Starting phenix.real_space_refine on Wed May 28 04:02:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ps1_17842/05_2025/8ps1_17842.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ps1_17842/05_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_17842/05_2025/8ps1_17842.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ps1_17842/05_2025/8ps1_17842.map" model { file = "/net/cci-nas-00/data/ceres_data/8ps1_17842/05_2025/8ps1_17842.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ps1_17842/05_2025/8ps1_17842.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 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): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 15.70, per 1000 atoms: 0.53 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: 7.14 Conformation dependent library (CDL) restraints added in 3.9 seconds 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: 4.38 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: 15.15 Time building geometry restraints manager: 8.38 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: 1.220 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 1.130 Check model and map are aligned: 0.210 Set scattering table: 0.260 Process input model: 68.140 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.120 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:11.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 82.620 ------------------------------------------------------------------------------- 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 : 2.02 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.062 0.011 TRP A1286 HIS 0.015 0.004 HIS A1358 PHE 0.067 0.008 PHE G 799 TYR 0.062 0.008 TYR A 753 ARG 0.018 0.002 ARG A1036 Details of bonding type rmsd hydrogen bonds : bond 0.23276 ( 1386) hydrogen bonds : angle 9.16976 ( 3861) covalent geometry : bond 0.01423 (30416) covalent geometry : angle 1.92308 (41226) *********************** 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 : 3.373 Fit side-chains REVERT: A 413 LEU cc_start: 0.9271 (OUTLIER) cc_final: 0.9053 (tm) REVERT: A 431 GLU cc_start: 0.8757 (tp30) cc_final: 0.8491 (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: 1.6376 time to fit residues: 390.5191 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 : 3.418 ------------------------------------------------------------------------------- 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 318 optimal weight: 8.9990 chunk 285 optimal weight: 10.0000 chunk 158 optimal weight: 6.9990 chunk 97 optimal weight: 20.0000 chunk 192 optimal weight: 5.9990 chunk 152 optimal weight: 7.9990 chunk 295 optimal weight: 0.7980 chunk 114 optimal weight: 20.0000 chunk 179 optimal weight: 5.9990 chunk 219 optimal weight: 8.9990 chunk 342 optimal weight: 6.9990 overall best weight: 5.3588 ------------------------------------------------------------------------------- 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 181 HIS G 221 ASN G 245 GLN G 365 GLN G 440 ASN G 500 HIS G 718 ASN G 747 HIS G1217 ASN G1241 ASN G1341 ASN G1355 ASN G1451 GLN G1512 HIS G1523 ASN G1697 HIS G1890 ASN G1895 ASN G1912 ASN G1983 ASN G2013 ASN G2020 GLN Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.064404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.048619 restraints weight = 89775.200| |-----------------------------------------------------------------------------| r_work (start): 0.2873 rms_B_bonded: 1.88 r_work: 0.2748 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2637 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.2637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8564 moved from start: 0.1641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 30416 Z= 0.207 Angle : 0.608 10.259 41226 Z= 0.321 Chirality : 0.045 0.199 4629 Planarity : 0.004 0.041 5302 Dihedral : 8.151 78.882 4254 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 1.26 % Allowed : 8.38 % Favored : 90.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.13), residues: 3764 helix: 0.02 (0.12), residues: 1689 sheet: -1.09 (0.21), residues: 532 loop : -0.43 (0.16), residues: 1543 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP G 832 HIS 0.007 0.001 HIS A1689 PHE 0.024 0.002 PHE A 35 TYR 0.023 0.002 TYR G 624 ARG 0.006 0.001 ARG G1849 Details of bonding type rmsd hydrogen bonds : bond 0.04800 ( 1386) hydrogen bonds : angle 5.11837 ( 3861) covalent geometry : bond 0.00483 (30416) covalent geometry : angle 0.60813 (41226) *********************** 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 158 residues out of total 3248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 117 time to evaluate : 3.301 Fit side-chains REVERT: A 75 HIS cc_start: 0.7977 (OUTLIER) cc_final: 0.7281 (p90) REVERT: A 518 LYS cc_start: 0.7922 (pttt) cc_final: 0.7549 (tptp) REVERT: A 1066 ASN cc_start: 0.6947 (t0) cc_final: 0.6431 (t0) REVERT: A 1127 VAL cc_start: 0.8292 (t) cc_final: 0.7963 (p) REVERT: A 1160 THR cc_start: 0.7836 (p) cc_final: 0.7281 (t) REVERT: A 1234 MET cc_start: 0.9054 (mtm) cc_final: 0.8765 (mtm) REVERT: A 1289 MET cc_start: 0.9231 (mtp) cc_final: 0.9014 (mtp) REVERT: A 1786 PHE cc_start: 0.7605 (t80) cc_final: 0.7237 (t80) REVERT: A 1838 GLU cc_start: 0.7653 (tt0) cc_final: 0.6982 (tm-30) REVERT: A 1850 GLU cc_start: 0.6327 (OUTLIER) cc_final: 0.5880 (tm-30) REVERT: B 237 MET cc_start: 0.8055 (mmm) cc_final: 0.7849 (mmt) REVERT: G 38 ASN cc_start: 0.7584 (OUTLIER) cc_final: 0.7333 (m110) REVERT: G 442 ASP cc_start: 0.7484 (m-30) cc_final: 0.7172 (m-30) REVERT: G 597 MET cc_start: 0.9146 (mtm) cc_final: 0.8717 (mtm) REVERT: G 850 MET cc_start: 0.7913 (mmt) cc_final: 0.7697 (mmm) REVERT: G 1074 MET cc_start: 0.8888 (mmp) cc_final: 0.8617 (mmm) REVERT: G 2036 GLU cc_start: 0.8096 (OUTLIER) cc_final: 0.7878 (mp0) outliers start: 41 outliers final: 19 residues processed: 152 average time/residue: 1.5296 time to fit residues: 274.1361 Evaluate side-chains 132 residues out of total 3248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 109 time to evaluate : 3.706 ------------------------------------------------------------------------------- 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 1164 SER Chi-restraints excluded: chain A residue 1305 CYS 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 1850 GLU Chi-restraints excluded: chain G residue 38 ASN Chi-restraints excluded: chain G residue 86 LEU Chi-restraints excluded: chain G residue 115 THR 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 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 194 optimal weight: 10.0000 chunk 134 optimal weight: 10.0000 chunk 187 optimal weight: 0.9980 chunk 156 optimal weight: 10.0000 chunk 131 optimal weight: 9.9990 chunk 129 optimal weight: 9.9990 chunk 370 optimal weight: 10.0000 chunk 130 optimal weight: 0.9990 chunk 84 optimal weight: 3.9990 chunk 106 optimal weight: 7.9990 chunk 58 optimal weight: 8.9990 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 527 GLN A1794 GLN G1564 HIS G2013 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.064876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.049328 restraints weight = 89676.033| |-----------------------------------------------------------------------------| r_work (start): 0.2896 rms_B_bonded: 1.78 r_work: 0.2767 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2655 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.2655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 0.1871 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= 0.180 Angle : 0.550 10.656 41226 Z= 0.289 Chirality : 0.044 0.182 4629 Planarity : 0.004 0.056 5302 Dihedral : 7.716 77.556 4240 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 1.17 % Allowed : 10.13 % Favored : 88.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.14), residues: 3764 helix: 1.01 (0.13), residues: 1673 sheet: -0.84 (0.22), residues: 516 loop : -0.17 (0.16), residues: 1575 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP G 832 HIS 0.007 0.001 HIS A1689 PHE 0.024 0.002 PHE A 35 TYR 0.021 0.002 TYR G 624 ARG 0.016 0.001 ARG A 632 Details of bonding type rmsd hydrogen bonds : bond 0.04485 ( 1386) hydrogen bonds : angle 4.81679 ( 3861) covalent geometry : bond 0.00417 (30416) covalent geometry : angle 0.54993 (41226) *********************** 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 150 residues out of total 3248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 112 time to evaluate : 3.585 Fit side-chains REVERT: A 59 ARG cc_start: 0.7852 (mtm110) cc_final: 0.7569 (mtt180) REVERT: A 75 HIS cc_start: 0.7949 (OUTLIER) cc_final: 0.7259 (p90) REVERT: A 518 LYS cc_start: 0.7888 (pttt) cc_final: 0.7516 (tptp) REVERT: A 1127 VAL cc_start: 0.8324 (t) cc_final: 0.8033 (p) REVERT: A 1160 THR cc_start: 0.7843 (p) cc_final: 0.7420 (t) REVERT: A 1234 MET cc_start: 0.9020 (mtm) cc_final: 0.8705 (mtm) REVERT: B 237 MET cc_start: 0.8078 (mmm) cc_final: 0.7866 (mmt) REVERT: G 442 ASP cc_start: 0.7344 (m-30) cc_final: 0.7005 (m-30) REVERT: G 597 MET cc_start: 0.9118 (mtm) cc_final: 0.8751 (mtm) REVERT: G 2036 GLU cc_start: 0.8108 (OUTLIER) cc_final: 0.7887 (mp0) outliers start: 38 outliers final: 23 residues processed: 145 average time/residue: 1.5518 time to fit residues: 266.4186 Evaluate side-chains 131 residues out of total 3248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 106 time to evaluate : 3.642 ------------------------------------------------------------------------------- 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 1001 VAL Chi-restraints excluded: chain A residue 1164 SER 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 86 LEU Chi-restraints excluded: chain G residue 115 THR Chi-restraints excluded: chain G residue 318 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 367 optimal weight: 10.0000 chunk 149 optimal weight: 8.9990 chunk 262 optimal weight: 9.9990 chunk 206 optimal weight: 10.0000 chunk 268 optimal weight: 10.0000 chunk 256 optimal weight: 0.0000 chunk 160 optimal weight: 0.0670 chunk 266 optimal weight: 8.9990 chunk 181 optimal weight: 20.0000 chunk 145 optimal weight: 20.0000 chunk 100 optimal weight: 10.0000 overall best weight: 5.6128 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 341 GLN A1794 GLN G 752 GLN ** 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 = 0.3330 r_free = 0.3330 target = 0.064864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.049717 restraints weight = 90381.057| |-----------------------------------------------------------------------------| r_work (start): 0.2906 rms_B_bonded: 1.78 r_work: 0.2763 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2653 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 moved from start: 0.2080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 30416 Z= 0.212 Angle : 0.568 10.955 41226 Z= 0.296 Chirality : 0.045 0.183 4629 Planarity : 0.004 0.042 5302 Dihedral : 7.473 74.133 4237 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 1.54 % Allowed : 10.96 % Favored : 87.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.14), residues: 3764 helix: 1.19 (0.13), residues: 1677 sheet: -0.78 (0.22), residues: 517 loop : -0.11 (0.16), residues: 1570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP G 865 HIS 0.007 0.001 HIS A1689 PHE 0.024 0.002 PHE A1376 TYR 0.022 0.002 TYR G 624 ARG 0.005 0.001 ARG A 801 Details of bonding type rmsd hydrogen bonds : bond 0.04544 ( 1386) hydrogen bonds : angle 4.79053 ( 3861) covalent geometry : bond 0.00495 (30416) covalent geometry : angle 0.56812 (41226) *********************** 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 160 residues out of total 3248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 110 time to evaluate : 3.637 Fit side-chains REVERT: A 75 HIS cc_start: 0.7927 (OUTLIER) cc_final: 0.7180 (p90) REVERT: A 518 LYS cc_start: 0.7967 (pttt) cc_final: 0.7550 (tptp) REVERT: A 1127 VAL cc_start: 0.8348 (t) cc_final: 0.8087 (p) REVERT: A 1160 THR cc_start: 0.7795 (p) cc_final: 0.7293 (t) REVERT: A 1234 MET cc_start: 0.9034 (mtm) cc_final: 0.8753 (mtm) REVERT: G 597 MET cc_start: 0.9107 (mtm) cc_final: 0.8841 (mtm) REVERT: G 1011 MET cc_start: 0.8168 (tpp) cc_final: 0.7937 (mmm) REVERT: G 1064 LYS cc_start: 0.8169 (OUTLIER) cc_final: 0.7441 (mmmm) REVERT: G 1881 ARG cc_start: 0.7845 (OUTLIER) cc_final: 0.7108 (tpm170) outliers start: 50 outliers final: 30 residues processed: 152 average time/residue: 1.5511 time to fit residues: 279.8139 Evaluate side-chains 139 residues out of total 3248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 106 time to evaluate : 3.779 ------------------------------------------------------------------------------- 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 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 1260 MET 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 86 LEU Chi-restraints excluded: chain G residue 115 THR Chi-restraints excluded: chain G residue 201 THR Chi-restraints excluded: chain G residue 318 SER Chi-restraints excluded: chain G residue 340 SER 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 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 101 optimal weight: 2.9990 chunk 296 optimal weight: 9.9990 chunk 126 optimal weight: 3.9990 chunk 257 optimal weight: 3.9990 chunk 180 optimal weight: 5.9990 chunk 262 optimal weight: 9.9990 chunk 294 optimal weight: 7.9990 chunk 58 optimal weight: 10.0000 chunk 33 optimal weight: 9.9990 chunk 62 optimal weight: 9.9990 chunk 320 optimal weight: 9.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1063 HIS A1794 GLN 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 = 0.3335 r_free = 0.3335 target = 0.065019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.049185 restraints weight = 89971.378| |-----------------------------------------------------------------------------| r_work (start): 0.2891 rms_B_bonded: 1.82 r_work: 0.2773 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2661 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 moved from start: 0.2178 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= 0.191 Angle : 0.546 10.572 41226 Z= 0.284 Chirality : 0.044 0.177 4629 Planarity : 0.004 0.070 5302 Dihedral : 7.309 72.188 4237 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 1.79 % Allowed : 11.46 % Favored : 86.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.14), residues: 3764 helix: 1.32 (0.13), residues: 1678 sheet: -0.70 (0.22), residues: 516 loop : -0.07 (0.16), residues: 1570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP G 865 HIS 0.006 0.001 HIS A1689 PHE 0.022 0.002 PHE A 35 TYR 0.020 0.002 TYR G 624 ARG 0.014 0.001 ARG A 632 Details of bonding type rmsd hydrogen bonds : bond 0.04361 ( 1386) hydrogen bonds : angle 4.71400 ( 3861) covalent geometry : bond 0.00445 (30416) covalent geometry : angle 0.54562 (41226) *********************** 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 167 residues out of total 3248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 109 time to evaluate : 3.325 Fit side-chains REVERT: A 75 HIS cc_start: 0.7890 (OUTLIER) cc_final: 0.7121 (p90) REVERT: A 518 LYS cc_start: 0.7946 (pttt) cc_final: 0.7513 (tptp) REVERT: A 1127 VAL cc_start: 0.8360 (t) cc_final: 0.8098 (p) REVERT: A 1160 THR cc_start: 0.7729 (p) cc_final: 0.7293 (t) REVERT: A 1234 MET cc_start: 0.9031 (mtm) cc_final: 0.8737 (mtm) REVERT: G 11 LEU cc_start: 0.7604 (OUTLIER) cc_final: 0.7290 (pp) REVERT: G 481 ASP cc_start: 0.8539 (OUTLIER) cc_final: 0.8205 (t70) REVERT: G 1011 MET cc_start: 0.8224 (tpp) cc_final: 0.7962 (mmm) REVERT: G 1881 ARG cc_start: 0.7847 (OUTLIER) cc_final: 0.7134 (tpm170) outliers start: 58 outliers final: 39 residues processed: 161 average time/residue: 1.3130 time to fit residues: 255.0252 Evaluate side-chains 150 residues out of total 3248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 107 time to evaluate : 3.542 ------------------------------------------------------------------------------- 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 428 VAL Chi-restraints excluded: chain A residue 461 THR 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 1209 ASP Chi-restraints excluded: chain A residue 1254 VAL Chi-restraints excluded: chain A residue 1260 MET 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 A residue 1849 VAL 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 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 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 236 optimal weight: 4.9990 chunk 157 optimal weight: 5.9990 chunk 6 optimal weight: 0.0270 chunk 72 optimal weight: 5.9990 chunk 179 optimal weight: 5.9990 chunk 195 optimal weight: 8.9990 chunk 301 optimal weight: 0.7980 chunk 255 optimal weight: 0.8980 chunk 36 optimal weight: 9.9990 chunk 198 optimal weight: 5.9990 chunk 123 optimal weight: 5.9990 overall best weight: 2.5442 ------------------------------------------------------------------------------- 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 ** 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 = 0.3353 r_free = 0.3353 target = 0.065768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.049544 restraints weight = 89847.058| |-----------------------------------------------------------------------------| r_work (start): 0.2906 rms_B_bonded: 1.89 r_work: 0.2795 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2684 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 moved from start: 0.2261 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= 0.122 Angle : 0.486 9.300 41226 Z= 0.254 Chirality : 0.042 0.159 4629 Planarity : 0.004 0.046 5302 Dihedral : 6.948 69.998 4236 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.66 % Allowed : 11.76 % Favored : 86.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.14), residues: 3764 helix: 1.61 (0.13), residues: 1676 sheet: -0.59 (0.22), residues: 519 loop : 0.04 (0.16), residues: 1569 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP G 865 HIS 0.006 0.001 HIS A1689 PHE 0.024 0.001 PHE A 35 TYR 0.016 0.001 TYR A 417 ARG 0.005 0.000 ARG A1070 Details of bonding type rmsd hydrogen bonds : bond 0.03841 ( 1386) hydrogen bonds : angle 4.53572 ( 3861) covalent geometry : bond 0.00278 (30416) covalent geometry : angle 0.48636 (41226) *********************** 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 166 residues out of total 3248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 112 time to evaluate : 3.448 Fit side-chains REVERT: A 74 LEU cc_start: 0.8827 (OUTLIER) cc_final: 0.8594 (pp) REVERT: A 75 HIS cc_start: 0.7905 (OUTLIER) cc_final: 0.7112 (p90) REVERT: A 518 LYS cc_start: 0.7954 (pttt) cc_final: 0.7511 (tptp) REVERT: A 1127 VAL cc_start: 0.8340 (t) cc_final: 0.8060 (p) REVERT: A 1160 THR cc_start: 0.7675 (p) cc_final: 0.7240 (t) REVERT: G 11 LEU cc_start: 0.7460 (OUTLIER) cc_final: 0.7176 (pt) REVERT: G 481 ASP cc_start: 0.8580 (OUTLIER) cc_final: 0.8260 (t70) REVERT: G 1011 MET cc_start: 0.8227 (tpp) cc_final: 0.7972 (mmm) REVERT: G 1854 MET cc_start: 0.7701 (mtt) cc_final: 0.6469 (mtm) REVERT: G 1881 ARG cc_start: 0.7858 (OUTLIER) cc_final: 0.7138 (tpm170) REVERT: G 1959 LYS cc_start: 0.7640 (OUTLIER) cc_final: 0.7272 (mmmm) outliers start: 54 outliers final: 33 residues processed: 160 average time/residue: 1.4413 time to fit residues: 275.8073 Evaluate side-chains 147 residues out of total 3248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 108 time to evaluate : 3.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 1209 ASP Chi-restraints excluded: chain A residue 1254 VAL 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 1417 THR Chi-restraints excluded: chain G residue 1479 ILE 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 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 19 optimal weight: 10.0000 chunk 347 optimal weight: 8.9990 chunk 322 optimal weight: 10.0000 chunk 261 optimal weight: 9.9990 chunk 222 optimal weight: 9.9990 chunk 168 optimal weight: 3.9990 chunk 61 optimal weight: 0.9990 chunk 253 optimal weight: 6.9990 chunk 21 optimal weight: 8.9990 chunk 13 optimal weight: 9.9990 chunk 124 optimal weight: 0.0670 overall best weight: 4.2126 ------------------------------------------------------------------------------- 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 G 331 ASN G1421 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 = 0.065393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.049629 restraints weight = 89640.257| |-----------------------------------------------------------------------------| r_work (start): 0.2902 rms_B_bonded: 1.87 r_work: 0.2786 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2674 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.2674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 moved from start: 0.2281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 30416 Z= 0.168 Angle : 0.523 10.046 41226 Z= 0.272 Chirality : 0.043 0.165 4629 Planarity : 0.004 0.069 5302 Dihedral : 6.959 68.942 4235 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.00 % Allowed : 11.89 % Favored : 86.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.14), residues: 3764 helix: 1.59 (0.13), residues: 1675 sheet: -0.60 (0.22), residues: 520 loop : 0.04 (0.16), residues: 1569 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP G 865 HIS 0.006 0.001 HIS A1689 PHE 0.022 0.002 PHE A 35 TYR 0.018 0.002 TYR G 624 ARG 0.018 0.001 ARG A 632 Details of bonding type rmsd hydrogen bonds : bond 0.04139 ( 1386) hydrogen bonds : angle 4.58645 ( 3861) covalent geometry : bond 0.00389 (30416) covalent geometry : angle 0.52329 (41226) *********************** 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 176 residues out of total 3248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 111 time to evaluate : 3.794 Fit side-chains REVERT: A 74 LEU cc_start: 0.8833 (OUTLIER) cc_final: 0.8599 (pp) REVERT: A 75 HIS cc_start: 0.7910 (OUTLIER) cc_final: 0.7137 (p90) REVERT: A 518 LYS cc_start: 0.7944 (pttt) cc_final: 0.7418 (tptp) REVERT: A 1127 VAL cc_start: 0.8358 (t) cc_final: 0.8085 (p) REVERT: A 1160 THR cc_start: 0.7702 (p) cc_final: 0.7274 (t) REVERT: B 167 PRO cc_start: 0.7500 (Cg_endo) cc_final: 0.7261 (Cg_exo) REVERT: G 11 LEU cc_start: 0.7488 (OUTLIER) cc_final: 0.7203 (pp) REVERT: G 481 ASP cc_start: 0.8545 (OUTLIER) cc_final: 0.8204 (t70) REVERT: G 1011 MET cc_start: 0.8222 (tpp) cc_final: 0.7976 (mmm) REVERT: G 1064 LYS cc_start: 0.8149 (OUTLIER) cc_final: 0.7427 (mmmm) REVERT: G 1747 LYS cc_start: 0.4424 (OUTLIER) cc_final: 0.4088 (pttp) REVERT: G 1881 ARG cc_start: 0.7816 (OUTLIER) cc_final: 0.7099 (tpm170) REVERT: G 1959 LYS cc_start: 0.7649 (OUTLIER) cc_final: 0.7276 (mmmm) outliers start: 65 outliers final: 41 residues processed: 170 average time/residue: 1.4025 time to fit residues: 287.1109 Evaluate side-chains 158 residues out of total 3248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 109 time to evaluate : 3.338 ------------------------------------------------------------------------------- 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 461 THR Chi-restraints excluded: chain A residue 509 ILE 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 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 1769 VAL 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 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 1417 THR Chi-restraints excluded: chain G residue 1472 VAL Chi-restraints excluded: chain G residue 1479 ILE Chi-restraints excluded: chain G residue 1511 SER Chi-restraints excluded: chain G residue 1565 VAL Chi-restraints excluded: chain G residue 1586 SER 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 1747 LYS 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 3 optimal weight: 4.9990 chunk 268 optimal weight: 10.0000 chunk 114 optimal weight: 8.9990 chunk 25 optimal weight: 9.9990 chunk 262 optimal weight: 10.0000 chunk 344 optimal weight: 10.0000 chunk 130 optimal weight: 3.9990 chunk 267 optimal weight: 3.9990 chunk 157 optimal weight: 20.0000 chunk 96 optimal weight: 0.9980 chunk 313 optimal weight: 9.9990 overall best weight: 4.5988 ------------------------------------------------------------------------------- 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 G1595 ASN ** G2013 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.065309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.049619 restraints weight = 89974.244| |-----------------------------------------------------------------------------| r_work (start): 0.2903 rms_B_bonded: 1.83 r_work: 0.2784 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2672 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 moved from start: 0.2327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 30416 Z= 0.178 Angle : 0.529 10.183 41226 Z= 0.275 Chirality : 0.044 0.166 4629 Planarity : 0.004 0.055 5302 Dihedral : 6.954 67.467 4235 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.97 % Allowed : 12.07 % Favored : 85.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.14), residues: 3764 helix: 1.57 (0.13), residues: 1675 sheet: -0.58 (0.22), residues: 518 loop : 0.05 (0.16), residues: 1571 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP G 865 HIS 0.006 0.001 HIS A1689 PHE 0.022 0.002 PHE A1376 TYR 0.018 0.002 TYR G 624 ARG 0.010 0.000 ARG A1070 Details of bonding type rmsd hydrogen bonds : bond 0.04200 ( 1386) hydrogen bonds : angle 4.61092 ( 3861) covalent geometry : bond 0.00414 (30416) covalent geometry : angle 0.52913 (41226) *********************** 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 173 residues out of total 3248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 109 time to evaluate : 3.284 Fit side-chains REVERT: A 74 LEU cc_start: 0.8872 (OUTLIER) cc_final: 0.8609 (pp) REVERT: A 75 HIS cc_start: 0.7916 (OUTLIER) cc_final: 0.7154 (p90) REVERT: A 518 LYS cc_start: 0.7953 (pttt) cc_final: 0.7438 (tptp) REVERT: A 1127 VAL cc_start: 0.8365 (t) cc_final: 0.8103 (p) REVERT: A 1160 THR cc_start: 0.7721 (p) cc_final: 0.7292 (t) REVERT: B 167 PRO cc_start: 0.7488 (Cg_endo) cc_final: 0.7243 (Cg_exo) REVERT: B 168 MET cc_start: 0.7031 (tpp) cc_final: 0.6548 (tmt) REVERT: G 11 LEU cc_start: 0.7480 (OUTLIER) cc_final: 0.7195 (pp) REVERT: G 481 ASP cc_start: 0.8544 (OUTLIER) cc_final: 0.8206 (t70) REVERT: G 1011 MET cc_start: 0.8210 (tpp) cc_final: 0.7969 (mmm) REVERT: G 1064 LYS cc_start: 0.8155 (OUTLIER) cc_final: 0.7424 (mmmm) REVERT: G 1074 MET cc_start: 0.8865 (mmp) cc_final: 0.8618 (mmm) REVERT: G 1747 LYS cc_start: 0.4058 (OUTLIER) cc_final: 0.3088 (pttt) REVERT: G 1881 ARG cc_start: 0.7835 (OUTLIER) cc_final: 0.7131 (tpm170) REVERT: G 1959 LYS cc_start: 0.7649 (OUTLIER) cc_final: 0.7294 (mmmm) REVERT: G 2036 GLU cc_start: 0.8074 (OUTLIER) cc_final: 0.7833 (mp0) REVERT: G 2047 LYS cc_start: 0.8321 (mttm) cc_final: 0.7826 (tmmm) outliers start: 64 outliers final: 48 residues processed: 167 average time/residue: 1.3255 time to fit residues: 265.5270 Evaluate side-chains 165 residues out of total 3248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 108 time to evaluate : 3.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 GLU 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 509 ILE 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 1121 MET 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 1769 VAL 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 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 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 1511 SER Chi-restraints excluded: chain G residue 1565 VAL Chi-restraints excluded: chain G residue 1586 SER 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 1747 LYS 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 69 optimal weight: 0.7980 chunk 47 optimal weight: 8.9990 chunk 302 optimal weight: 3.9990 chunk 257 optimal weight: 0.5980 chunk 147 optimal weight: 6.9990 chunk 345 optimal weight: 10.0000 chunk 366 optimal weight: 8.9990 chunk 303 optimal weight: 10.0000 chunk 328 optimal weight: 4.9990 chunk 217 optimal weight: 4.9990 chunk 331 optimal weight: 20.0000 overall best weight: 3.0786 ------------------------------------------------------------------------------- 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 ** 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 = 0.3352 r_free = 0.3352 target = 0.065720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.049967 restraints weight = 89480.317| |-----------------------------------------------------------------------------| r_work (start): 0.2915 rms_B_bonded: 1.82 r_work: 0.2798 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2686 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.2686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 moved from start: 0.2359 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= 0.135 Angle : 0.498 9.649 41226 Z= 0.259 Chirality : 0.042 0.153 4629 Planarity : 0.004 0.090 5302 Dihedral : 6.777 65.571 4235 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.69 % Allowed : 12.41 % Favored : 85.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.14), residues: 3764 helix: 1.68 (0.13), residues: 1677 sheet: -0.54 (0.22), residues: 517 loop : 0.09 (0.16), residues: 1570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP G 865 HIS 0.006 0.001 HIS A1689 PHE 0.023 0.001 PHE A 35 TYR 0.015 0.001 TYR G 624 ARG 0.018 0.000 ARG A 632 Details of bonding type rmsd hydrogen bonds : bond 0.03897 ( 1386) hydrogen bonds : angle 4.51995 ( 3861) covalent geometry : bond 0.00312 (30416) covalent geometry : angle 0.49830 (41226) *********************** 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 163 residues out of total 3248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 108 time to evaluate : 3.385 Fit side-chains REVERT: A 74 LEU cc_start: 0.8853 (OUTLIER) cc_final: 0.8602 (pp) REVERT: A 75 HIS cc_start: 0.7906 (OUTLIER) cc_final: 0.7135 (p90) REVERT: A 518 LYS cc_start: 0.8001 (pttt) cc_final: 0.7469 (tptp) REVERT: A 1127 VAL cc_start: 0.8356 (t) cc_final: 0.8075 (p) REVERT: A 1160 THR cc_start: 0.7700 (p) cc_final: 0.7274 (t) REVERT: B 167 PRO cc_start: 0.7469 (Cg_endo) cc_final: 0.7250 (Cg_exo) REVERT: G 11 LEU cc_start: 0.7497 (OUTLIER) cc_final: 0.7229 (pt) REVERT: G 481 ASP cc_start: 0.8561 (OUTLIER) cc_final: 0.8244 (t70) REVERT: G 1011 MET cc_start: 0.8211 (tpp) cc_final: 0.7968 (mmm) REVERT: G 1881 ARG cc_start: 0.7830 (OUTLIER) cc_final: 0.7118 (tpm170) REVERT: G 1959 LYS cc_start: 0.7659 (OUTLIER) cc_final: 0.7280 (mmmm) REVERT: G 2036 GLU cc_start: 0.8067 (OUTLIER) cc_final: 0.7823 (mp0) REVERT: G 2047 LYS cc_start: 0.8392 (mttm) cc_final: 0.7880 (tmmm) outliers start: 55 outliers final: 43 residues processed: 159 average time/residue: 1.4147 time to fit residues: 270.0100 Evaluate side-chains 158 residues out of total 3248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 108 time to evaluate : 3.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 1769 VAL 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 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 1479 ILE Chi-restraints excluded: chain G residue 1511 SER Chi-restraints excluded: chain G residue 1565 VAL Chi-restraints excluded: chain G residue 1586 SER 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 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 169 optimal weight: 0.4980 chunk 47 optimal weight: 9.9990 chunk 210 optimal weight: 10.0000 chunk 61 optimal weight: 2.9990 chunk 97 optimal weight: 5.9990 chunk 359 optimal weight: 10.0000 chunk 53 optimal weight: 8.9990 chunk 83 optimal weight: 9.9990 chunk 30 optimal weight: 20.0000 chunk 95 optimal weight: 8.9990 chunk 73 optimal weight: 2.9990 overall best weight: 4.2988 ------------------------------------------------------------------------------- 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 ** G2013 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.065411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.049670 restraints weight = 90452.836| |-----------------------------------------------------------------------------| r_work (start): 0.2903 rms_B_bonded: 1.86 r_work: 0.2786 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2674 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.2674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 moved from start: 0.2369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 30416 Z= 0.170 Angle : 0.526 9.916 41226 Z= 0.273 Chirality : 0.044 0.165 4629 Planarity : 0.004 0.059 5302 Dihedral : 6.824 64.664 4235 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 1.63 % Allowed : 12.50 % Favored : 85.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.14), residues: 3764 helix: 1.62 (0.13), residues: 1674 sheet: -0.56 (0.22), residues: 518 loop : 0.09 (0.16), residues: 1572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP G 865 HIS 0.005 0.001 HIS A1689 PHE 0.022 0.002 PHE A1376 TYR 0.017 0.002 TYR G 624 ARG 0.012 0.000 ARG A1070 Details of bonding type rmsd hydrogen bonds : bond 0.04154 ( 1386) hydrogen bonds : angle 4.59026 ( 3861) covalent geometry : bond 0.00395 (30416) covalent geometry : angle 0.52618 (41226) ********************** 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 164 residues out of total 3248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 111 time to evaluate : 3.340 Fit side-chains REVERT: A 75 HIS cc_start: 0.7872 (OUTLIER) cc_final: 0.7113 (p90) REVERT: A 518 LYS cc_start: 0.8018 (pttt) cc_final: 0.7457 (tptp) REVERT: A 1127 VAL cc_start: 0.8366 (t) cc_final: 0.8090 (p) REVERT: A 1160 THR cc_start: 0.7726 (p) cc_final: 0.7294 (t) REVERT: A 1782 GLU cc_start: 0.7071 (mp0) cc_final: 0.6858 (mp0) REVERT: B 167 PRO cc_start: 0.7425 (Cg_endo) cc_final: 0.7217 (Cg_exo) REVERT: B 168 MET cc_start: 0.6987 (tpp) cc_final: 0.6716 (tmt) REVERT: G 11 LEU cc_start: 0.7433 (OUTLIER) cc_final: 0.7153 (pp) REVERT: G 481 ASP cc_start: 0.8563 (OUTLIER) cc_final: 0.8228 (t70) REVERT: G 1011 MET cc_start: 0.8209 (tpp) cc_final: 0.7964 (mmm) REVERT: G 1881 ARG cc_start: 0.7804 (OUTLIER) cc_final: 0.7098 (tpm170) REVERT: G 1959 LYS cc_start: 0.7653 (OUTLIER) cc_final: 0.7288 (mmmm) REVERT: G 2036 GLU cc_start: 0.8099 (OUTLIER) cc_final: 0.7869 (mp0) outliers start: 53 outliers final: 45 residues processed: 158 average time/residue: 1.3563 time to fit residues: 257.2382 Evaluate side-chains 160 residues out of total 3248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 109 time to evaluate : 3.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET 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 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 1769 VAL 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 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 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 1511 SER Chi-restraints excluded: chain G residue 1565 VAL Chi-restraints excluded: chain G residue 1586 SER 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 1740 THR 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 346 optimal weight: 8.9990 chunk 197 optimal weight: 0.7980 chunk 316 optimal weight: 10.0000 chunk 147 optimal weight: 6.9990 chunk 211 optimal weight: 20.0000 chunk 363 optimal weight: 5.9990 chunk 33 optimal weight: 3.9990 chunk 175 optimal weight: 0.4980 chunk 253 optimal weight: 5.9990 chunk 15 optimal weight: 7.9990 chunk 124 optimal weight: 9.9990 overall best weight: 3.4586 ------------------------------------------------------------------------------- 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 969 ASN A1482 GLN A1794 GLN ** 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 = 0.3350 r_free = 0.3350 target = 0.065679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.049962 restraints weight = 89757.604| |-----------------------------------------------------------------------------| r_work (start): 0.2912 rms_B_bonded: 1.86 r_work: 0.2796 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2684 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.2684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.2395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 30416 Z= 0.146 Angle : 0.507 9.823 41226 Z= 0.264 Chirality : 0.043 0.160 4629 Planarity : 0.004 0.096 5302 Dihedral : 6.720 63.246 4235 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.72 % Allowed : 12.38 % Favored : 85.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.14), residues: 3764 helix: 1.67 (0.13), residues: 1677 sheet: -0.53 (0.22), residues: 517 loop : 0.11 (0.16), residues: 1570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP G 865 HIS 0.006 0.001 HIS A1689 PHE 0.023 0.001 PHE A 35 TYR 0.016 0.001 TYR G 624 ARG 0.020 0.000 ARG A 632 Details of bonding type rmsd hydrogen bonds : bond 0.03971 ( 1386) hydrogen bonds : angle 4.53657 ( 3861) covalent geometry : bond 0.00337 (30416) covalent geometry : angle 0.50667 (41226) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 21477.61 seconds wall clock time: 371 minutes 30.99 seconds (22290.99 seconds total)