Starting phenix.real_space_refine on Sat Apr 13 21:52:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8psm_17856/04_2024/8psm_17856_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8psm_17856/04_2024/8psm_17856.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8psm_17856/04_2024/8psm_17856_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8psm_17856/04_2024/8psm_17856_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8psm_17856/04_2024/8psm_17856_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8psm_17856/04_2024/8psm_17856.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8psm_17856/04_2024/8psm_17856.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8psm_17856/04_2024/8psm_17856_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8psm_17856/04_2024/8psm_17856_updated.pdb" } resolution = 3.1 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= 0.010 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 2 5.49 5 S 107 5.16 5 C 18878 2.51 5 N 4956 2.21 5 O 5682 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 8": "OE1" <-> "OE2" Residue "A TYR 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 329": "OE1" <-> "OE2" Residue "A ASP 334": "OD1" <-> "OD2" Residue "A ASP 355": "OD1" <-> "OD2" Residue "A GLU 633": "OE1" <-> "OE2" Residue "A PHE 710": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 716": "OD1" <-> "OD2" Residue "A GLU 746": "OE1" <-> "OE2" Residue "A ASP 785": "OD1" <-> "OD2" Residue "A GLU 949": "OE1" <-> "OE2" Residue "A TYR 977": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 991": "OD1" <-> "OD2" Residue "A GLU 994": "OE1" <-> "OE2" Residue "A GLU 1016": "OE1" <-> "OE2" Residue "A GLU 1120": "OE1" <-> "OE2" Residue "A GLU 1124": "OE1" <-> "OE2" Residue "A GLU 1128": "OE1" <-> "OE2" Residue "A GLU 1142": "OE1" <-> "OE2" Residue "A GLU 1159": "OE1" <-> "OE2" Residue "A ASP 1202": "OD1" <-> "OD2" Residue "A GLU 1317": "OE1" <-> "OE2" Residue "A TYR 1332": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1354": "OE1" <-> "OE2" Residue "A PHE 1376": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1511": "OD1" <-> "OD2" Residue "A PHE 1576": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1579": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1612": "OD1" <-> "OD2" Residue "A GLU 1681": "OE1" <-> "OE2" Residue "A GLU 1751": "OE1" <-> "OE2" Residue "A PHE 1791": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1797": "OE1" <-> "OE2" Residue "B PHE 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 280": "OE1" <-> "OE2" Residue "B TYR 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 100": "OD1" <-> "OD2" Residue "G ASP 138": "OD1" <-> "OD2" Residue "G GLU 193": "OE1" <-> "OE2" Residue "G GLU 290": "OE1" <-> "OE2" Residue "G TYR 311": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 491": "OE1" <-> "OE2" Residue "G GLU 546": "OE1" <-> "OE2" Residue "G GLU 580": "OE1" <-> "OE2" Residue "G GLU 642": "OE1" <-> "OE2" Residue "G GLU 668": "OE1" <-> "OE2" Residue "G TYR 702": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 780": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 849": "OE1" <-> "OE2" Residue "G GLU 870": "OE1" <-> "OE2" Residue "G GLU 1038": "OE1" <-> "OE2" Residue "G GLU 1216": "OE1" <-> "OE2" Residue "G GLU 1256": "OE1" <-> "OE2" Residue "G ASP 1272": "OD1" <-> "OD2" Residue "G GLU 1291": "OE1" <-> "OE2" Residue "G ASP 1391": "OD1" <-> "OD2" Residue "G PHE 1450": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 1456": "OD1" <-> "OD2" Residue "G GLU 1469": "OE1" <-> "OE2" Residue "G GLU 1500": "OE1" <-> "OE2" Residue "G GLU 1507": "OE1" <-> "OE2" Residue "G ASP 1599": "OD1" <-> "OD2" Residue "G ASP 1708": "OD1" <-> "OD2" Residue "G GLU 1757": "OE1" <-> "OE2" Residue "G ASP 1923": "OD1" <-> "OD2" Residue "G GLU 1935": "OE1" <-> "OE2" Residue "G GLU 1942": "OE1" <-> "OE2" Residue "G PHE 2026": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 29625 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 12346 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1579, 12346 Classifications: {'peptide': 1579} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 61, 'TRANS': 1517} Chain breaks: 4 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: 16004 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2034, 16004 Classifications: {'peptide': 2034} Link IDs: {'PCIS': 1, 'PTRANS': 108, 'TRANS': 1924} Chain breaks: 1 Chain: "B" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 21 Unusual residues: {'PNS': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Chain: "G" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'FMN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 15.53, per 1000 atoms: 0.52 Number of scatterers: 29625 At special positions: 0 Unit cell: (184.625, 182.515, 173.02, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 107 16.00 P 2 15.00 O 5682 8.00 N 4956 7.00 C 18878 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A1246 " - pdb=" SG CYS A1327 " distance=2.87 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 10.90 Conformation dependent library (CDL) restraints added in 5.4 seconds 7520 Ramachandran restraints generated. 3760 Oldfield, 0 Emsley, 3760 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7026 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 170 helices and 26 sheets defined 44.1% alpha, 11.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 10.59 Creating SS restraints... Processing helix chain 'A' and resid 3 through 23 removed outlier: 3.544A pdb=" N GLU A 8 " --> pdb=" O GLU A 4 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N TYR A 20 " --> pdb=" O GLU A 16 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N ALA A 23 " --> pdb=" O ALA A 19 " (cutoff:3.500A) Processing helix chain 'A' and resid 28 through 37 Processing helix chain 'A' and resid 52 through 64 Processing helix chain 'A' and resid 66 through 71 Processing helix chain 'A' and resid 85 through 88 No H-bonds generated for 'chain 'A' and resid 85 through 88' Processing helix chain 'A' and resid 330 through 350 Processing helix chain 'A' and resid 356 through 381 Processing helix chain 'A' and resid 384 through 389 Processing helix chain 'A' and resid 396 through 398 No H-bonds generated for 'chain 'A' and resid 396 through 398' Processing helix chain 'A' and resid 405 through 421 removed outlier: 4.338A pdb=" N LYS A 410 " --> pdb=" O TRP A 406 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLN A 411 " --> pdb=" O ASN A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 442 Processing helix chain 'A' and resid 445 through 456 Processing helix chain 'A' and resid 460 through 462 No H-bonds generated for 'chain 'A' and resid 460 through 462' Processing helix chain 'A' and resid 464 through 484 removed outlier: 3.575A pdb=" N GLU A 478 " --> pdb=" O GLU A 474 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU A 484 " --> pdb=" O CYS A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 531 Processing helix chain 'A' and resid 609 through 615 removed outlier: 3.622A pdb=" N SER A 615 " --> pdb=" O LYS A 611 " (cutoff:3.500A) Processing helix chain 'A' and resid 653 through 668 Processing helix chain 'A' and resid 688 through 698 Processing helix chain 'A' and resid 712 through 724 Processing helix chain 'A' and resid 742 through 753 Processing helix chain 'A' and resid 756 through 758 No H-bonds generated for 'chain 'A' and resid 756 through 758' Processing helix chain 'A' and resid 781 through 783 No H-bonds generated for 'chain 'A' and resid 781 through 783' Processing helix chain 'A' and resid 786 through 795 Processing helix chain 'A' and resid 797 through 812 Processing helix chain 'A' and resid 839 through 855 removed outlier: 3.571A pdb=" N LEU A 846 " --> pdb=" O SER A 842 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N GLU A 847 " --> pdb=" O LYS A 843 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N THR A 848 " --> pdb=" O LEU A 844 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N LEU A 849 " --> pdb=" O SER A 845 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N PHE A 850 " --> pdb=" O LEU A 846 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N ASN A 851 " --> pdb=" O GLU A 847 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N HIS A 854 " --> pdb=" O PHE A 850 " (cutoff:3.500A) Processing helix chain 'A' and resid 858 through 860 No H-bonds generated for 'chain 'A' and resid 858 through 860' Processing helix chain 'A' and resid 885 through 891 removed outlier: 3.886A pdb=" N MET A 891 " --> pdb=" O GLY A 887 " (cutoff:3.500A) Processing helix chain 'A' and resid 898 through 909 removed outlier: 3.715A pdb=" N LEU A 908 " --> pdb=" O ASN A 904 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N LEU A 909 " --> pdb=" O LEU A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 911 through 919 removed outlier: 3.571A pdb=" N LYS A 919 " --> pdb=" O GLU A 915 " (cutoff:3.500A) Processing helix chain 'A' and resid 936 through 968 removed outlier: 3.502A pdb=" N LEU A 947 " --> pdb=" O LEU A 943 " (cutoff:3.500A) Processing helix chain 'A' and resid 998 through 1004 removed outlier: 3.587A pdb=" N ILE A1004 " --> pdb=" O GLN A1000 " (cutoff:3.500A) Processing helix chain 'A' and resid 1007 through 1009 No H-bonds generated for 'chain 'A' and resid 1007 through 1009' Processing helix chain 'A' and resid 1015 through 1017 No H-bonds generated for 'chain 'A' and resid 1015 through 1017' Processing helix chain 'A' and resid 1033 through 1041 Processing helix chain 'A' and resid 1047 through 1057 Processing helix chain 'A' and resid 1086 through 1099 removed outlier: 4.069A pdb=" N LYS A1090 " --> pdb=" O ASP A1086 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N ALA A1091 " --> pdb=" O LYS A1087 " (cutoff:3.500A) removed outlier: 5.085A pdb=" N THR A1095 " --> pdb=" O ALA A1091 " (cutoff:3.500A) removed outlier: 5.801A pdb=" N SER A1096 " --> pdb=" O LYS A1092 " (cutoff:3.500A) Processing helix chain 'A' and resid 1108 through 1110 No H-bonds generated for 'chain 'A' and resid 1108 through 1110' Processing helix chain 'A' and resid 1138 through 1151 removed outlier: 7.221A pdb=" N ASP A1150 " --> pdb=" O HIS A1146 " (cutoff:3.500A) removed outlier: 7.492A pdb=" N LYS A1151 " --> pdb=" O GLN A1147 " (cutoff:3.500A) Processing helix chain 'A' and resid 1195 through 1198 No H-bonds generated for 'chain 'A' and resid 1195 through 1198' Processing helix chain 'A' and resid 1202 through 1205 No H-bonds generated for 'chain 'A' and resid 1202 through 1205' Processing helix chain 'A' and resid 1210 through 1225 removed outlier: 3.547A pdb=" N PHE A1214 " --> pdb=" O PRO A1210 " (cutoff:3.500A) Processing helix chain 'A' and resid 1231 through 1236 Processing helix chain 'A' and resid 1240 through 1242 No H-bonds generated for 'chain 'A' and resid 1240 through 1242' Processing helix chain 'A' and resid 1254 through 1261 Processing helix chain 'A' and resid 1272 through 1277 removed outlier: 4.466A pdb=" N LEU A1275 " --> pdb=" O ASN A1272 " (cutoff:3.500A) Processing helix chain 'A' and resid 1280 through 1290 removed outlier: 4.658A pdb=" N SER A1284 " --> pdb=" O ILE A1280 " (cutoff:3.500A) Processing helix chain 'A' and resid 1304 through 1321 removed outlier: 4.693A pdb=" N SER A1308 " --> pdb=" O CYS A1305 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VAL A1309 " --> pdb=" O ALA A1306 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N SER A1311 " --> pdb=" O SER A1308 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N THR A1318 " --> pdb=" O GLY A1315 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N SER A1321 " --> pdb=" O THR A1318 " (cutoff:3.500A) Processing helix chain 'A' and resid 1337 through 1345 Processing helix chain 'A' and resid 1352 through 1357 Processing helix chain 'A' and resid 1362 through 1364 No H-bonds generated for 'chain 'A' and resid 1362 through 1364' Processing helix chain 'A' and resid 1390 through 1396 Processing helix chain 'A' and resid 1424 through 1429 Processing helix chain 'A' and resid 1445 through 1468 Processing helix chain 'A' and resid 1472 through 1476 removed outlier: 4.197A pdb=" N GLU A1476 " --> pdb=" O LEU A1472 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1472 through 1476' Processing helix chain 'A' and resid 1482 through 1508 removed outlier: 3.587A pdb=" N GLU A1492 " --> pdb=" O GLU A1488 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE A1493 " --> pdb=" O ARG A1489 " (cutoff:3.500A) Processing helix chain 'A' and resid 1521 through 1529 removed outlier: 3.724A pdb=" N LEU A1526 " --> pdb=" O LEU A1522 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N TYR A1529 " --> pdb=" O ALA A1525 " (cutoff:3.500A) Processing helix chain 'A' and resid 1533 through 1535 No H-bonds generated for 'chain 'A' and resid 1533 through 1535' Processing helix chain 'A' and resid 1547 through 1563 removed outlier: 3.882A pdb=" N LYS A1551 " --> pdb=" O LYS A1547 " (cutoff:3.500A) Processing helix chain 'A' and resid 1577 through 1581 removed outlier: 3.892A pdb=" N THR A1581 " --> pdb=" O LYS A1578 " (cutoff:3.500A) Processing helix chain 'A' and resid 1585 through 1602 removed outlier: 4.139A pdb=" N GLY A1589 " --> pdb=" O GLY A1586 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ASN A1601 " --> pdb=" O GLN A1598 " (cutoff:3.500A) Processing helix chain 'A' and resid 1616 through 1620 removed outlier: 3.669A pdb=" N GLN A1620 " --> pdb=" O ILE A1617 " (cutoff:3.500A) Processing helix chain 'A' and resid 1658 through 1664 removed outlier: 3.519A pdb=" N TYR A1662 " --> pdb=" O ASP A1659 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N GLY A1663 " --> pdb=" O TYR A1660 " (cutoff:3.500A) Processing helix chain 'A' and resid 1667 through 1693 Processing helix chain 'A' and resid 1711 through 1716 Processing helix chain 'A' and resid 1735 through 1737 No H-bonds generated for 'chain 'A' and resid 1735 through 1737' Processing helix chain 'A' and resid 1741 through 1744 No H-bonds generated for 'chain 'A' and resid 1741 through 1744' Processing helix chain 'A' and resid 1747 through 1759 Processing helix chain 'A' and resid 1776 through 1778 No H-bonds generated for 'chain 'A' and resid 1776 through 1778' Processing helix chain 'A' and resid 1784 through 1789 Processing helix chain 'A' and resid 1793 through 1800 removed outlier: 3.598A pdb=" N GLU A1797 " --> pdb=" O PRO A1793 " (cutoff:3.500A) Processing helix chain 'A' and resid 1805 through 1823 Processing helix chain 'A' and resid 1854 through 1861 removed outlier: 3.741A pdb=" N GLU A1860 " --> pdb=" O LYS A1856 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N GLU A1861 " --> pdb=" O LYS A1857 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 158 Processing helix chain 'B' and resid 172 through 176 Processing helix chain 'B' and resid 180 through 192 removed outlier: 3.628A pdb=" N GLN B 183 " --> pdb=" O SER B 180 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU B 187 " --> pdb=" O ASN B 184 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLY B 188 " --> pdb=" O GLU B 185 " (cutoff:3.500A) Processing helix chain 'B' and resid 207 through 216 removed outlier: 4.230A pdb=" N THR B 216 " --> pdb=" O THR B 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 236 Processing helix chain 'B' and resid 243 through 252 removed outlier: 3.986A pdb=" N LEU B 250 " --> pdb=" O ALA B 246 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 269 removed outlier: 4.036A pdb=" N GLY B 263 " --> pdb=" O GLY B 259 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL B 267 " --> pdb=" O GLY B 263 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 285 Processing helix chain 'B' and resid 290 through 298 Processing helix chain 'G' and resid 24 through 26 No H-bonds generated for 'chain 'G' and resid 24 through 26' Processing helix chain 'G' and resid 28 through 40 Processing helix chain 'G' and resid 57 through 71 Processing helix chain 'G' and resid 81 through 95 removed outlier: 3.551A pdb=" N THR G 89 " --> pdb=" O ASN G 85 " (cutoff:3.500A) Processing helix chain 'G' and resid 101 through 110 Processing helix chain 'G' and resid 116 through 132 Processing helix chain 'G' and resid 144 through 151 Processing helix chain 'G' and resid 169 through 179 removed outlier: 4.394A pdb=" N ARG G 174 " --> pdb=" O GLU G 171 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ASP G 175 " --> pdb=" O GLU G 172 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N THR G 179 " --> pdb=" O LEU G 176 " (cutoff:3.500A) Processing helix chain 'G' and resid 181 through 201 removed outlier: 5.306A pdb=" N ASP G 186 " --> pdb=" O VAL G 182 " (cutoff:3.500A) removed outlier: 5.047A pdb=" N LEU G 187 " --> pdb=" O LEU G 183 " (cutoff:3.500A) Processing helix chain 'G' and resid 215 through 220 Processing helix chain 'G' and resid 228 through 232 Processing helix chain 'G' and resid 234 through 256 Proline residue: G 239 - end of helix Processing helix chain 'G' and resid 260 through 265 Processing helix chain 'G' and resid 274 through 285 removed outlier: 3.708A pdb=" N VAL G 281 " --> pdb=" O VAL G 278 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ILE G 283 " --> pdb=" O ALA G 280 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ALA G 284 " --> pdb=" O VAL G 281 " (cutoff:3.500A) Processing helix chain 'G' and resid 292 through 313 Processing helix chain 'G' and resid 321 through 329 Processing helix chain 'G' and resid 346 through 359 removed outlier: 4.107A pdb=" N HIS G 359 " --> pdb=" O LYS G 355 " (cutoff:3.500A) Processing helix chain 'G' and resid 362 through 364 No H-bonds generated for 'chain 'G' and resid 362 through 364' Processing helix chain 'G' and resid 383 through 396 removed outlier: 3.544A pdb=" N ALA G 396 " --> pdb=" O THR G 392 " (cutoff:3.500A) Processing helix chain 'G' and resid 409 through 411 No H-bonds generated for 'chain 'G' and resid 409 through 411' Processing helix chain 'G' and resid 430 through 446 Proline residue: G 434 - end of helix removed outlier: 4.476A pdb=" N ASP G 437 " --> pdb=" O PRO G 434 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ASN G 440 " --> pdb=" O ASP G 437 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N LEU G 443 " --> pdb=" O ASN G 440 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N VAL G 444 " --> pdb=" O LYS G 441 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N LYS G 445 " --> pdb=" O ASP G 442 " (cutoff:3.500A) Processing helix chain 'G' and resid 475 through 484 Processing helix chain 'G' and resid 490 through 493 No H-bonds generated for 'chain 'G' and resid 490 through 493' Processing helix chain 'G' and resid 508 through 510 No H-bonds generated for 'chain 'G' and resid 508 through 510' Processing helix chain 'G' and resid 512 through 520 removed outlier: 3.730A pdb=" N ASN G 519 " --> pdb=" O LEU G 515 " (cutoff:3.500A) Processing helix chain 'G' and resid 544 through 548 Processing helix chain 'G' and resid 561 through 564 No H-bonds generated for 'chain 'G' and resid 561 through 564' Processing helix chain 'G' and resid 582 through 587 removed outlier: 3.650A pdb=" N LEU G 586 " --> pdb=" O LYS G 582 " (cutoff:3.500A) Processing helix chain 'G' and resid 604 through 612 Processing helix chain 'G' and resid 627 through 640 Processing helix chain 'G' and resid 656 through 671 removed outlier: 3.748A 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 688 through 697 Processing helix chain 'G' and resid 710 through 723 Processing helix chain 'G' and resid 748 through 758 removed outlier: 5.172A pdb=" N SER G 755 " --> pdb=" O LEU G 751 " (cutoff:3.500A) removed outlier: 5.187A pdb=" N LYS G 756 " --> pdb=" O GLN G 752 " (cutoff:3.500A) Processing helix chain 'G' and resid 778 through 782 Processing helix chain 'G' and resid 784 through 788 removed outlier: 3.504A pdb=" N THR G 787 " --> pdb=" O GLU G 784 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N LYS G 788 " --> pdb=" O TRP G 785 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 784 through 788' Processing helix chain 'G' and resid 803 through 805 No H-bonds generated for 'chain 'G' and resid 803 through 805' Processing helix chain 'G' and resid 815 through 823 Processing helix chain 'G' and resid 832 through 835 Processing helix chain 'G' and resid 860 through 871 Processing helix chain 'G' and resid 877 through 886 removed outlier: 4.220A pdb=" N VAL G 881 " --> pdb=" O LYS G 877 " (cutoff:3.500A) Proline residue: G 882 - end of helix removed outlier: 3.807A pdb=" N GLU G 885 " --> pdb=" O VAL G 881 " (cutoff:3.500A) Processing helix chain 'G' and resid 888 through 897 Processing helix chain 'G' and resid 914 through 916 No H-bonds generated for 'chain 'G' and resid 914 through 916' Processing helix chain 'G' and resid 919 through 930 Processing helix chain 'G' and resid 941 through 958 Processing helix chain 'G' and resid 970 through 974 Processing helix chain 'G' and resid 976 through 986 Processing helix chain 'G' and resid 988 through 991 Processing helix chain 'G' and resid 997 through 1008 removed outlier: 3.541A pdb=" N ASP G1001 " --> pdb=" O ALA G 997 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLN G1008 " --> pdb=" O LEU G1004 " (cutoff:3.500A) Processing helix chain 'G' and resid 1023 through 1030 removed outlier: 4.150A pdb=" N GLU G1026 " --> pdb=" O ARG G1023 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N PHE G1029 " --> pdb=" O GLU G1026 " (cutoff:3.500A) Processing helix chain 'G' and resid 1035 through 1038 Processing helix chain 'G' and resid 1040 through 1042 No H-bonds generated for 'chain 'G' and resid 1040 through 1042' Processing helix chain 'G' and resid 1048 through 1050 No H-bonds generated for 'chain 'G' and resid 1048 through 1050' Processing helix chain 'G' and resid 1059 through 1061 No H-bonds generated for 'chain 'G' and resid 1059 through 1061' Processing helix chain 'G' and resid 1070 through 1089 Processing helix chain 'G' and resid 1094 through 1096 No H-bonds generated for 'chain 'G' and resid 1094 through 1096' Processing helix chain 'G' and resid 1135 through 1143 Processing helix chain 'G' and resid 1149 through 1155 Processing helix chain 'G' and resid 1169 through 1174 Processing helix chain 'G' and resid 1258 through 1270 removed outlier: 3.524A pdb=" N LYS G1268 " --> pdb=" O GLU G1264 " (cutoff:3.500A) Processing helix chain 'G' and resid 1294 through 1304 Processing helix chain 'G' and resid 1309 through 1311 No H-bonds generated for 'chain 'G' and resid 1309 through 1311' Processing helix chain 'G' and resid 1323 through 1338 removed outlier: 3.926A pdb=" N GLY G1330 " --> pdb=" O ILE G1327 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N TRP G1331 " --> pdb=" O VAL G1328 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N ARG G1332 " --> pdb=" O VAL G1329 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ILE G1334 " --> pdb=" O TRP G1331 " (cutoff:3.500A) removed outlier: 5.248A pdb=" N ILE G1335 " --> pdb=" O ARG G1332 " (cutoff:3.500A) Processing helix chain 'G' and resid 1341 through 1343 No H-bonds generated for 'chain 'G' and resid 1341 through 1343' Processing helix chain 'G' and resid 1419 through 1421 No H-bonds generated for 'chain 'G' and resid 1419 through 1421' Processing helix chain 'G' and resid 1439 through 1446 Processing helix chain 'G' and resid 1515 through 1522 Processing helix chain 'G' and resid 1551 through 1557 Processing helix chain 'G' and resid 1562 through 1564 No H-bonds generated for 'chain 'G' and resid 1562 through 1564' Processing helix chain 'G' and resid 1567 through 1572 Processing helix chain 'G' and resid 1582 through 1596 Processing helix chain 'G' and resid 1678 through 1683 removed outlier: 3.705A pdb=" N THR G1683 " --> pdb=" O ASP G1679 " (cutoff:3.500A) Processing helix chain 'G' and resid 1686 through 1702 Processing helix chain 'G' and resid 1706 through 1712 Processing helix chain 'G' and resid 1723 through 1734 Processing helix chain 'G' and resid 1774 through 1794 Proline residue: G1779 - end of helix Processing helix chain 'G' and resid 1808 through 1818 removed outlier: 3.576A pdb=" N GLU G1811 " --> pdb=" O SER G1808 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ALA G1814 " --> pdb=" O GLU G1811 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N LEU G1818 " --> pdb=" O LEU G1815 " (cutoff:3.500A) Processing helix chain 'G' and resid 1824 through 1838 Processing helix chain 'G' and resid 1859 through 1862 No H-bonds generated for 'chain 'G' and resid 1859 through 1862' Processing helix chain 'G' and resid 1868 through 1882 Processing helix chain 'G' and resid 1904 through 1913 removed outlier: 3.656A pdb=" N VAL G1910 " --> pdb=" O ALA G1906 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ASN G1912 " --> pdb=" O ASP G1908 " (cutoff:3.500A) Processing helix chain 'G' and resid 1917 through 1920 No H-bonds generated for 'chain 'G' and resid 1917 through 1920' Processing helix chain 'G' and resid 1925 through 1928 No H-bonds generated for 'chain 'G' and resid 1925 through 1928' Processing helix chain 'G' and resid 1935 through 1951 removed outlier: 4.322A pdb=" N LEU G1940 " --> pdb=" O GLU G1937 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N PHE G1941 " --> pdb=" O GLY G1938 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ILE G1944 " --> pdb=" O PHE G1941 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLU G1946 " --> pdb=" O ILE G1943 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N SER G1948 " --> pdb=" O ASP G1945 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LYS G1949 " --> pdb=" O GLU G1946 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N SER G1951 " --> pdb=" O SER G1948 " (cutoff:3.500A) Processing helix chain 'G' and resid 1980 through 1994 removed outlier: 4.391A pdb=" N ASN G1983 " --> pdb=" O TYR G1980 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLY G1984 " --> pdb=" O LEU G1981 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LYS G1986 " --> pdb=" O ASN G1983 " (cutoff:3.500A) Proline residue: G1987 - end of helix removed outlier: 3.603A pdb=" N SER G1990 " --> pdb=" O PRO G1987 " (cutoff:3.500A) Processing helix chain 'G' and resid 1998 through 2000 No H-bonds generated for 'chain 'G' and resid 1998 through 2000' Processing helix chain 'G' and resid 2023 through 2032 removed outlier: 3.568A pdb=" N LEU G2032 " --> pdb=" O ASP G2028 " (cutoff:3.500A) Processing helix chain 'G' and resid 2036 through 2043 Processing helix chain 'G' and resid 2045 through 2049 Processing sheet with id= A, first strand: chain 'A' and resid 44 through 46 Processing sheet with id= B, first strand: chain 'A' and resid 400 through 402 removed outlier: 6.549A pdb=" N ALA A 767 " --> pdb=" O LEU A 679 " (cutoff:3.500A) removed outlier: 8.415A pdb=" N THR A 681 " --> pdb=" O ALA A 767 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N ILE A 769 " --> pdb=" O THR A 681 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 497 through 503 Processing sheet with id= D, first strand: chain 'A' and resid 649 through 651 removed outlier: 4.343A pdb=" N MET A 923 " --> pdb=" O ARG A 641 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N ALA A 820 " --> pdb=" O THR A 863 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N CYS A 865 " --> pdb=" O ALA A 820 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N VAL A 822 " --> pdb=" O CYS A 865 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N ALA A 867 " --> pdb=" O VAL A 822 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N LEU A 824 " --> pdb=" O ALA A 867 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N ILE A 869 " --> pdb=" O LEU A 824 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N MET A 826 " --> pdb=" O ILE A 869 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 1243 through 1245 removed outlier: 6.699A pdb=" N ILE A1326 " --> pdb=" O GLY A1244 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N MET A1388 " --> pdb=" O VAL A1021 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N VAL A1021 " --> pdb=" O MET A1388 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N ILE A1019 " --> pdb=" O VAL A1404 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N GLY A1402 " --> pdb=" O VAL A1021 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N ILE A1654 " --> pdb=" O ALA A1405 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N ALA A1407 " --> pdb=" O GLN A1652 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N GLN A1652 " --> pdb=" O ALA A1407 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N THR A1409 " --> pdb=" O GLY A1650 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N GLY A1650 " --> pdb=" O THR A1409 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 1060 through 1066 Processing sheet with id= G, first strand: chain 'A' and resid 1102 through 1105 removed outlier: 4.165A pdb=" N GLY A1102 " --> pdb=" O GLN A1188 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLN A1188 " --> pdb=" O GLY A1102 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 1121 through 1126 Processing sheet with id= I, first strand: chain 'A' and resid 1134 through 1136 Processing sheet with id= J, first strand: chain 'A' and resid 1538 through 1540 removed outlier: 5.735A pdb=" N ILE A1573 " --> pdb=" O ALA A1539 " (cutoff:3.500A) No H-bonds generated for sheet with id= J Processing sheet with id= K, first strand: chain 'A' and resid 1769 through 1775 removed outlier: 3.629A pdb=" N ASP A1866 " --> pdb=" O THR A1885 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'A' and resid 1837 through 1840 Processing sheet with id= M, first strand: chain 'G' and resid 6 through 13 removed outlier: 3.818A pdb=" N LEU G 16 " --> pdb=" O HIS G 13 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'G' and resid 526 through 529 removed outlier: 7.934A pdb=" N ALA G 158 " --> pdb=" O LYS G 268 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N ALA G 270 " --> pdb=" O ALA G 158 " (cutoff:3.500A) removed outlier: 7.383A pdb=" N PHE G 160 " --> pdb=" O ALA G 270 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N GLY G 272 " --> pdb=" O PHE G 160 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'G' and resid 338 through 342 removed outlier: 5.950A pdb=" N SER G 380 " --> pdb=" O ILE G 368 " (cutoff:3.500A) removed outlier: 5.514A pdb=" N ILE G 368 " --> pdb=" O SER G 380 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'G' and resid 568 through 571 Processing sheet with id= Q, first strand: chain 'G' and resid 618 through 620 removed outlier: 6.530A pdb=" N GLY G 648 " --> pdb=" O LEU G 619 " (cutoff:3.500A) removed outlier: 7.868A pdb=" N ILE G 649 " --> pdb=" O GLN G 677 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N LEU G 679 " --> pdb=" O ILE G 649 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N LEU G 651 " --> pdb=" O LEU G 679 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N ILE G 681 " --> pdb=" O LEU G 651 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N TYR G 702 " --> pdb=" O LEU G 679 " (cutoff:3.500A) removed outlier: 8.407A pdb=" N ILE G 681 " --> pdb=" O TYR G 702 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N GLY G 704 " --> pdb=" O ILE G 681 " (cutoff:3.500A) removed outlier: 7.874A pdb=" N LEU G 705 " --> pdb=" O PRO G 727 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N ALA G 729 " --> pdb=" O LEU G 705 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'G' and resid 843 through 847 Processing sheet with id= S, first strand: chain 'G' and resid 1125 through 1128 removed outlier: 3.511A pdb=" N VAL G1209 " --> pdb=" O LEU G1197 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N GLU G1199 " --> pdb=" O PRO G1207 " (cutoff:3.500A) removed outlier: 5.351A pdb=" N THR G1208 " --> pdb=" O ILE G1224 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'G' and resid 1158 through 1161 Processing sheet with id= U, first strand: chain 'G' and resid 1372 through 1375 removed outlier: 6.034A pdb=" N ARG G1398 " --> pdb=" O PRO G1402 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N SER G1354 " --> pdb=" O SER G1409 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N PHE G1411 " --> pdb=" O HIS G1352 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N HIS G1352 " --> pdb=" O PHE G1411 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N ARG G1413 " --> pdb=" O LEU G1350 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N LEU G1350 " --> pdb=" O ARG G1413 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N ARG G1606 " --> pdb=" O MET G1359 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N GLU G1656 " --> pdb=" O ARG G1606 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N TYR G1608 " --> pdb=" O GLU G1654 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N GLU G1654 " --> pdb=" O TYR G1608 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N CYS G1610 " --> pdb=" O THR G1652 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N THR G1652 " --> pdb=" O CYS G1610 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N THR G1642 " --> pdb=" O VAL G1650 " (cutoff:3.500A) removed outlier: 4.943A pdb=" N THR G1652 " --> pdb=" O PHE G1640 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N PHE G1640 " --> pdb=" O THR G1652 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N GLU G1654 " --> pdb=" O ILE G1638 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N ILE G1638 " --> pdb=" O GLU G1654 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N GLU G1656 " --> pdb=" O LYS G1636 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N LYS G1636 " --> pdb=" O GLU G1656 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N LYS G1639 " --> pdb=" O HIS G1628 " (cutoff:3.500A) removed outlier: 5.144A pdb=" N HIS G1628 " --> pdb=" O LYS G1639 " (cutoff:3.500A) removed outlier: 7.613A pdb=" N GLU G1641 " --> pdb=" O ILE G1626 " (cutoff:3.500A) removed outlier: 5.553A pdb=" N ILE G1626 " --> pdb=" O GLU G1641 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N ARG G1643 " --> pdb=" O THR G1624 " (cutoff:3.500A) removed outlier: 5.431A pdb=" N THR G1624 " --> pdb=" O ARG G1643 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ALA G1540 " --> pdb=" O ILE G1626 " (cutoff:3.500A) removed outlier: 5.976A pdb=" N HIS G1628 " --> pdb=" O PRO G1538 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'G' and resid 1431 through 1435 removed outlier: 3.655A pdb=" N TYR G1431 " --> pdb=" O PHE G1466 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LYS G1462 " --> pdb=" O ILE G1435 " (cutoff:3.500A) removed outlier: 5.157A pdb=" N THR G1463 " --> pdb=" O GLU G1492 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N GLY G1487 " --> pdb=" O VAL G1504 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N VAL G1491 " --> pdb=" O GLU G1500 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N GLU G1500 " --> pdb=" O VAL G1491 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'G' and resid 1663 through 1666 removed outlier: 6.783A pdb=" N THR G1803 " --> pdb=" O PHE G1664 " (cutoff:3.500A) removed outlier: 8.570A pdb=" N PHE G1666 " --> pdb=" O THR G1803 " (cutoff:3.500A) removed outlier: 7.262A pdb=" N ALA G1805 " --> pdb=" O PHE G1666 " (cutoff:3.500A) No H-bonds generated for sheet with id= W Processing sheet with id= X, first strand: chain 'G' and resid 1716 through 1720 Processing sheet with id= Y, first strand: chain 'G' and resid 1966 through 1968 removed outlier: 6.337A pdb=" N ALA G1901 " --> pdb=" O ILE G1888 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N ILE G1888 " --> pdb=" O ALA G1901 " (cutoff:3.500A) removed outlier: 7.549A pdb=" N ASP G1903 " --> pdb=" O VAL G1886 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N VAL G1886 " --> pdb=" O ASP G1903 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'G' and resid 1378 through 1383 removed outlier: 6.922A pdb=" N ASP G1391 " --> pdb=" O GLU G1379 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N VAL G1381 " --> pdb=" O ILE G1389 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N ILE G1389 " --> pdb=" O VAL G1381 " (cutoff:3.500A) 1134 hydrogen bonds defined for protein. 3069 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: 13.84 Time building geometry restraints manager: 11.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.31: 5071 1.31 - 1.45: 7647 1.45 - 1.59: 17333 1.59 - 1.72: 3 1.72 - 1.86: 188 Bond restraints: 30242 Sorted by residual: bond pdb=" CD GLU A1317 " pdb=" OE2 GLU A1317 " ideal model delta sigma weight residual 1.249 1.380 -0.131 1.90e-02 2.77e+03 4.72e+01 bond pdb=" NE ARG A1515 " pdb=" CZ ARG A1515 " ideal model delta sigma weight residual 1.326 1.398 -0.072 1.10e-02 8.26e+03 4.30e+01 bond pdb=" C39 PNS B1901 " pdb=" N41 PNS B1901 " ideal model delta sigma weight residual 1.452 1.341 0.111 2.00e-02 2.50e+03 3.09e+01 bond pdb=" C TYR A1174 " pdb=" O TYR A1174 " ideal model delta sigma weight residual 1.236 1.299 -0.063 1.14e-02 7.69e+03 3.06e+01 bond pdb=" N ILE G1798 " pdb=" CA ILE G1798 " ideal model delta sigma weight residual 1.458 1.498 -0.040 7.70e-03 1.69e+04 2.76e+01 ... (remaining 30237 not shown) Histogram of bond angle deviations from ideal: 95.49 - 103.32: 311 103.32 - 111.15: 9661 111.15 - 118.99: 17708 118.99 - 126.82: 13000 126.82 - 134.65: 282 Bond angle restraints: 40962 Sorted by residual: angle pdb=" CB GLU A1317 " pdb=" CG GLU A1317 " pdb=" CD GLU A1317 " ideal model delta sigma weight residual 112.60 125.57 -12.97 1.70e+00 3.46e-01 5.82e+01 angle pdb=" C SER G 233 " pdb=" N ILE G 234 " pdb=" CA ILE G 234 " ideal model delta sigma weight residual 120.24 124.94 -4.70 6.30e-01 2.52e+00 5.57e+01 angle pdb=" N SER B 180 " pdb=" CA SER B 180 " pdb=" C SER B 180 " ideal model delta sigma weight residual 111.07 118.52 -7.45 1.07e+00 8.73e-01 4.84e+01 angle pdb=" CA GLY G1577 " pdb=" C GLY G1577 " pdb=" O GLY G1577 " ideal model delta sigma weight residual 122.33 116.81 5.52 8.10e-01 1.52e+00 4.65e+01 angle pdb=" CA ASP A1612 " pdb=" CB ASP A1612 " pdb=" CG ASP A1612 " ideal model delta sigma weight residual 112.60 119.30 -6.70 1.00e+00 1.00e+00 4.50e+01 ... (remaining 40957 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.89: 16536 18.89 - 37.79: 1385 37.79 - 56.68: 233 56.68 - 75.57: 71 75.57 - 94.46: 30 Dihedral angle restraints: 18255 sinusoidal: 7346 harmonic: 10909 Sorted by residual: dihedral pdb=" CB CYS A1246 " pdb=" SG CYS A1246 " pdb=" SG CYS A1327 " pdb=" CB CYS A1327 " ideal model delta sinusoidal sigma weight residual 93.00 37.41 55.59 1 1.00e+01 1.00e-02 4.18e+01 dihedral pdb=" C5' FMN G2101 " pdb=" O5' FMN G2101 " pdb=" P FMN G2101 " pdb=" O1P FMN G2101 " ideal model delta sinusoidal sigma weight residual 75.26 169.72 -94.46 1 2.00e+01 2.50e-03 2.59e+01 dihedral pdb=" CA SER G 769 " pdb=" C SER G 769 " pdb=" N GLY G 770 " pdb=" CA GLY G 770 " ideal model delta harmonic sigma weight residual 180.00 154.78 25.22 0 5.00e+00 4.00e-02 2.54e+01 ... (remaining 18252 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 2135 0.062 - 0.124: 1718 0.124 - 0.185: 608 0.185 - 0.247: 128 0.247 - 0.309: 14 Chirality restraints: 4603 Sorted by residual: chirality pdb=" CA ILE A1403 " pdb=" N ILE A1403 " pdb=" C ILE A1403 " pdb=" CB ILE A1403 " both_signs ideal model delta sigma weight residual False 2.43 2.74 -0.31 2.00e-01 2.50e+01 2.38e+00 chirality pdb=" CA VAL G1616 " pdb=" N VAL G1616 " pdb=" C VAL G1616 " pdb=" CB VAL G1616 " both_signs ideal model delta sigma weight residual False 2.44 2.75 -0.31 2.00e-01 2.50e+01 2.33e+00 chirality pdb=" CA VAL A 893 " pdb=" N VAL A 893 " pdb=" C VAL A 893 " pdb=" CB VAL A 893 " both_signs ideal model delta sigma weight residual False 2.44 2.75 -0.30 2.00e-01 2.50e+01 2.32e+00 ... (remaining 4600 not shown) Planarity restraints: 5286 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C32 PNS B1901 " -0.064 2.00e-02 2.50e+03 6.56e-02 5.37e+01 pdb=" C34 PNS B1901 " 0.036 2.00e-02 2.50e+03 pdb=" C37 PNS B1901 " -0.079 2.00e-02 2.50e+03 pdb=" N36 PNS B1901 " 0.099 2.00e-02 2.50e+03 pdb=" O35 PNS B1901 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' FMN G2101 " 0.008 2.00e-02 2.50e+03 2.72e-02 3.51e+01 pdb=" C10 FMN G2101 " 0.010 2.00e-02 2.50e+03 pdb=" C2 FMN G2101 " -0.028 2.00e-02 2.50e+03 pdb=" C4 FMN G2101 " -0.008 2.00e-02 2.50e+03 pdb=" C4A FMN G2101 " 0.026 2.00e-02 2.50e+03 pdb=" C5A FMN G2101 " 0.054 2.00e-02 2.50e+03 pdb=" C6 FMN G2101 " 0.026 2.00e-02 2.50e+03 pdb=" C7 FMN G2101 " -0.010 2.00e-02 2.50e+03 pdb=" C7M FMN G2101 " -0.063 2.00e-02 2.50e+03 pdb=" C8 FMN G2101 " -0.010 2.00e-02 2.50e+03 pdb=" C8M FMN G2101 " -0.019 2.00e-02 2.50e+03 pdb=" C9 FMN G2101 " 0.001 2.00e-02 2.50e+03 pdb=" C9A FMN G2101 " 0.022 2.00e-02 2.50e+03 pdb=" N1 FMN G2101 " -0.014 2.00e-02 2.50e+03 pdb=" N10 FMN G2101 " 0.017 2.00e-02 2.50e+03 pdb=" N3 FMN G2101 " -0.029 2.00e-02 2.50e+03 pdb=" N5 FMN G2101 " 0.045 2.00e-02 2.50e+03 pdb=" O2 FMN G2101 " -0.018 2.00e-02 2.50e+03 pdb=" O4 FMN G2101 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 722 " 0.066 2.00e-02 2.50e+03 3.54e-02 2.50e+01 pdb=" CG TYR A 722 " -0.061 2.00e-02 2.50e+03 pdb=" CD1 TYR A 722 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 TYR A 722 " -0.016 2.00e-02 2.50e+03 pdb=" CE1 TYR A 722 " -0.020 2.00e-02 2.50e+03 pdb=" CE2 TYR A 722 " -0.006 2.00e-02 2.50e+03 pdb=" CZ TYR A 722 " 0.010 2.00e-02 2.50e+03 pdb=" OH TYR A 722 " 0.034 2.00e-02 2.50e+03 ... (remaining 5283 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 469 2.66 - 3.22: 27718 3.22 - 3.78: 45779 3.78 - 4.34: 66244 4.34 - 4.90: 106839 Nonbonded interactions: 247049 Sorted by model distance: nonbonded pdb=" O PHE A 35 " pdb=" OG1 THR A 41 " model vdw 2.097 2.440 nonbonded pdb=" O TRP A1030 " pdb=" OG1 THR A1035 " model vdw 2.209 2.440 nonbonded pdb=" O3P FMN G2101 " pdb=" O4' FMN G2101 " model vdw 2.215 2.440 nonbonded pdb=" OH TYR G 778 " pdb=" OE1 GLN G1088 " model vdw 2.244 2.440 nonbonded pdb=" OH TYR A1694 " pdb=" OD2 ASP G1001 " model vdw 2.259 2.440 ... (remaining 247044 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.620 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: 0.030 Extract box with map and model: 4.750 Check model and map are aligned: 0.490 Set scattering table: 0.290 Process input model: 80.010 Find NCS groups from input model: 0.810 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:3.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 90.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8861 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 0.131 30242 Z= 0.889 Angle : 1.880 12.974 40962 Z= 1.374 Chirality : 0.089 0.309 4603 Planarity : 0.007 0.066 5286 Dihedral : 15.082 94.463 11226 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.48 % Allowed : 6.38 % Favored : 93.14 % Rotamer: Outliers : 0.55 % Allowed : 4.07 % Favored : 95.38 % 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: -3.52 (0.11), residues: 3760 helix: -2.83 (0.09), residues: 1627 sheet: -2.17 (0.20), residues: 502 loop : -1.61 (0.14), residues: 1631 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.007 TRP G 943 HIS 0.017 0.004 HIS A1689 PHE 0.043 0.007 PHE G 799 TYR 0.066 0.007 TYR A 722 ARG 0.010 0.001 ARG A1104 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7520 Ramachandran restraints generated. 3760 Oldfield, 0 Emsley, 3760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7520 Ramachandran restraints generated. 3760 Oldfield, 0 Emsley, 3760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 3245 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 232 time to evaluate : 3.244 Fit side-chains REVERT: A 56 MET cc_start: 0.9267 (mtt) cc_final: 0.9060 (mtt) REVERT: A 431 GLU cc_start: 0.9253 (mm-30) cc_final: 0.8888 (mp0) REVERT: A 917 CYS cc_start: 0.9446 (OUTLIER) cc_final: 0.9219 (m) REVERT: A 1112 ASN cc_start: 0.8961 (t0) cc_final: 0.8485 (t0) REVERT: A 1317 GLU cc_start: 0.7055 (tt0) cc_final: 0.5657 (mm-30) REVERT: A 1741 LYS cc_start: 0.4000 (mmmt) cc_final: 0.3573 (mmmt) REVERT: A 1755 MET cc_start: 0.8796 (mmp) cc_final: 0.8338 (mtp) REVERT: A 1790 ASN cc_start: 0.8494 (m110) cc_final: 0.8289 (m110) REVERT: B 168 MET cc_start: 0.8707 (tpp) cc_final: 0.8118 (tpp) REVERT: B 200 LYS cc_start: 0.7663 (ptmm) cc_final: 0.7277 (ttmt) REVERT: B 237 MET cc_start: 0.6924 (mmp) cc_final: 0.6425 (mmt) REVERT: B 290 MET cc_start: 0.3282 (mmm) cc_final: 0.3049 (mmm) REVERT: G 132 MET cc_start: 0.9398 (mmm) cc_final: 0.9154 (mmm) REVERT: G 553 ASN cc_start: 0.9113 (m-40) cc_final: 0.8047 (t0) REVERT: G 1216 GLU cc_start: 0.8659 (OUTLIER) cc_final: 0.8440 (pm20) outliers start: 18 outliers final: 10 residues processed: 249 average time/residue: 0.4451 time to fit residues: 178.6242 Evaluate side-chains 198 residues out of total 3245 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 186 time to evaluate : 3.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 395 SER Chi-restraints excluded: chain A residue 434 SER Chi-restraints excluded: chain A residue 811 SER Chi-restraints excluded: chain A residue 917 CYS Chi-restraints excluded: chain A residue 1044 GLU Chi-restraints excluded: chain A residue 1255 SER Chi-restraints excluded: chain A residue 1333 ASP Chi-restraints excluded: chain A residue 1366 SER Chi-restraints excluded: chain A residue 1540 SER Chi-restraints excluded: chain G residue 1216 GLU Chi-restraints excluded: chain G residue 1586 SER Chi-restraints excluded: chain G residue 1761 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 317 optimal weight: 5.9990 chunk 284 optimal weight: 5.9990 chunk 158 optimal weight: 5.9990 chunk 97 optimal weight: 1.9990 chunk 192 optimal weight: 2.9990 chunk 152 optimal weight: 8.9990 chunk 294 optimal weight: 20.0000 chunk 114 optimal weight: 2.9990 chunk 179 optimal weight: 6.9990 chunk 219 optimal weight: 6.9990 chunk 341 optimal weight: 7.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 379 ASN A 457 ASN A 713 GLN A 969 ASN A1123 GLN A1549 ASN A1689 HIS ** B 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 271 ASN G 110 GLN G 718 ASN G1186 ASN G1868 GLN G2050 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8828 moved from start: 0.1288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 30242 Z= 0.284 Angle : 0.531 7.132 40962 Z= 0.281 Chirality : 0.042 0.161 4603 Planarity : 0.004 0.049 5286 Dihedral : 5.481 87.313 4053 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.47 % Favored : 97.47 % Rotamer: Outliers : 0.59 % Allowed : 7.27 % Favored : 92.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.79 (0.13), residues: 3760 helix: 0.05 (0.12), residues: 1658 sheet: -1.58 (0.21), residues: 527 loop : -0.57 (0.16), residues: 1575 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP G 661 HIS 0.004 0.001 HIS G1939 PHE 0.019 0.002 PHE A 35 TYR 0.020 0.001 TYR A 722 ARG 0.005 0.000 ARG G1765 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7520 Ramachandran restraints generated. 3760 Oldfield, 0 Emsley, 3760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7520 Ramachandran restraints generated. 3760 Oldfield, 0 Emsley, 3760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 3245 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 194 time to evaluate : 3.575 Fit side-chains revert: symmetry clash REVERT: A 56 MET cc_start: 0.9298 (mtt) cc_final: 0.8956 (mtt) REVERT: A 75 HIS cc_start: 0.8145 (m90) cc_final: 0.7742 (m-70) REVERT: A 431 GLU cc_start: 0.9244 (mm-30) cc_final: 0.8801 (mp0) REVERT: A 1121 MET cc_start: 0.8598 (mtp) cc_final: 0.8356 (mtm) REVERT: A 1377 MET cc_start: 0.9142 (tpp) cc_final: 0.8941 (tpp) REVERT: A 1797 GLU cc_start: 0.8356 (tm-30) cc_final: 0.8015 (tm-30) REVERT: B 168 MET cc_start: 0.8689 (tpp) cc_final: 0.8321 (tpp) REVERT: B 290 MET cc_start: 0.3172 (mmm) cc_final: 0.2951 (tpp) REVERT: G 553 ASN cc_start: 0.9171 (m-40) cc_final: 0.8180 (t0) REVERT: G 1981 LEU cc_start: 0.9115 (OUTLIER) cc_final: 0.8901 (pp) outliers start: 19 outliers final: 9 residues processed: 209 average time/residue: 0.4599 time to fit residues: 154.9748 Evaluate side-chains 187 residues out of total 3245 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 177 time to evaluate : 3.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 811 SER Chi-restraints excluded: chain A residue 1333 ASP Chi-restraints excluded: chain A residue 1498 GLU Chi-restraints excluded: chain A residue 1557 ILE Chi-restraints excluded: chain A residue 1759 MET Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain G residue 516 THR Chi-restraints excluded: chain G residue 616 THR Chi-restraints excluded: chain G residue 1381 VAL Chi-restraints excluded: chain G residue 1981 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 189 optimal weight: 9.9990 chunk 105 optimal weight: 1.9990 chunk 284 optimal weight: 4.9990 chunk 232 optimal weight: 2.9990 chunk 94 optimal weight: 0.9980 chunk 342 optimal weight: 5.9990 chunk 369 optimal weight: 7.9990 chunk 304 optimal weight: 0.9980 chunk 339 optimal weight: 4.9990 chunk 116 optimal weight: 3.9990 chunk 274 optimal weight: 7.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 821 GLN A 971 ASN A1689 HIS ** B 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 110 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8804 moved from start: 0.1509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 30242 Z= 0.176 Angle : 0.461 7.930 40962 Z= 0.240 Chirality : 0.040 0.152 4603 Planarity : 0.003 0.055 5286 Dihedral : 4.745 74.653 4039 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.77 % Favored : 97.18 % Rotamer: Outliers : 0.74 % Allowed : 8.17 % Favored : 91.09 % 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: 0.24 (0.14), residues: 3760 helix: 1.10 (0.13), residues: 1641 sheet: -1.27 (0.20), residues: 555 loop : -0.14 (0.16), residues: 1564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP G 661 HIS 0.006 0.001 HIS A1689 PHE 0.024 0.001 PHE A 22 TYR 0.015 0.001 TYR A 722 ARG 0.006 0.000 ARG G1765 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7520 Ramachandran restraints generated. 3760 Oldfield, 0 Emsley, 3760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7520 Ramachandran restraints generated. 3760 Oldfield, 0 Emsley, 3760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 3245 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 195 time to evaluate : 3.476 Fit side-chains REVERT: A 56 MET cc_start: 0.9260 (mtt) cc_final: 0.8871 (mtt) REVERT: A 431 GLU cc_start: 0.9243 (mm-30) cc_final: 0.8798 (mp0) REVERT: A 949 GLU cc_start: 0.8551 (OUTLIER) cc_final: 0.8121 (mp0) REVERT: A 1121 MET cc_start: 0.8613 (mtp) cc_final: 0.8383 (mtm) REVERT: A 1377 MET cc_start: 0.9173 (tpp) cc_final: 0.8935 (tpp) REVERT: A 1797 GLU cc_start: 0.8278 (tm-30) cc_final: 0.7958 (tm-30) REVERT: B 168 MET cc_start: 0.8622 (tpp) cc_final: 0.8370 (tpp) REVERT: B 193 GLU cc_start: 0.7723 (OUTLIER) cc_final: 0.7317 (mm-30) REVERT: G 326 ASP cc_start: 0.9109 (t70) cc_final: 0.8702 (t0) REVERT: G 553 ASN cc_start: 0.9107 (m-40) cc_final: 0.8132 (t0) REVERT: G 1964 PHE cc_start: 0.8285 (m-80) cc_final: 0.7980 (m-10) outliers start: 24 outliers final: 10 residues processed: 210 average time/residue: 0.4563 time to fit residues: 155.8196 Evaluate side-chains 192 residues out of total 3245 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 180 time to evaluate : 3.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 949 GLU Chi-restraints excluded: chain A residue 1131 LEU Chi-restraints excluded: chain A residue 1327 CYS Chi-restraints excluded: chain A residue 1333 ASP Chi-restraints excluded: chain A residue 1745 ILE Chi-restraints excluded: chain B residue 157 HIS Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 193 GLU Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain G residue 167 ASP Chi-restraints excluded: chain G residue 215 ILE Chi-restraints excluded: chain G residue 1381 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 337 optimal weight: 5.9990 chunk 257 optimal weight: 4.9990 chunk 177 optimal weight: 20.0000 chunk 37 optimal weight: 5.9990 chunk 163 optimal weight: 7.9990 chunk 229 optimal weight: 3.9990 chunk 343 optimal weight: 3.9990 chunk 363 optimal weight: 0.5980 chunk 179 optimal weight: 8.9990 chunk 325 optimal weight: 5.9990 chunk 97 optimal weight: 8.9990 overall best weight: 3.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 713 GLN A 821 GLN A 971 ASN A1194 ASN A1689 HIS ** B 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 110 GLN G1633 ASN ** G1897 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8819 moved from start: 0.1597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 30242 Z= 0.277 Angle : 0.488 8.266 40962 Z= 0.253 Chirality : 0.041 0.149 4603 Planarity : 0.004 0.055 5286 Dihedral : 4.759 73.170 4038 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.82 % Favored : 97.13 % Rotamer: Outliers : 1.05 % Allowed : 8.75 % Favored : 90.20 % 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: 0.49 (0.14), residues: 3760 helix: 1.21 (0.13), residues: 1662 sheet: -1.04 (0.21), residues: 540 loop : 0.02 (0.16), residues: 1558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP G1138 HIS 0.005 0.001 HIS A1689 PHE 0.020 0.001 PHE A 35 TYR 0.019 0.001 TYR A 722 ARG 0.006 0.000 ARG G1765 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7520 Ramachandran restraints generated. 3760 Oldfield, 0 Emsley, 3760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7520 Ramachandran restraints generated. 3760 Oldfield, 0 Emsley, 3760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 3245 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 184 time to evaluate : 3.522 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 56 MET cc_start: 0.9317 (mtt) cc_final: 0.8977 (mtt) REVERT: A 328 LEU cc_start: 0.6880 (OUTLIER) cc_final: 0.6601 (tt) REVERT: A 431 GLU cc_start: 0.9240 (mm-30) cc_final: 0.8786 (mp0) REVERT: A 856 GLU cc_start: 0.7062 (OUTLIER) cc_final: 0.6248 (mt-10) REVERT: A 949 GLU cc_start: 0.8531 (OUTLIER) cc_final: 0.8159 (mp0) REVERT: A 1121 MET cc_start: 0.8627 (mtp) cc_final: 0.8389 (mtm) REVERT: A 1377 MET cc_start: 0.9209 (tpp) cc_final: 0.8974 (tpp) REVERT: A 1797 GLU cc_start: 0.8307 (tm-30) cc_final: 0.7979 (tm-30) REVERT: G 553 ASN cc_start: 0.9119 (m-40) cc_final: 0.8132 (t0) outliers start: 34 outliers final: 18 residues processed: 210 average time/residue: 0.4626 time to fit residues: 156.0133 Evaluate side-chains 196 residues out of total 3245 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 175 time to evaluate : 3.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 421 ILE Chi-restraints excluded: chain A residue 856 GLU Chi-restraints excluded: chain A residue 922 VAL Chi-restraints excluded: chain A residue 949 GLU Chi-restraints excluded: chain A residue 967 VAL Chi-restraints excluded: chain A residue 1044 GLU Chi-restraints excluded: chain A residue 1131 LEU Chi-restraints excluded: chain A residue 1327 CYS Chi-restraints excluded: chain A residue 1333 ASP Chi-restraints excluded: chain A residue 1745 ILE Chi-restraints excluded: chain B residue 157 HIS Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain G residue 167 ASP Chi-restraints excluded: chain G residue 215 ILE Chi-restraints excluded: chain G residue 240 LEU Chi-restraints excluded: chain G residue 322 SER Chi-restraints excluded: chain G residue 516 THR Chi-restraints excluded: chain G residue 616 THR Chi-restraints excluded: chain G residue 1324 ASP Chi-restraints excluded: chain G residue 1381 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 302 optimal weight: 0.0470 chunk 206 optimal weight: 3.9990 chunk 5 optimal weight: 6.9990 chunk 270 optimal weight: 1.9990 chunk 149 optimal weight: 9.9990 chunk 310 optimal weight: 7.9990 chunk 251 optimal weight: 1.9990 chunk 0 optimal weight: 20.0000 chunk 185 optimal weight: 7.9990 chunk 326 optimal weight: 8.9990 chunk 91 optimal weight: 2.9990 overall best weight: 2.2086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 713 GLN A 821 GLN A1601 ASN A1689 HIS ** B 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 110 GLN G1633 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8800 moved from start: 0.1703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 30242 Z= 0.175 Angle : 0.449 7.266 40962 Z= 0.231 Chirality : 0.040 0.148 4603 Planarity : 0.003 0.056 5286 Dihedral : 4.582 73.309 4038 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.77 % Favored : 97.21 % Rotamer: Outliers : 0.96 % Allowed : 9.71 % Favored : 89.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.73 (0.14), residues: 3760 helix: 1.43 (0.13), residues: 1648 sheet: -0.87 (0.21), residues: 550 loop : 0.13 (0.16), residues: 1562 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP G1138 HIS 0.005 0.001 HIS A1689 PHE 0.023 0.001 PHE A 35 TYR 0.013 0.001 TYR A 722 ARG 0.005 0.000 ARG G1023 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7520 Ramachandran restraints generated. 3760 Oldfield, 0 Emsley, 3760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7520 Ramachandran restraints generated. 3760 Oldfield, 0 Emsley, 3760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 3245 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 193 time to evaluate : 3.332 Fit side-chains REVERT: A 328 LEU cc_start: 0.6890 (OUTLIER) cc_final: 0.6641 (tt) REVERT: A 431 GLU cc_start: 0.9224 (mm-30) cc_final: 0.8790 (mp0) REVERT: A 856 GLU cc_start: 0.6973 (OUTLIER) cc_final: 0.6155 (mt-10) REVERT: A 949 GLU cc_start: 0.8560 (OUTLIER) cc_final: 0.8195 (mp0) REVERT: A 1121 MET cc_start: 0.8623 (mtp) cc_final: 0.8392 (mtm) REVERT: A 1332 TYR cc_start: 0.9253 (OUTLIER) cc_final: 0.7865 (p90) REVERT: A 1377 MET cc_start: 0.9159 (tpp) cc_final: 0.8919 (tpp) REVERT: A 1797 GLU cc_start: 0.8294 (tm-30) cc_final: 0.7973 (tm-30) REVERT: G 326 ASP cc_start: 0.9106 (t70) cc_final: 0.8712 (t0) REVERT: G 553 ASN cc_start: 0.9137 (m-40) cc_final: 0.8154 (t0) outliers start: 31 outliers final: 18 residues processed: 217 average time/residue: 0.4601 time to fit residues: 161.7967 Evaluate side-chains 198 residues out of total 3245 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 176 time to evaluate : 3.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 421 ILE Chi-restraints excluded: chain A residue 856 GLU Chi-restraints excluded: chain A residue 922 VAL Chi-restraints excluded: chain A residue 949 GLU Chi-restraints excluded: chain A residue 967 VAL Chi-restraints excluded: chain A residue 1044 GLU Chi-restraints excluded: chain A residue 1125 VAL Chi-restraints excluded: chain A residue 1131 LEU Chi-restraints excluded: chain A residue 1327 CYS Chi-restraints excluded: chain A residue 1332 TYR Chi-restraints excluded: chain A residue 1333 ASP Chi-restraints excluded: chain A residue 1557 ILE Chi-restraints excluded: chain A residue 1745 ILE Chi-restraints excluded: chain B residue 157 HIS Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 167 ASP Chi-restraints excluded: chain G residue 322 SER Chi-restraints excluded: chain G residue 616 THR Chi-restraints excluded: chain G residue 1131 SER Chi-restraints excluded: chain G residue 1324 ASP Chi-restraints excluded: chain G residue 1381 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 122 optimal weight: 2.9990 chunk 327 optimal weight: 10.0000 chunk 71 optimal weight: 2.9990 chunk 213 optimal weight: 0.6980 chunk 89 optimal weight: 10.0000 chunk 363 optimal weight: 8.9990 chunk 301 optimal weight: 0.3980 chunk 168 optimal weight: 40.0000 chunk 30 optimal weight: 0.9990 chunk 120 optimal weight: 3.9990 chunk 190 optimal weight: 0.1980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 713 GLN A 821 GLN ** B 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 110 GLN G1341 ASN G1633 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8779 moved from start: 0.1843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 30242 Z= 0.122 Angle : 0.431 9.113 40962 Z= 0.221 Chirality : 0.039 0.146 4603 Planarity : 0.003 0.056 5286 Dihedral : 4.392 73.508 4038 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.45 % Favored : 97.53 % Rotamer: Outliers : 0.86 % Allowed : 10.20 % Favored : 88.93 % 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: 3760 helix: 1.57 (0.13), residues: 1640 sheet: -0.75 (0.21), residues: 554 loop : 0.19 (0.16), residues: 1566 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP G 661 HIS 0.004 0.001 HIS G1002 PHE 0.024 0.001 PHE A 35 TYR 0.011 0.001 TYR A 417 ARG 0.005 0.000 ARG A1789 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7520 Ramachandran restraints generated. 3760 Oldfield, 0 Emsley, 3760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7520 Ramachandran restraints generated. 3760 Oldfield, 0 Emsley, 3760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 3245 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 189 time to evaluate : 3.588 Fit side-chains revert: symmetry clash REVERT: A 328 LEU cc_start: 0.6820 (OUTLIER) cc_final: 0.6591 (tt) REVERT: A 431 GLU cc_start: 0.9210 (mm-30) cc_final: 0.8801 (mp0) REVERT: A 949 GLU cc_start: 0.8544 (OUTLIER) cc_final: 0.8182 (mp0) REVERT: A 1121 MET cc_start: 0.8620 (mtp) cc_final: 0.8364 (mtm) REVERT: A 1332 TYR cc_start: 0.9217 (OUTLIER) cc_final: 0.7822 (p90) REVERT: A 1741 LYS cc_start: 0.4202 (mmmt) cc_final: 0.3761 (mmmt) REVERT: A 1797 GLU cc_start: 0.8280 (tm-30) cc_final: 0.7974 (tm-30) REVERT: G 128 THR cc_start: 0.9520 (OUTLIER) cc_final: 0.9315 (t) REVERT: G 326 ASP cc_start: 0.9134 (t70) cc_final: 0.8671 (t0) REVERT: G 553 ASN cc_start: 0.9086 (m-40) cc_final: 0.8134 (t0) REVERT: G 1180 MET cc_start: 0.8552 (OUTLIER) cc_final: 0.8138 (mtp) outliers start: 28 outliers final: 19 residues processed: 208 average time/residue: 0.4542 time to fit residues: 152.7226 Evaluate side-chains 203 residues out of total 3245 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 179 time to evaluate : 3.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 395 SER Chi-restraints excluded: chain A residue 421 ILE Chi-restraints excluded: chain A residue 922 VAL Chi-restraints excluded: chain A residue 949 GLU Chi-restraints excluded: chain A residue 1125 VAL Chi-restraints excluded: chain A residue 1131 LEU Chi-restraints excluded: chain A residue 1327 CYS Chi-restraints excluded: chain A residue 1332 TYR Chi-restraints excluded: chain A residue 1333 ASP Chi-restraints excluded: chain A residue 1498 GLU Chi-restraints excluded: chain A residue 1745 ILE Chi-restraints excluded: chain B residue 157 HIS Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 128 THR Chi-restraints excluded: chain G residue 215 ILE Chi-restraints excluded: chain G residue 616 THR Chi-restraints excluded: chain G residue 1131 SER Chi-restraints excluded: chain G residue 1180 MET Chi-restraints excluded: chain G residue 1324 ASP Chi-restraints excluded: chain G residue 1381 VAL Chi-restraints excluded: chain G residue 1625 SER Chi-restraints excluded: chain G residue 1944 ILE Chi-restraints excluded: chain G residue 1958 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 350 optimal weight: 5.9990 chunk 41 optimal weight: 7.9990 chunk 207 optimal weight: 9.9990 chunk 265 optimal weight: 0.9980 chunk 205 optimal weight: 0.9990 chunk 306 optimal weight: 0.0270 chunk 203 optimal weight: 7.9990 chunk 362 optimal weight: 20.0000 chunk 226 optimal weight: 0.7980 chunk 220 optimal weight: 0.9980 chunk 167 optimal weight: 5.9990 overall best weight: 0.7640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 713 GLN A1873 HIS ** B 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 110 GLN G1055 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8765 moved from start: 0.1978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 30242 Z= 0.112 Angle : 0.431 10.187 40962 Z= 0.218 Chirality : 0.039 0.146 4603 Planarity : 0.003 0.056 5286 Dihedral : 4.220 73.134 4038 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.31 % Favored : 97.66 % Rotamer: Outliers : 1.02 % Allowed : 10.27 % Favored : 88.72 % 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: 1.03 (0.14), residues: 3760 helix: 1.65 (0.13), residues: 1646 sheet: -0.57 (0.21), residues: 550 loop : 0.24 (0.16), residues: 1564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP G 661 HIS 0.004 0.001 HIS G1002 PHE 0.034 0.001 PHE B 286 TYR 0.019 0.001 TYR B 294 ARG 0.008 0.000 ARG G1023 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7520 Ramachandran restraints generated. 3760 Oldfield, 0 Emsley, 3760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7520 Ramachandran restraints generated. 3760 Oldfield, 0 Emsley, 3760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 3245 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 197 time to evaluate : 3.409 Fit side-chains revert: symmetry clash REVERT: A 328 LEU cc_start: 0.6889 (OUTLIER) cc_final: 0.6686 (tt) REVERT: A 431 GLU cc_start: 0.9185 (mm-30) cc_final: 0.8797 (mp0) REVERT: A 856 GLU cc_start: 0.6889 (OUTLIER) cc_final: 0.6057 (mt-10) REVERT: A 949 GLU cc_start: 0.8544 (OUTLIER) cc_final: 0.8162 (mp0) REVERT: A 1121 MET cc_start: 0.8653 (mtp) cc_final: 0.8396 (mtm) REVERT: A 1332 TYR cc_start: 0.9175 (OUTLIER) cc_final: 0.8330 (p90) REVERT: A 1741 LYS cc_start: 0.4022 (mmmt) cc_final: 0.3614 (mmmt) REVERT: A 1775 LEU cc_start: 0.8553 (mt) cc_final: 0.8338 (mp) REVERT: A 1797 GLU cc_start: 0.8301 (tm-30) cc_final: 0.7992 (tm-30) REVERT: G 128 THR cc_start: 0.9518 (OUTLIER) cc_final: 0.9304 (t) REVERT: G 326 ASP cc_start: 0.9125 (t70) cc_final: 0.8722 (t0) REVERT: G 553 ASN cc_start: 0.9085 (m-40) cc_final: 0.8187 (t0) outliers start: 33 outliers final: 19 residues processed: 223 average time/residue: 0.4611 time to fit residues: 169.3952 Evaluate side-chains 204 residues out of total 3245 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 180 time to evaluate : 3.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 395 SER Chi-restraints excluded: chain A residue 421 ILE Chi-restraints excluded: chain A residue 856 GLU Chi-restraints excluded: chain A residue 922 VAL Chi-restraints excluded: chain A residue 949 GLU Chi-restraints excluded: chain A residue 1044 GLU Chi-restraints excluded: chain A residue 1125 VAL Chi-restraints excluded: chain A residue 1131 LEU Chi-restraints excluded: chain A residue 1327 CYS Chi-restraints excluded: chain A residue 1332 TYR Chi-restraints excluded: chain A residue 1745 ILE Chi-restraints excluded: chain B residue 157 HIS Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 111 GLU Chi-restraints excluded: chain G residue 128 THR Chi-restraints excluded: chain G residue 215 ILE Chi-restraints excluded: chain G residue 616 THR Chi-restraints excluded: chain G residue 1324 ASP Chi-restraints excluded: chain G residue 1348 LEU Chi-restraints excluded: chain G residue 1381 VAL Chi-restraints excluded: chain G residue 1944 ILE Chi-restraints excluded: chain G residue 1958 LEU Chi-restraints excluded: chain G residue 1979 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 224 optimal weight: 10.0000 chunk 144 optimal weight: 6.9990 chunk 216 optimal weight: 2.9990 chunk 109 optimal weight: 1.9990 chunk 71 optimal weight: 4.9990 chunk 70 optimal weight: 0.9980 chunk 230 optimal weight: 9.9990 chunk 246 optimal weight: 20.0000 chunk 179 optimal weight: 0.5980 chunk 33 optimal weight: 0.6980 chunk 284 optimal weight: 5.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1873 HIS ** B 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 110 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8774 moved from start: 0.2006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 30242 Z= 0.141 Angle : 0.438 11.337 40962 Z= 0.222 Chirality : 0.040 0.318 4603 Planarity : 0.003 0.056 5286 Dihedral : 4.134 72.190 4036 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.42 % Favored : 97.55 % Rotamer: Outliers : 0.96 % Allowed : 10.60 % Favored : 88.44 % 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: 1.11 (0.14), residues: 3760 helix: 1.72 (0.13), residues: 1641 sheet: -0.44 (0.21), residues: 563 loop : 0.27 (0.16), residues: 1556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP G 661 HIS 0.004 0.001 HIS A1873 PHE 0.033 0.001 PHE B 286 TYR 0.017 0.001 TYR B 294 ARG 0.008 0.000 ARG G1023 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7520 Ramachandran restraints generated. 3760 Oldfield, 0 Emsley, 3760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7520 Ramachandran restraints generated. 3760 Oldfield, 0 Emsley, 3760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 3245 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 189 time to evaluate : 3.536 Fit side-chains revert: symmetry clash REVERT: A 431 GLU cc_start: 0.9181 (mm-30) cc_final: 0.8800 (mp0) REVERT: A 856 GLU cc_start: 0.6892 (OUTLIER) cc_final: 0.6036 (mt-10) REVERT: A 949 GLU cc_start: 0.8544 (OUTLIER) cc_final: 0.8177 (mp0) REVERT: A 1121 MET cc_start: 0.8656 (mtp) cc_final: 0.8391 (mtm) REVERT: A 1332 TYR cc_start: 0.9202 (OUTLIER) cc_final: 0.7911 (p90) REVERT: A 1741 LYS cc_start: 0.4111 (mmmt) cc_final: 0.3688 (mmmt) REVERT: A 1775 LEU cc_start: 0.8581 (mt) cc_final: 0.8366 (mp) REVERT: A 1797 GLU cc_start: 0.8310 (tm-30) cc_final: 0.7998 (tm-30) REVERT: G 128 THR cc_start: 0.9517 (OUTLIER) cc_final: 0.9294 (t) REVERT: G 326 ASP cc_start: 0.9145 (t70) cc_final: 0.8733 (t0) REVERT: G 553 ASN cc_start: 0.9070 (m-40) cc_final: 0.8189 (t0) outliers start: 31 outliers final: 20 residues processed: 213 average time/residue: 0.4446 time to fit residues: 155.4255 Evaluate side-chains 204 residues out of total 3245 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 180 time to evaluate : 3.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 395 SER Chi-restraints excluded: chain A residue 421 ILE Chi-restraints excluded: chain A residue 856 GLU Chi-restraints excluded: chain A residue 922 VAL Chi-restraints excluded: chain A residue 949 GLU Chi-restraints excluded: chain A residue 1044 GLU Chi-restraints excluded: chain A residue 1125 VAL Chi-restraints excluded: chain A residue 1131 LEU Chi-restraints excluded: chain A residue 1327 CYS Chi-restraints excluded: chain A residue 1332 TYR Chi-restraints excluded: chain A residue 1498 GLU Chi-restraints excluded: chain A residue 1745 ILE Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 111 GLU Chi-restraints excluded: chain G residue 128 THR Chi-restraints excluded: chain G residue 215 ILE Chi-restraints excluded: chain G residue 555 LEU Chi-restraints excluded: chain G residue 616 THR Chi-restraints excluded: chain G residue 1324 ASP Chi-restraints excluded: chain G residue 1348 LEU Chi-restraints excluded: chain G residue 1381 VAL Chi-restraints excluded: chain G residue 1944 ILE Chi-restraints excluded: chain G residue 1958 LEU Chi-restraints excluded: chain G residue 1979 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 329 optimal weight: 0.0980 chunk 347 optimal weight: 0.0770 chunk 316 optimal weight: 2.9990 chunk 337 optimal weight: 5.9990 chunk 203 optimal weight: 3.9990 chunk 147 optimal weight: 10.0000 chunk 265 optimal weight: 4.9990 chunk 103 optimal weight: 0.0470 chunk 305 optimal weight: 9.9990 chunk 319 optimal weight: 10.0000 chunk 336 optimal weight: 0.5980 overall best weight: 0.7638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1873 HIS ** B 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 110 GLN G 112 ASN G 163 GLN G1220 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8756 moved from start: 0.2134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 30242 Z= 0.112 Angle : 0.434 12.308 40962 Z= 0.218 Chirality : 0.040 0.262 4603 Planarity : 0.003 0.055 5286 Dihedral : 4.007 71.042 4036 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.50 % Favored : 97.47 % Rotamer: Outliers : 0.83 % Allowed : 10.85 % Favored : 88.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.16 (0.14), residues: 3760 helix: 1.71 (0.13), residues: 1668 sheet: -0.37 (0.22), residues: 557 loop : 0.32 (0.17), residues: 1535 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP G 661 HIS 0.004 0.001 HIS A1873 PHE 0.024 0.001 PHE A 35 TYR 0.015 0.001 TYR B 294 ARG 0.008 0.000 ARG G1023 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7520 Ramachandran restraints generated. 3760 Oldfield, 0 Emsley, 3760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7520 Ramachandran restraints generated. 3760 Oldfield, 0 Emsley, 3760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 3245 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 199 time to evaluate : 3.504 Fit side-chains revert: symmetry clash REVERT: A 352 MET cc_start: 0.8411 (ttm) cc_final: 0.8187 (ptp) REVERT: A 431 GLU cc_start: 0.9156 (mm-30) cc_final: 0.8783 (mp0) REVERT: A 891 MET cc_start: 0.8913 (mmm) cc_final: 0.8554 (tpp) REVERT: A 949 GLU cc_start: 0.8547 (OUTLIER) cc_final: 0.8150 (mp0) REVERT: A 1121 MET cc_start: 0.8713 (mtp) cc_final: 0.8458 (mtm) REVERT: A 1332 TYR cc_start: 0.9171 (OUTLIER) cc_final: 0.8578 (p90) REVERT: A 1741 LYS cc_start: 0.4471 (mmmt) cc_final: 0.4073 (mmmt) REVERT: A 1775 LEU cc_start: 0.8577 (mt) cc_final: 0.8356 (mp) REVERT: A 1797 GLU cc_start: 0.8311 (tm-30) cc_final: 0.8010 (tm-30) REVERT: G 326 ASP cc_start: 0.9144 (t70) cc_final: 0.8740 (t0) REVERT: G 553 ASN cc_start: 0.9074 (m-40) cc_final: 0.8205 (t0) outliers start: 27 outliers final: 22 residues processed: 220 average time/residue: 0.4911 time to fit residues: 177.2314 Evaluate side-chains 209 residues out of total 3245 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 185 time to evaluate : 3.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 395 SER Chi-restraints excluded: chain A residue 421 ILE Chi-restraints excluded: chain A residue 949 GLU Chi-restraints excluded: chain A residue 1044 GLU Chi-restraints excluded: chain A residue 1125 VAL Chi-restraints excluded: chain A residue 1131 LEU Chi-restraints excluded: chain A residue 1327 CYS Chi-restraints excluded: chain A residue 1332 TYR Chi-restraints excluded: chain A residue 1498 GLU Chi-restraints excluded: chain A residue 1745 ILE Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 111 GLU Chi-restraints excluded: chain G residue 128 THR Chi-restraints excluded: chain G residue 163 GLN Chi-restraints excluded: chain G residue 215 ILE Chi-restraints excluded: chain G residue 234 ILE Chi-restraints excluded: chain G residue 555 LEU Chi-restraints excluded: chain G residue 616 THR Chi-restraints excluded: chain G residue 1324 ASP Chi-restraints excluded: chain G residue 1348 LEU Chi-restraints excluded: chain G residue 1381 VAL Chi-restraints excluded: chain G residue 1944 ILE Chi-restraints excluded: chain G residue 1958 LEU Chi-restraints excluded: chain G residue 1979 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 221 optimal weight: 0.6980 chunk 357 optimal weight: 9.9990 chunk 217 optimal weight: 0.0980 chunk 169 optimal weight: 10.0000 chunk 248 optimal weight: 2.9990 chunk 374 optimal weight: 5.9990 chunk 344 optimal weight: 10.0000 chunk 298 optimal weight: 1.9990 chunk 30 optimal weight: 8.9990 chunk 230 optimal weight: 9.9990 chunk 182 optimal weight: 10.0000 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1873 HIS ** B 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 110 GLN ** G1892 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1897 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8786 moved from start: 0.2041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 30242 Z= 0.187 Angle : 0.464 12.432 40962 Z= 0.234 Chirality : 0.040 0.261 4603 Planarity : 0.003 0.055 5286 Dihedral : 4.135 69.281 4036 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.69 % Favored : 97.29 % Rotamer: Outliers : 0.83 % Allowed : 10.97 % Favored : 88.19 % 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: 1.22 (0.14), residues: 3760 helix: 1.74 (0.13), residues: 1653 sheet: -0.29 (0.22), residues: 546 loop : 0.36 (0.16), residues: 1561 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G1138 HIS 0.004 0.001 HIS A1689 PHE 0.034 0.001 PHE B 286 TYR 0.021 0.001 TYR B 294 ARG 0.010 0.000 ARG G 518 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7520 Ramachandran restraints generated. 3760 Oldfield, 0 Emsley, 3760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7520 Ramachandran restraints generated. 3760 Oldfield, 0 Emsley, 3760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 3245 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 187 time to evaluate : 3.351 Fit side-chains revert: symmetry clash REVERT: A 431 GLU cc_start: 0.9180 (mm-30) cc_final: 0.8794 (mp0) REVERT: A 856 GLU cc_start: 0.7092 (OUTLIER) cc_final: 0.6260 (mt-10) REVERT: A 949 GLU cc_start: 0.8555 (OUTLIER) cc_final: 0.8205 (mp0) REVERT: A 1121 MET cc_start: 0.8649 (mtp) cc_final: 0.8379 (mtm) REVERT: A 1332 TYR cc_start: 0.9235 (OUTLIER) cc_final: 0.7884 (p90) REVERT: A 1468 GLU cc_start: 0.8931 (mt-10) cc_final: 0.8710 (mt-10) REVERT: A 1775 LEU cc_start: 0.8567 (mt) cc_final: 0.8360 (mp) REVERT: A 1797 GLU cc_start: 0.8299 (tm-30) cc_final: 0.7987 (tm-30) REVERT: G 553 ASN cc_start: 0.9058 (m-40) cc_final: 0.8188 (t0) outliers start: 27 outliers final: 23 residues processed: 207 average time/residue: 0.5033 time to fit residues: 170.2269 Evaluate side-chains 207 residues out of total 3245 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 181 time to evaluate : 3.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 395 SER Chi-restraints excluded: chain A residue 421 ILE Chi-restraints excluded: chain A residue 856 GLU Chi-restraints excluded: chain A residue 949 GLU Chi-restraints excluded: chain A residue 1044 GLU Chi-restraints excluded: chain A residue 1125 VAL Chi-restraints excluded: chain A residue 1131 LEU Chi-restraints excluded: chain A residue 1327 CYS Chi-restraints excluded: chain A residue 1332 TYR Chi-restraints excluded: chain A residue 1498 GLU Chi-restraints excluded: chain A residue 1745 ILE Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 111 GLU Chi-restraints excluded: chain G residue 128 THR Chi-restraints excluded: chain G residue 167 ASP Chi-restraints excluded: chain G residue 215 ILE Chi-restraints excluded: chain G residue 234 ILE Chi-restraints excluded: chain G residue 555 LEU Chi-restraints excluded: chain G residue 616 THR Chi-restraints excluded: chain G residue 1131 SER Chi-restraints excluded: chain G residue 1324 ASP Chi-restraints excluded: chain G residue 1348 LEU Chi-restraints excluded: chain G residue 1381 VAL Chi-restraints excluded: chain G residue 1944 ILE Chi-restraints excluded: chain G residue 1958 LEU Chi-restraints excluded: chain G residue 1979 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 236 optimal weight: 4.9990 chunk 317 optimal weight: 2.9990 chunk 91 optimal weight: 0.7980 chunk 275 optimal weight: 9.9990 chunk 44 optimal weight: 4.9990 chunk 82 optimal weight: 20.0000 chunk 298 optimal weight: 0.9990 chunk 125 optimal weight: 9.9990 chunk 306 optimal weight: 9.9990 chunk 37 optimal weight: 5.9990 chunk 55 optimal weight: 1.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1873 HIS ** B 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1892 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1897 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.079056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.057993 restraints weight = 80222.927| |-----------------------------------------------------------------------------| r_work (start): 0.2830 rms_B_bonded: 2.49 r_work: 0.2711 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2594 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8795 moved from start: 0.2040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 30242 Z= 0.185 Angle : 0.462 12.110 40962 Z= 0.234 Chirality : 0.041 0.255 4603 Planarity : 0.003 0.056 5286 Dihedral : 4.184 69.412 4036 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.61 % Favored : 97.37 % Rotamer: Outliers : 0.92 % Allowed : 10.97 % Favored : 88.10 % 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: 1.23 (0.14), residues: 3760 helix: 1.74 (0.13), residues: 1644 sheet: -0.28 (0.22), residues: 546 loop : 0.37 (0.16), residues: 1570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G1138 HIS 0.004 0.001 HIS A1873 PHE 0.025 0.001 PHE A 22 TYR 0.019 0.001 TYR B 294 ARG 0.010 0.000 ARG G 518 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6277.51 seconds wall clock time: 116 minutes 14.60 seconds (6974.60 seconds total)