue 1209 ASP Chi-restraints excluded: chain A residue 1254 VAL Chi-restraints excluded: chain A residue 1284 SER Chi-restraints excluded: chain A residue 1333 ASP Chi-restraints excluded: chain A residue 1773 VAL Chi-restraints excluded: chain A residue 1808 SER Chi-restraints excluded: chain A residue 1836 ASP Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 86 LEU Chi-restraints excluded: chain G residue 201 THR Chi-restraints excluded: chain G residue 281 VAL Chi-restraints excluded: chain G residue 340 SER Chi-restraints excluded: chain G residue 481 ASP Chi-restraints excluded: chain G residue 777 THR Chi-restraints excluded: chain G residue 845 THR Chi-restraints excluded: chain G residue 981 GLU Chi-restraints excluded: chain G residue 1190 SER Chi-restraints excluded: chain G residue 1380 SER Chi-restraints excluded: chain G residue 1381 VAL Chi-restraints excluded: chain G residue 1392 VAL Chi-restraints excluded: chain G residue 1472 VAL Chi-restraints excluded: chain G residue 1565 VAL Chi-restraints excluded: chain G residue 1650 VAL Chi-restraints excluded: chain G residue 1708 ASP Chi-restraints excluded: chain G residue 1736 MET Chi-restraints excluded: chain G residue 1772 SER Chi-restraints excluded: chain G residue 1881 ARG Chi-restraints excluded: chain G residue 1925 ILE Chi-restraints excluded: chain G residue 1939 HIS Chi-restraints excluded: chain G residue 1948 SER Chi-restraints excluded: chain G residue 1959 LYS Chi-restraints excluded: chain G residue 2036 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 42 optimal weight: 2.9990 chunk 9 optimal weight: 0.0370 chunk 311 optimal weight: 7.9990 chunk 276 optimal weight: 4.9990 chunk 236 optimal weight: 9.9990 chunk 109 optimal weight: 7.9990 chunk 124 optimal weight: 5.9990 chunk 159 optimal weight: 7.9990 chunk 57 optimal weight: 20.0000 chunk 3 optimal weight: 2.9990 chunk 178 optimal weight: 5.9990 overall best weight: 3.4066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1794 GLN ** B 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G2013 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.065688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.049853 restraints weight = 89469.786| |-----------------------------------------------------------------------------| r_work (start): 0.2911 rms_B_bonded: 1.85 r_work: 0.2794 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2682 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 moved from start: 0.2358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 30416 Z= 0.144 Angle : 0.502 9.790 41226 Z= 0.261 Chirality : 0.043 0.158 4629 Planarity : 0.004 0.050 5302 Dihedral : 6.733 64.690 4235 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 1.60 % Allowed : 12.07 % Favored : 86.33 % 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: 1.05 (0.14), residues: 3764 helix: 1.73 (0.13), residues: 1677 sheet: -0.55 (0.22), residues: 531 loop : 0.13 (0.16), residues: 1556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A1070 TYR 0.016 0.001 TYR G 624 PHE 0.023 0.001 PHE A 35 TRP 0.011 0.001 TRP G 865 HIS 0.006 0.001 HIS A1689 Details of bonding type rmsd covalent geometry : bond 0.00332 (30416) covalent geometry : angle 0.50152 (41226) hydrogen bonds : bond 0.03946 ( 1386) hydrogen bonds : angle 4.50529 ( 3861) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 3248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 108 time to evaluate : 1.266 Fit side-chains REVERT: A 52 THR cc_start: 0.8876 (OUTLIER) cc_final: 0.8389 (m) REVERT: A 74 LEU cc_start: 0.8883 (OUTLIER) cc_final: 0.8648 (pp) REVERT: A 75 HIS cc_start: 0.7886 (OUTLIER) cc_final: 0.7122 (p90) REVERT: A 518 LYS cc_start: 0.7966 (pttt) cc_final: 0.7540 (tptp) REVERT: A 1066 ASN cc_start: 0.6980 (t0) cc_final: 0.6584 (t0) REVERT: A 1127 VAL cc_start: 0.8361 (t) cc_final: 0.8089 (p) REVERT: A 1160 THR cc_start: 0.7687 (p) cc_final: 0.7277 (t) REVERT: A 1180 ARG cc_start: 0.6632 (mmt180) cc_final: 0.6045 (mmt180) REVERT: B 167 PRO cc_start: 0.7346 (Cg_endo) cc_final: 0.7135 (Cg_exo) REVERT: B 168 MET cc_start: 0.7005 (tpp) cc_final: 0.6603 (tmt) REVERT: G 11 LEU cc_start: 0.7481 (OUTLIER) cc_final: 0.7203 (pt) REVERT: G 481 ASP cc_start: 0.8564 (OUTLIER) cc_final: 0.8252 (t70) REVERT: G 1881 ARG cc_start: 0.7852 (OUTLIER) cc_final: 0.7160 (tpm170) REVERT: G 1959 LYS cc_start: 0.7636 (OUTLIER) cc_final: 0.7270 (mmmm) REVERT: G 2036 GLU cc_start: 0.8140 (OUTLIER) cc_final: 0.7921 (mp0) outliers start: 52 outliers final: 40 residues processed: 156 average time/residue: 0.7315 time to fit residues: 135.6293 Evaluate side-chains 154 residues out of total 3248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 106 time to evaluate : 1.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 THR Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 75 HIS Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 412 SER Chi-restraints excluded: chain A residue 428 VAL Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 744 ASP Chi-restraints excluded: chain A residue 888 ILE Chi-restraints excluded: chain A residue 940 THR Chi-restraints excluded: chain A residue 1001 VAL Chi-restraints excluded: chain A residue 1189 ILE Chi-restraints excluded: chain A residue 1209 ASP Chi-restraints excluded: chain A residue 1254 VAL Chi-restraints excluded: chain A residue 1284 SER Chi-restraints excluded: chain A residue 1333 ASP Chi-restraints excluded: chain A residue 1380 GLN Chi-restraints excluded: chain A residue 1435 SER Chi-restraints excluded: chain A residue 1773 VAL Chi-restraints excluded: chain A residue 1808 SER Chi-restraints excluded: chain A residue 1836 ASP Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 86 LEU Chi-restraints excluded: chain G residue 201 THR Chi-restraints excluded: chain G residue 281 VAL Chi-restraints excluded: chain G residue 340 SER Chi-restraints excluded: chain G residue 481 ASP Chi-restraints excluded: chain G residue 777 THR Chi-restraints excluded: chain G residue 845 THR Chi-restraints excluded: chain G residue 981 GLU Chi-restraints excluded: chain G residue 1190 SER Chi-restraints excluded: chain G residue 1380 SER Chi-restraints excluded: chain G residue 1381 VAL Chi-restraints excluded: chain G residue 1392 VAL Chi-restraints excluded: chain G residue 1417 THR Chi-restraints excluded: chain G residue 1472 VAL Chi-restraints excluded: chain G residue 1511 SER Chi-restraints excluded: chain G residue 1565 VAL Chi-restraints excluded: chain G residue 1650 VAL Chi-restraints excluded: chain G residue 1708 ASP Chi-restraints excluded: chain G residue 1736 MET Chi-restraints excluded: chain G residue 1772 SER Chi-restraints excluded: chain G residue 1881 ARG Chi-restraints excluded: chain G residue 1925 ILE Chi-restraints excluded: chain G residue 1939 HIS Chi-restraints excluded: chain G residue 1948 SER Chi-restraints excluded: chain G residue 1959 LYS Chi-restraints excluded: chain G residue 2036 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 200 optimal weight: 30.0000 chunk 202 optimal weight: 9.9990 chunk 92 optimal weight: 3.9990 chunk 335 optimal weight: 9.9990 chunk 182 optimal weight: 6.9990 chunk 268 optimal weight: 9.9990 chunk 224 optimal weight: 8.9990 chunk 183 optimal weight: 6.9990 chunk 73 optimal weight: 3.9990 chunk 213 optimal weight: 7.9990 chunk 222 optimal weight: 2.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1794 GLN ** B 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G2013 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.065294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.049556 restraints weight = 90340.234| |-----------------------------------------------------------------------------| r_work (start): 0.2901 rms_B_bonded: 1.82 r_work: 0.2782 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2670 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.2361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 30416 Z= 0.190 Angle : 0.542 10.292 41226 Z= 0.281 Chirality : 0.044 0.168 4629 Planarity : 0.004 0.098 5302 Dihedral : 6.861 63.910 4235 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 1.48 % Allowed : 12.23 % Favored : 86.30 % 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: 0.94 (0.14), residues: 3764 helix: 1.60 (0.13), residues: 1681 sheet: -0.58 (0.22), residues: 532 loop : 0.11 (0.16), residues: 1551 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.001 ARG A 632 TYR 0.018 0.002 TYR G 624 PHE 0.024 0.002 PHE A1376 TRP 0.011 0.001 TRP G 865 HIS 0.006 0.001 HIS A1689 Details of bonding type rmsd covalent geometry : bond 0.00442 (30416) covalent geometry : angle 0.54227 (41226) hydrogen bonds : bond 0.04271 ( 1386) hydrogen bonds : angle 4.60766 ( 3861) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11023.40 seconds wall clock time: 188 minutes 22.49 seconds (11302.49 seconds total)