Starting phenix.real_space_refine on Thu Mar 21 09:19:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8psj_17853/03_2024/8psj_17853_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8psj_17853/03_2024/8psj_17853.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8psj_17853/03_2024/8psj_17853_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8psj_17853/03_2024/8psj_17853_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8psj_17853/03_2024/8psj_17853_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8psj_17853/03_2024/8psj_17853.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8psj_17853/03_2024/8psj_17853.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8psj_17853/03_2024/8psj_17853_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8psj_17853/03_2024/8psj_17853_updated.pdb" } resolution = 3.4 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= 0.008 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 108 5.16 5 C 18920 2.51 5 N 4969 2.21 5 O 5696 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 403": "OD1" <-> "OD2" Residue "A GLU 435": "OE1" <-> "OE2" Residue "A ASP 492": "OD1" <-> "OD2" Residue "A ASP 648": "OD1" <-> "OD2" Residue "A PHE 710": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 764": "OD1" <-> "OD2" Residue "A GLU 780": "OE1" <-> "OE2" Residue "A GLU 847": "OE1" <-> "OE2" Residue "A ASP 991": "OD1" <-> "OD2" Residue "A ASP 1085": "OD1" <-> "OD2" Residue "A ASP 1088": "OD1" <-> "OD2" Residue "A GLU 1120": "OE1" <-> "OE2" Residue "A GLU 1124": "OE1" <-> "OE2" Residue "A PHE 1134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1139": "OE1" <-> "OE2" Residue "A ASP 1209": "OD1" <-> "OD2" Residue "A GLU 1221": "OE1" <-> "OE2" Residue "A ASP 1263": "OD1" <-> "OD2" Residue "A ASP 1267": "OD1" <-> "OD2" Residue "A ASP 1313": "OD1" <-> "OD2" Residue "A TYR 1332": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1337": "OE1" <-> "OE2" Residue "A GLU 1354": "OE1" <-> "OE2" Residue "A GLU 1355": "OE1" <-> "OE2" Residue "A GLU 1378": "OE1" <-> "OE2" Residue "A ASP 1391": "OD1" <-> "OD2" Residue "A ASP 1412": "OD1" <-> "OD2" Residue "A GLU 1456": "OE1" <-> "OE2" Residue "A GLU 1473": "OE1" <-> "OE2" Residue "A PHE 1485": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1512": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1579": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1622": "OE1" <-> "OE2" Residue "A ASP 1668": "OD1" <-> "OD2" Residue "A PHE 1820": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1874": "OD1" <-> "OD2" Residue "B ASP 174": "OD1" <-> "OD2" Residue "B GLU 208": "OE1" <-> "OE2" Residue "B PHE 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 272": "OE1" <-> "OE2" Residue "G PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 186": "OD1" <-> "OD2" Residue "G GLU 197": "OE1" <-> "OE2" Residue "G PHE 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 312": "OE1" <-> "OE2" Residue "G PHE 548": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 702": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 744": "OE1" <-> "OE2" Residue "G GLU 849": "OE1" <-> "OE2" Residue "G GLU 885": "OE1" <-> "OE2" Residue "G PHE 1003": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 1026": "OE1" <-> "OE2" Residue "G TYR 1298": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 1311": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 1357": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 1412": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 1423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 1456": "OD1" <-> "OD2" Residue "G GLU 1551": "OE1" <-> "OE2" Residue "G ASP 1559": "OD1" <-> "OD2" Residue "G PHE 1569": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 1866": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 1869": "OE1" <-> "OE2" Residue "G TYR 1873": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 1935": "OE1" <-> "OE2" Residue "G PHE 1941": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 1961": "OE1" <-> "OE2" Residue "G TYR 1980": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 29695 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 12402 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1589, 12402 Classifications: {'peptide': 1589} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 61, 'TRANS': 1527} Chain breaks: 2 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 1223 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1223 Classifications: {'peptide': 163} Link IDs: {'PTRANS': 8, 'TRANS': 154} Chain: "G" Number of atoms: 16018 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2036, 16018 Classifications: {'peptide': 2036} Link IDs: {'PCIS': 1, 'PTRANS': 108, 'TRANS': 1926} Chain breaks: 1 Chain: "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: 14.43, per 1000 atoms: 0.49 Number of scatterers: 29695 At special positions: 0 Unit cell: (179.35, 185.68, 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 108 16.00 P 2 15.00 O 5696 8.00 N 4969 7.00 C 18920 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=2.12 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: 11.24 Conformation dependent library (CDL) restraints added in 5.8 seconds 7552 Ramachandran restraints generated. 3776 Oldfield, 0 Emsley, 3776 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7042 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 166 helices and 30 sheets defined 44.0% alpha, 11.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 10.00 Creating SS restraints... Processing helix chain 'A' and resid 3 through 22 removed outlier: 3.822A pdb=" N GLU A 8 " --> pdb=" O GLU A 4 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLN A 21 " --> pdb=" O LEU A 17 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N PHE A 22 " --> pdb=" O LEU A 18 " (cutoff:3.500A) Processing helix chain 'A' and resid 28 through 35 Processing helix chain 'A' and resid 53 through 64 Processing helix chain 'A' and resid 68 through 72 Processing helix chain 'A' and resid 85 through 89 Processing helix chain 'A' and resid 330 through 350 Processing helix chain 'A' and resid 356 through 382 removed outlier: 3.505A pdb=" N ALA A 369 " --> pdb=" O LYS A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 389 Processing helix chain 'A' and resid 405 through 422 removed outlier: 4.455A pdb=" N LYS A 410 " --> pdb=" O TRP A 406 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLN A 411 " --> pdb=" O ASN A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 442 removed outlier: 3.582A pdb=" N SER A 434 " --> pdb=" O GLU A 431 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N ASN A 441 " --> pdb=" O ASN A 438 " (cutoff:3.500A) 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 483 Processing helix chain 'A' and resid 522 through 530 removed outlier: 3.656A pdb=" N GLN A 527 " --> pdb=" O SER A 523 " (cutoff:3.500A) Processing helix chain 'A' and resid 609 through 614 removed outlier: 3.511A pdb=" N ALA A 614 " --> pdb=" O THR A 610 " (cutoff:3.500A) Processing helix chain 'A' and resid 653 through 669 Processing helix chain 'A' and resid 688 through 699 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 840 through 855 removed outlier: 3.710A pdb=" N LEU A 846 " --> pdb=" O SER A 842 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N GLU A 847 " --> pdb=" O LYS A 843 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N THR A 848 " --> pdb=" O LEU A 844 " (cutoff:3.500A) removed outlier: 4.901A pdb=" N LEU A 849 " --> pdb=" O SER A 845 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N PHE A 850 " --> pdb=" O LEU A 846 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ASN A 851 " --> pdb=" O GLU A 847 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N HIS A 854 " --> pdb=" O PHE A 850 " (cutoff:3.500A) Processing helix chain 'A' and resid 879 through 891 removed outlier: 6.013A pdb=" N ILE A 883 " --> pdb=" O ALA A 880 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N GLU A 886 " --> pdb=" O ILE A 883 " (cutoff:3.500A) Processing helix chain 'A' and resid 898 through 909 removed outlier: 3.705A pdb=" N LEU A 908 " --> pdb=" O ASN A 904 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N LEU A 909 " --> pdb=" O LEU A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 911 through 917 Processing helix chain 'A' and resid 930 through 932 No H-bonds generated for 'chain 'A' and resid 930 through 932' Processing helix chain 'A' and resid 936 through 968 removed outlier: 3.637A pdb=" N GLU A 960 " --> pdb=" O ALA A 956 " (cutoff:3.500A) Processing helix chain 'A' and resid 998 through 1001 No H-bonds generated for 'chain 'A' and resid 998 through 1001' 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 1033 through 1042 Processing helix chain 'A' and resid 1047 through 1057 Processing helix chain 'A' and resid 1086 through 1100 removed outlier: 4.200A pdb=" N LYS A1090 " --> pdb=" O ASP A1086 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N ALA A1091 " --> pdb=" O LYS A1087 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N THR A1095 " --> pdb=" O ALA A1091 " (cutoff:3.500A) removed outlier: 5.600A pdb=" N SER A1096 " --> pdb=" O LYS A1092 " (cutoff:3.500A) Processing helix chain 'A' and resid 1109 through 1111 No H-bonds generated for 'chain 'A' and resid 1109 through 1111' Processing helix chain 'A' and resid 1138 through 1151 removed outlier: 7.412A pdb=" N ASP A1150 " --> pdb=" O HIS A1146 " (cutoff:3.500A) removed outlier: 7.295A 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 1207 removed outlier: 3.868A pdb=" N GLN A1207 " --> pdb=" O ASP A1203 " (cutoff:3.500A) Processing helix chain 'A' and resid 1210 through 1225 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 1274 through 1278 Processing helix chain 'A' and resid 1280 through 1290 removed outlier: 3.765A pdb=" N MET A1283 " --> pdb=" O ILE A1280 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N MET A1289 " --> pdb=" O TRP A1286 " (cutoff:3.500A) Processing helix chain 'A' and resid 1304 through 1320 removed outlier: 4.670A pdb=" N SER A1308 " --> pdb=" O CYS A1305 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N SER A1311 " --> pdb=" O SER A1308 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL A1316 " --> pdb=" O ASP A1313 " (cutoff:3.500A) Processing helix chain 'A' and resid 1337 through 1346 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 1425 through 1429 Processing helix chain 'A' and resid 1441 through 1443 No H-bonds generated for 'chain 'A' and resid 1441 through 1443' Processing helix chain 'A' and resid 1445 through 1473 removed outlier: 3.623A pdb=" N ARG A1455 " --> pdb=" O GLN A1451 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLU A1473 " --> pdb=" O ALA A1469 " (cutoff:3.500A) Processing helix chain 'A' and resid 1482 through 1509 removed outlier: 3.598A pdb=" N GLU A1496 " --> pdb=" O GLU A1492 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N TRP A1508 " --> pdb=" O ALA A1504 " (cutoff:3.500A) Processing helix chain 'A' and resid 1521 through 1529 removed outlier: 4.940A 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: 4.137A pdb=" N LYS A1551 " --> pdb=" O LYS A1547 " (cutoff:3.500A) Processing helix chain 'A' and resid 1577 through 1581 removed outlier: 3.934A pdb=" N THR A1581 " --> pdb=" O LYS A1578 " (cutoff:3.500A) Processing helix chain 'A' and resid 1585 through 1600 removed outlier: 4.542A pdb=" N GLY A1589 " --> pdb=" O GLY A1586 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N MET A1593 " --> pdb=" O ALA A1590 " (cutoff:3.500A) Processing helix chain 'A' and resid 1616 through 1620 Processing helix chain 'A' and resid 1658 through 1664 removed outlier: 3.502A pdb=" N TYR A1662 " --> pdb=" O ASP A1659 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N GLY A1663 " --> pdb=" O TYR A1660 " (cutoff:3.500A) Processing helix chain 'A' and resid 1667 through 1694 Processing helix chain 'A' and resid 1711 through 1716 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 1790 Processing helix chain 'A' and resid 1793 through 1801 removed outlier: 3.553A pdb=" N TYR A1798 " --> pdb=" O GLN A1794 " (cutoff:3.500A) Processing helix chain 'A' and resid 1805 through 1823 Processing helix chain 'A' and resid 1854 through 1861 Processing helix chain 'B' and resid 147 through 159 removed outlier: 3.784A pdb=" N LEU B 151 " --> pdb=" O ALA B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 176 Processing helix chain 'B' and resid 180 through 193 removed outlier: 4.208A pdb=" N GLU B 185 " --> pdb=" O THR B 181 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 214 Processing helix chain 'B' and resid 224 through 236 removed outlier: 3.530A pdb=" N SER B 234 " --> pdb=" O SER B 230 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N SER B 235 " --> pdb=" O ARG B 231 " (cutoff:3.500A) Processing helix chain 'B' and resid 243 through 253 Processing helix chain 'B' and resid 258 through 270 removed outlier: 4.454A pdb=" N GLY B 263 " --> pdb=" O GLY B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 298 removed outlier: 3.590A pdb=" N ALA B 291 " --> pdb=" O LEU B 287 " (cutoff:3.500A) Processing helix chain 'G' and resid 24 through 40 removed outlier: 3.594A pdb=" N PHE G 27 " --> pdb=" O THR G 24 " (cutoff:3.500A) removed outlier: 5.762A pdb=" N PHE G 28 " --> pdb=" O ALA G 25 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ILE G 29 " --> pdb=" O SER G 26 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N SER G 31 " --> pdb=" O PHE G 28 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N LEU G 33 " --> pdb=" O ALA G 30 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N GLN G 34 " --> pdb=" O SER G 31 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N GLU G 35 " --> pdb=" O GLN G 32 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLN G 36 " --> pdb=" O LEU G 33 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N PHE G 37 " --> pdb=" O GLN G 34 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LYS G 39 " --> pdb=" O GLN G 36 " (cutoff:3.500A) Processing helix chain 'G' and resid 57 through 69 Processing helix chain 'G' and resid 79 through 84 removed outlier: 3.513A pdb=" N GLN G 82 " --> pdb=" O GLN G 79 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N VAL G 83 " --> pdb=" O PHE G 80 " (cutoff:3.500A) Processing helix chain 'G' and resid 87 through 94 Processing helix chain 'G' and resid 101 through 111 removed outlier: 3.589A pdb=" N GLN G 110 " --> pdb=" O ALA G 106 " (cutoff:3.500A) Processing helix chain 'G' and resid 116 through 132 Processing helix chain 'G' and resid 144 through 151 Processing helix chain 'G' and resid 170 through 179 Processing helix chain 'G' and resid 184 through 201 removed outlier: 4.039A pdb=" N ILE G 188 " --> pdb=" O GLY G 185 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N LYS G 189 " --> pdb=" O ASP G 186 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N PHE G 190 " --> pdb=" O LEU G 187 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N LEU G 195 " --> pdb=" O ALA G 192 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N SER G 196 " --> pdb=" O GLU G 193 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLU G 197 " --> pdb=" O THR G 194 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N ILE G 199 " --> pdb=" O SER G 196 " (cutoff:3.500A) Processing helix chain 'G' and resid 205 through 208 No H-bonds generated for 'chain 'G' and resid 205 through 208' Processing helix chain 'G' and resid 215 through 220 Processing helix chain 'G' and resid 234 through 256 Proline residue: G 239 - end of helix removed outlier: 3.552A pdb=" N LEU G 246 " --> pdb=" O GLY G 242 " (cutoff:3.500A) Processing helix chain 'G' and resid 260 through 266 Processing helix chain 'G' and resid 277 through 285 Processing helix chain 'G' and resid 295 through 313 Processing helix chain 'G' and resid 321 through 329 removed outlier: 3.960A pdb=" N ASP G 326 " --> pdb=" O SER G 322 " (cutoff:3.500A) Processing helix chain 'G' and resid 346 through 358 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 394 removed outlier: 3.720A pdb=" N THR G 392 " --> pdb=" O GLY G 388 " (cutoff:3.500A) Processing helix chain 'G' and resid 430 through 446 Proline residue: G 434 - end of helix removed outlier: 4.721A pdb=" N ASP G 437 " --> pdb=" O PRO G 434 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ILE G 439 " --> pdb=" O SER G 436 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU G 443 " --> pdb=" O ASN G 440 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL G 444 " --> pdb=" O LYS G 441 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N LYS G 445 " --> pdb=" O ASP G 442 " (cutoff:3.500A) Processing helix chain 'G' and resid 475 through 484 removed outlier: 3.542A pdb=" N VAL G 480 " --> pdb=" O SER G 476 " (cutoff:3.500A) Processing helix chain 'G' and resid 490 through 495 removed outlier: 4.707A pdb=" N GLN G 495 " --> pdb=" O GLU G 491 " (cutoff:3.500A) 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 Processing helix chain 'G' and resid 544 through 548 removed outlier: 3.563A pdb=" N PHE G 548 " --> pdb=" O GLN G 545 " (cutoff:3.500A) 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 584 through 587 No H-bonds generated for 'chain 'G' and resid 584 through 587' Processing helix chain 'G' and resid 604 through 611 removed outlier: 3.500A pdb=" N ALA G 608 " --> pdb=" O PRO G 604 " (cutoff:3.500A) Processing helix chain 'G' and resid 621 through 623 No H-bonds generated for 'chain 'G' and resid 621 through 623' Processing helix chain 'G' and resid 627 through 640 removed outlier: 3.659A pdb=" N ALA G 633 " --> pdb=" O GLY G 629 " (cutoff:3.500A) Processing helix chain 'G' and resid 656 through 671 Proline residue: G 664 - end of helix Processing helix chain 'G' and resid 688 through 697 Processing helix chain 'G' and resid 710 through 722 Processing helix chain 'G' and resid 748 through 758 removed outlier: 6.362A pdb=" N SER G 755 " --> pdb=" O LEU G 751 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N LYS G 756 " --> pdb=" O GLN G 752 " (cutoff:3.500A) Processing helix chain 'G' and resid 774 through 782 Proline residue: G 779 - end of helix Processing helix chain 'G' and resid 784 through 786 No H-bonds generated for 'chain 'G' and resid 784 through 786' Processing helix chain 'G' and resid 803 through 807 removed outlier: 4.248A pdb=" N ILE G 807 " --> pdb=" O ARG G 804 " (cutoff:3.500A) Processing helix chain 'G' and resid 815 through 823 removed outlier: 3.635A pdb=" N LYS G 819 " --> pdb=" O PRO G 815 " (cutoff:3.500A) Processing helix chain 'G' and resid 829 through 836 removed outlier: 4.564A pdb=" N GLU G 833 " --> pdb=" O ASP G 830 " (cutoff:3.500A) Processing helix chain 'G' and resid 860 through 871 Processing helix chain 'G' and resid 877 through 886 removed outlier: 4.203A pdb=" N VAL G 881 " --> pdb=" O LYS G 877 " (cutoff:3.500A) Proline residue: G 882 - end of helix Processing helix chain 'G' and resid 888 through 897 Processing helix chain 'G' and resid 919 through 930 Processing helix chain 'G' and resid 942 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 1007 Processing helix chain 'G' and resid 1023 through 1030 removed outlier: 4.135A pdb=" N GLU G1026 " --> pdb=" O ARG G1023 " (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 1044 through 1046 No H-bonds generated for 'chain 'G' and resid 1044 through 1046' 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 1190 through 1192 No H-bonds generated for 'chain 'G' and resid 1190 through 1192' Processing helix chain 'G' and resid 1258 through 1270 removed outlier: 3.528A 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 1324 through 1338 removed outlier: 4.023A pdb=" N ARG G1332 " --> pdb=" O VAL G1329 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ILE G1334 " --> pdb=" O TRP G1331 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N ILE G1335 " --> pdb=" O ARG G1332 " (cutoff:3.500A) 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 1523 Processing helix chain 'G' and resid 1551 through 1556 Processing helix chain 'G' and resid 1562 through 1565 No H-bonds generated for 'chain 'G' and resid 1562 through 1565' Processing helix chain 'G' and resid 1567 through 1572 Processing helix chain 'G' and resid 1582 through 1596 removed outlier: 5.080A pdb=" N LEU G1592 " --> pdb=" O SER G1588 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ASN G1595 " --> pdb=" O ALA G1591 " (cutoff:3.500A) Processing helix chain 'G' and resid 1678 through 1683 removed outlier: 3.695A pdb=" N THR G1683 " --> pdb=" O ASP G1679 " (cutoff:3.500A) Processing helix chain 'G' and resid 1685 through 1702 Processing helix chain 'G' and resid 1706 through 1712 Processing helix chain 'G' and resid 1724 through 1733 Processing helix chain 'G' and resid 1774 through 1795 Proline residue: G1779 - end of helix Processing helix chain 'G' and resid 1810 through 1818 Processing helix chain 'G' and resid 1824 through 1839 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 1920 removed outlier: 3.844A pdb=" N LYS G1918 " --> pdb=" O LEU G1914 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU G1919 " --> pdb=" O ASN G1915 " (cutoff:3.500A) Processing helix chain 'G' and resid 1925 through 1930 removed outlier: 4.022A pdb=" N LYS G1929 " --> pdb=" O ILE G1925 " (cutoff:3.500A) Processing helix chain 'G' and resid 1935 through 1951 removed outlier: 3.888A pdb=" N GLU G1942 " --> pdb=" O GLY G1938 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ILE G1943 " --> pdb=" O HIS G1939 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N GLU G1946 " --> pdb=" O GLU G1942 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N LYS G1950 " --> pdb=" O GLU G1946 " (cutoff:3.500A) Processing helix chain 'G' and resid 1980 through 1995 removed outlier: 4.476A pdb=" N ASN G1983 " --> pdb=" O TYR G1980 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LYS G1986 " --> pdb=" O ASN G1983 " (cutoff:3.500A) Proline residue: G1987 - end of helix removed outlier: 3.875A pdb=" N LEU G1992 " --> pdb=" O LYS G1989 " (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 2003 through 2006 No H-bonds generated for 'chain 'G' and resid 2003 through 2006' Processing helix chain 'G' and resid 2023 through 2032 Processing helix chain 'G' and resid 2036 through 2043 removed outlier: 4.374A pdb=" N ILE G2041 " --> pdb=" O PRO G2037 " (cutoff:3.500A) Processing helix chain 'G' and resid 2045 through 2049 Processing sheet with id= A, first strand: chain 'A' and resid 43 through 46 removed outlier: 6.555A pdb=" N GLU A 77 " --> pdb=" O VAL A 44 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N GLU A 46 " --> pdb=" O GLU A 77 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N LEU A 79 " --> pdb=" O GLU A 46 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'A' and resid 400 through 402 removed outlier: 6.551A pdb=" N VAL A 703 " --> pdb=" O ILE A 733 " (cutoff:3.500A) removed outlier: 7.754A pdb=" N VAL A 735 " --> pdb=" O VAL A 703 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N VAL A 705 " --> pdb=" O VAL A 735 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N THR A 706 " --> pdb=" O ILE A 680 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N ALA A 767 " --> pdb=" O LEU A 679 " (cutoff:3.500A) removed outlier: 8.408A pdb=" N THR A 681 " --> pdb=" O ALA A 767 " (cutoff:3.500A) removed outlier: 6.539A 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: 4.166A pdb=" N MET A 923 " --> pdb=" O ARG A 641 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 820 through 822 Processing sheet with id= F, first strand: chain 'A' and resid 1060 through 1067 Processing sheet with id= G, first strand: chain 'A' and resid 1103 through 1105 Processing sheet with id= H, first strand: chain 'A' and resid 1123 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 1326 through 1333 removed outlier: 3.787A pdb=" N GLY A1023 " --> pdb=" O ILE A1386 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N MET A1388 " --> pdb=" O VAL A1021 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N VAL A1021 " --> pdb=" O MET A1388 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'A' and resid 1406 through 1409 removed outlier: 3.916A pdb=" N MET A1406 " --> pdb=" O ILE A1654 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N VAL A1538 " --> pdb=" O SER A1640 " (cutoff:3.500A) removed outlier: 8.409A pdb=" N THR A1642 " --> pdb=" O VAL A1538 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N SER A1540 " --> pdb=" O THR A1642 " (cutoff:3.500A) removed outlier: 8.846A pdb=" N PHE A1644 " --> pdb=" O SER A1540 " (cutoff:3.500A) removed outlier: 5.619A pdb=" N ILE A1573 " --> pdb=" O ALA A1539 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N PHE A1541 " --> pdb=" O ILE A1573 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N VAL A1575 " --> pdb=" O PHE A1541 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'A' and resid 1768 through 1775 Processing sheet with id= M, first strand: chain 'A' and resid 1837 through 1840 Processing sheet with id= N, first strand: chain 'G' and resid 6 through 13 removed outlier: 3.710A pdb=" N LEU G 16 " --> pdb=" O HIS G 13 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'G' and resid 458 through 460 removed outlier: 4.660A pdb=" N GLY G 272 " --> pdb=" O TYR G 460 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLY G 269 " --> pdb=" O LEU G 156 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ALA G 158 " --> pdb=" O GLY G 269 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N HIS G 500 " --> pdb=" O VAL G 157 " (cutoff:3.500A) removed outlier: 8.008A pdb=" N ILE G 159 " --> pdb=" O HIS G 500 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N LEU G 502 " --> pdb=" O ILE G 159 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N ARG G 526 " --> pdb=" O ILE G 501 " (cutoff:3.500A) removed outlier: 8.363A pdb=" N ASP G 503 " --> pdb=" O ARG G 526 " (cutoff:3.500A) removed outlier: 7.320A pdb=" N ILE G 528 " --> pdb=" O ASP G 503 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'G' and resid 418 through 420 removed outlier: 3.611A pdb=" N LEU G 377 " --> pdb=" O ILE G 341 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VAL G 378 " --> pdb=" O LEU G 370 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N SER G 380 " --> pdb=" O ILE G 368 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N ILE G 368 " --> pdb=" O SER G 380 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'G' and resid 568 through 571 Processing sheet with id= R, first strand: chain 'G' and resid 618 through 620 removed outlier: 6.669A pdb=" N GLY G 648 " --> pdb=" O LEU G 619 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N TYR G 702 " --> pdb=" O LEU G 679 " (cutoff:3.500A) removed outlier: 8.284A pdb=" N ILE G 681 " --> pdb=" O TYR G 702 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N GLY G 704 " --> pdb=" O ILE G 681 " (cutoff:3.500A) removed outlier: 8.405A pdb=" N LEU G 705 " --> pdb=" O PRO G 727 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N ALA G 729 " --> pdb=" O LEU G 705 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'G' and resid 843 through 847 Processing sheet with id= T, first strand: chain 'G' and resid 1125 through 1128 removed outlier: 6.453A pdb=" N GLU G1199 " --> pdb=" O PRO G1207 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N VAL G1201 " --> pdb=" O LEU G1205 " (cutoff:3.500A) removed outlier: 5.100A pdb=" N LEU G1205 " --> pdb=" O VAL G1201 " (cutoff:3.500A) removed outlier: 5.319A pdb=" N THR G1208 " --> pdb=" O ILE G1224 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N ILE G1218 " --> pdb=" O LEU G1214 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N LEU G1238 " --> pdb=" O MET G1221 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'G' and resid 1158 through 1161 Processing sheet with id= V, first strand: chain 'G' and resid 1285 through 1287 removed outlier: 4.115A pdb=" N THR G1374 " --> pdb=" O GLY G1287 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N ASP G1391 " --> pdb=" O GLU G1379 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N VAL G1381 " --> pdb=" O ILE G1389 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ILE G1389 " --> pdb=" O VAL G1381 " (cutoff:3.500A) removed outlier: 5.065A pdb=" N ASN G1383 " --> pdb=" O GLY G1387 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N GLY G1387 " --> pdb=" O ASN G1383 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N MET G1404 " --> pdb=" O LEU G1396 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N ARG G1398 " --> pdb=" O PRO G1402 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N PHE G1411 " --> pdb=" O HIS G1352 " (cutoff:3.500A) removed outlier: 5.414A pdb=" N HIS G1352 " --> pdb=" O PHE G1411 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N ARG G1413 " --> pdb=" O LEU G1350 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N LEU G1350 " --> pdb=" O ARG G1413 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'G' and resid 1431 through 1435 removed outlier: 3.748A pdb=" N LYS G1462 " --> pdb=" O ILE G1435 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLY G1487 " --> pdb=" O VAL G1504 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLY G1502 " --> pdb=" O ILE G1489 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'G' and resid 1490 through 1492 Processing sheet with id= Y, first strand: chain 'G' and resid 1530 through 1532 removed outlier: 3.552A pdb=" N GLU G1641 " --> pdb=" O SER G1625 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N LEU G1637 " --> pdb=" O VAL G1629 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N MET G1631 " --> pdb=" O ARG G1635 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N ARG G1635 " --> pdb=" O MET G1631 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLY G1607 " --> pdb=" O GLU G1656 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N GLU G1658 " --> pdb=" O VAL G1605 " (cutoff:3.500A) removed outlier: 5.644A pdb=" N VAL G1605 " --> pdb=" O GLU G1658 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'G' and resid 1663 through 1666 removed outlier: 6.561A pdb=" N THR G1803 " --> pdb=" O PHE G1664 " (cutoff:3.500A) removed outlier: 8.354A pdb=" N PHE G1666 " --> pdb=" O THR G1803 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N ALA G1805 " --> pdb=" O PHE G1666 " (cutoff:3.500A) No H-bonds generated for sheet with id= Z Processing sheet with id= AA, first strand: chain 'G' and resid 1716 through 1720 Processing sheet with id= AB, first strand: chain 'G' and resid 1852 through 1857 removed outlier: 6.324A pdb=" N ALA G1901 " --> pdb=" O ILE G1888 " (cutoff:3.500A) removed outlier: 5.208A pdb=" N ILE G1888 " --> pdb=" O ALA G1901 " (cutoff:3.500A) removed outlier: 7.413A pdb=" N ASP G1903 " --> pdb=" O VAL G1886 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N VAL G1886 " --> pdb=" O ASP G1903 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'G' and resid 1471 through 1474 Processing sheet with id= AD, first strand: chain 'G' and resid 1537 through 1543 removed outlier: 7.180A pdb=" N ILE G1626 " --> pdb=" O ILE G1539 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N VAL G1541 " --> pdb=" O THR G1624 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N THR G1624 " --> pdb=" O VAL G1541 " (cutoff:3.500A) 1145 hydrogen bonds defined for protein. 3057 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: 13.40 Time building geometry restraints manager: 12.28 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: 5080 1.31 - 1.45: 7664 1.45 - 1.58: 17377 1.58 - 1.72: 3 1.72 - 1.85: 190 Bond restraints: 30314 Sorted by residual: bond pdb=" C TYR A1174 " pdb=" O TYR A1174 " ideal model delta sigma weight residual 1.236 1.305 -0.069 1.14e-02 7.69e+03 3.63e+01 bond pdb=" C34 PNS B1901 " pdb=" N36 PNS B1901 " ideal model delta sigma weight residual 1.452 1.334 0.118 2.00e-02 2.50e+03 3.51e+01 bond pdb=" C7 FMN G2101 " pdb=" C8 FMN G2101 " ideal model delta sigma weight residual 1.390 1.491 -0.101 2.00e-02 2.50e+03 2.53e+01 bond pdb=" N ILE G1537 " pdb=" CA ILE G1537 " ideal model delta sigma weight residual 1.458 1.496 -0.038 7.70e-03 1.69e+04 2.47e+01 bond pdb=" C4 FMN G2101 " pdb=" C4A FMN G2101 " ideal model delta sigma weight residual 1.390 1.489 -0.099 2.00e-02 2.50e+03 2.45e+01 ... (remaining 30309 not shown) Histogram of bond angle deviations from ideal: 96.22 - 103.92: 389 103.92 - 111.63: 11265 111.63 - 119.33: 16804 119.33 - 127.04: 12321 127.04 - 134.74: 281 Bond angle restraints: 41060 Sorted by residual: angle pdb=" C GLY G 662 " pdb=" N ILE G 663 " pdb=" CA ILE G 663 " ideal model delta sigma weight residual 120.33 126.10 -5.77 8.00e-01 1.56e+00 5.21e+01 angle pdb=" CB GLU A 381 " pdb=" CG GLU A 381 " pdb=" CD GLU A 381 " ideal model delta sigma weight residual 112.60 123.14 -10.54 1.70e+00 3.46e-01 3.84e+01 angle pdb=" CA ASP G 186 " pdb=" CB ASP G 186 " pdb=" CG ASP G 186 " ideal model delta sigma weight residual 112.60 118.67 -6.07 1.00e+00 1.00e+00 3.68e+01 angle pdb=" N ARG A1502 " pdb=" CA ARG A1502 " pdb=" C ARG A1502 " ideal model delta sigma weight residual 111.07 104.65 6.42 1.07e+00 8.73e-01 3.60e+01 angle pdb=" CB GLU A1378 " pdb=" CG GLU A1378 " pdb=" CD GLU A1378 " ideal model delta sigma weight residual 112.60 122.73 -10.13 1.70e+00 3.46e-01 3.55e+01 ... (remaining 41055 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 16458 17.98 - 35.95: 1470 35.95 - 53.93: 253 53.93 - 71.91: 77 71.91 - 89.89: 39 Dihedral angle restraints: 18297 sinusoidal: 7358 harmonic: 10939 Sorted by residual: dihedral pdb=" CA ILE G1503 " pdb=" C ILE G1503 " pdb=" N VAL G1504 " pdb=" CA VAL G1504 " ideal model delta harmonic sigma weight residual 180.00 156.32 23.68 0 5.00e+00 4.00e-02 2.24e+01 dihedral pdb=" CA ASP G 974 " pdb=" C ASP G 974 " pdb=" N LYS G 975 " pdb=" CA LYS G 975 " ideal model delta harmonic sigma weight residual 180.00 156.73 23.27 0 5.00e+00 4.00e-02 2.17e+01 dihedral pdb=" CA LEU G 370 " pdb=" C LEU G 370 " pdb=" N VAL G 371 " pdb=" CA VAL G 371 " ideal model delta harmonic sigma weight residual 180.00 156.97 23.03 0 5.00e+00 4.00e-02 2.12e+01 ... (remaining 18294 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 1973 0.056 - 0.112: 1611 0.112 - 0.167: 829 0.167 - 0.223: 178 0.223 - 0.279: 23 Chirality restraints: 4614 Sorted by residual: 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 2.72 -0.28 2.00e-01 2.50e+01 1.95e+00 chirality pdb=" CA ILE A1328 " pdb=" N ILE A1328 " pdb=" C ILE A1328 " pdb=" CB ILE A1328 " both_signs ideal model delta sigma weight residual False 2.43 2.70 -0.27 2.00e-01 2.50e+01 1.82e+00 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 2.70 -0.27 2.00e-01 2.50e+01 1.76e+00 ... (remaining 4611 not shown) Planarity restraints: 5299 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A1401 " -0.065 2.00e-02 2.50e+03 3.40e-02 2.31e+01 pdb=" CG TYR A1401 " 0.046 2.00e-02 2.50e+03 pdb=" CD1 TYR A1401 " 0.019 2.00e-02 2.50e+03 pdb=" CD2 TYR A1401 " 0.042 2.00e-02 2.50e+03 pdb=" CE1 TYR A1401 " 0.007 2.00e-02 2.50e+03 pdb=" CE2 TYR A1401 " -0.013 2.00e-02 2.50e+03 pdb=" CZ TYR A1401 " -0.016 2.00e-02 2.50e+03 pdb=" OH TYR A1401 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP G1449 " -0.050 2.00e-02 2.50e+03 2.51e-02 1.57e+01 pdb=" CG TRP G1449 " 0.049 2.00e-02 2.50e+03 pdb=" CD1 TRP G1449 " 0.021 2.00e-02 2.50e+03 pdb=" CD2 TRP G1449 " 0.015 2.00e-02 2.50e+03 pdb=" NE1 TRP G1449 " -0.017 2.00e-02 2.50e+03 pdb=" CE2 TRP G1449 " -0.014 2.00e-02 2.50e+03 pdb=" CE3 TRP G1449 " 0.011 2.00e-02 2.50e+03 pdb=" CZ2 TRP G1449 " -0.010 2.00e-02 2.50e+03 pdb=" CZ3 TRP G1449 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP G1449 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A1529 " 0.045 2.00e-02 2.50e+03 2.39e-02 1.14e+01 pdb=" CG TYR A1529 " -0.025 2.00e-02 2.50e+03 pdb=" CD1 TYR A1529 " -0.033 2.00e-02 2.50e+03 pdb=" CD2 TYR A1529 " -0.013 2.00e-02 2.50e+03 pdb=" CE1 TYR A1529 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 TYR A1529 " -0.012 2.00e-02 2.50e+03 pdb=" CZ TYR A1529 " 0.013 2.00e-02 2.50e+03 pdb=" OH TYR A1529 " 0.018 2.00e-02 2.50e+03 ... (remaining 5296 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 371 2.64 - 3.20: 27255 3.20 - 3.77: 46617 3.77 - 4.33: 66271 4.33 - 4.90: 107810 Nonbonded interactions: 248324 Sorted by model distance: nonbonded pdb=" OH TYR B 249 " pdb=" OD1 ASP B 288 " model vdw 2.072 2.440 nonbonded pdb=" OH TYR G 177 " pdb=" OE2 GLU G 220 " model vdw 2.113 2.440 nonbonded pdb=" OG1 THR A1812 " pdb=" NH1 ARG A1841 " model vdw 2.227 2.520 nonbonded pdb=" OH TYR A1694 " pdb=" OD2 ASP G1001 " model vdw 2.227 2.440 nonbonded pdb=" OG1 THR G1663 " pdb=" O THR G1803 " model vdw 2.227 2.440 ... (remaining 248319 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: 0.590 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: 4.600 Check model and map are aligned: 0.410 Set scattering table: 0.240 Process input model: 78.140 Find NCS groups from input model: 0.770 Set up NCS constraints: 0.100 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:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 87.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 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 0.118 30314 Z= 0.913 Angle : 1.911 10.537 41060 Z= 1.394 Chirality : 0.088 0.279 4614 Planarity : 0.007 0.034 5299 Dihedral : 14.915 89.885 11252 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.32 % Allowed : 7.68 % Favored : 92.00 % Rotamer: Outliers : 0.62 % Allowed : 5.29 % Favored : 94.09 % 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: -3.68 (0.11), residues: 3776 helix: -2.84 (0.09), residues: 1667 sheet: -2.34 (0.21), residues: 459 loop : -1.82 (0.14), residues: 1650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.007 TRP G1449 HIS 0.015 0.003 HIS A1689 PHE 0.037 0.005 PHE G 799 TYR 0.065 0.006 TYR A1401 ARG 0.012 0.001 ARG A1017 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7552 Ramachandran restraints generated. 3776 Oldfield, 0 Emsley, 3776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7552 Ramachandran restraints generated. 3776 Oldfield, 0 Emsley, 3776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 3252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 291 time to evaluate : 2.943 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 841 GLU cc_start: 0.9233 (mp0) cc_final: 0.8509 (tp30) REVERT: A 923 MET cc_start: 0.9304 (tpp) cc_final: 0.9049 (tpp) REVERT: A 981 GLU cc_start: 0.9027 (mp0) cc_final: 0.8818 (mm-30) REVERT: A 1123 GLN cc_start: 0.9298 (tm-30) cc_final: 0.8719 (tm-30) REVERT: A 1124 GLU cc_start: 0.8942 (tp30) cc_final: 0.8495 (tp30) REVERT: A 1130 ASP cc_start: 0.9042 (m-30) cc_final: 0.8722 (m-30) REVERT: A 1396 MET cc_start: 0.9490 (mtp) cc_final: 0.9187 (mtp) REVERT: A 1461 ASP cc_start: 0.9418 (m-30) cc_final: 0.9179 (m-30) REVERT: A 1751 GLU cc_start: 0.8781 (OUTLIER) cc_final: 0.8389 (mp0) REVERT: A 1789 ARG cc_start: 0.8406 (tmt170) cc_final: 0.7837 (tpt90) REVERT: A 1794 GLN cc_start: 0.8440 (tm-30) cc_final: 0.8126 (tm-30) REVERT: A 1797 GLU cc_start: 0.8747 (tm-30) cc_final: 0.8347 (pp20) REVERT: B 149 LEU cc_start: 0.9267 (mp) cc_final: 0.8908 (pp) REVERT: B 202 GLU cc_start: 0.8304 (tt0) cc_final: 0.8102 (tt0) REVERT: B 211 GLU cc_start: 0.7522 (tm-30) cc_final: 0.6951 (tp30) REVERT: B 277 LEU cc_start: 0.5008 (OUTLIER) cc_final: 0.4633 (mt) REVERT: G 169 TYR cc_start: 0.8037 (p90) cc_final: 0.7609 (p90) REVERT: G 174 ARG cc_start: 0.7720 (mtt180) cc_final: 0.6918 (mmm-85) REVERT: G 209 PHE cc_start: 0.7335 (m-80) cc_final: 0.7062 (m-80) REVERT: G 311 TYR cc_start: 0.8379 (t80) cc_final: 0.8157 (t80) REVERT: G 553 ASN cc_start: 0.7811 (p0) cc_final: 0.7368 (p0) REVERT: G 618 GLU cc_start: 0.8666 (mt-10) cc_final: 0.8411 (mt-10) REVERT: G 765 LEU cc_start: 0.9436 (tp) cc_final: 0.9023 (tp) REVERT: G 1180 MET cc_start: 0.8383 (mtp) cc_final: 0.8033 (mtm) REVERT: G 1265 MET cc_start: 0.9344 (ttp) cc_final: 0.9045 (ttp) REVERT: G 1456 ASP cc_start: 0.9215 (m-30) cc_final: 0.8632 (p0) REVERT: G 1633 ASN cc_start: 0.9028 (t0) cc_final: 0.8787 (t0) REVERT: G 1656 GLU cc_start: 0.9077 (pm20) cc_final: 0.8675 (pm20) REVERT: G 1658 GLU cc_start: 0.9268 (mt-10) cc_final: 0.9012 (mt-10) REVERT: G 1784 MET cc_start: 0.9322 (tmm) cc_final: 0.8952 (tmm) REVERT: G 1822 MET cc_start: 0.8992 (mtm) cc_final: 0.8768 (mtm) REVERT: G 1982 MET cc_start: 0.9057 (mmp) cc_final: 0.8783 (mmm) outliers start: 20 outliers final: 3 residues processed: 309 average time/residue: 0.4029 time to fit residues: 202.2101 Evaluate side-chains 213 residues out of total 3252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 208 time to evaluate : 3.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1751 GLU Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain G residue 626 SER Chi-restraints excluded: chain G residue 1641 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 318 optimal weight: 8.9990 chunk 285 optimal weight: 8.9990 chunk 158 optimal weight: 20.0000 chunk 97 optimal weight: 3.9990 chunk 192 optimal weight: 5.9990 chunk 152 optimal weight: 9.9990 chunk 295 optimal weight: 10.0000 chunk 114 optimal weight: 10.0000 chunk 179 optimal weight: 6.9990 chunk 219 optimal weight: 8.9990 chunk 342 optimal weight: 1.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 32 GLN A 379 ASN A 527 GLN A 654 GLN A 758 ASN A 829 ASN ** A 987 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 989 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1146 HIS A1188 GLN A1239 HIS A1458 GLN A1549 ASN A1671 ASN B 183 GLN G 36 GLN G 110 GLN G 224 ASN G 248 HIS ** G 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 440 ASN G 718 ASN ** G 993 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G1055 HIS G1078 HIS G1186 ASN ** G1220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G1355 ASN G1451 GLN ** G1535 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G1595 ASN G1674 GLN G1872 GLN G1912 ASN G1983 ASN G2044 ASN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.1482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 30314 Z= 0.335 Angle : 0.593 10.308 41060 Z= 0.311 Chirality : 0.043 0.200 4614 Planarity : 0.005 0.188 5299 Dihedral : 5.607 62.772 4061 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.99 % Favored : 96.98 % Rotamer: Outliers : 0.98 % Allowed : 8.83 % Favored : 90.19 % 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: -1.29 (0.13), residues: 3776 helix: -0.54 (0.12), residues: 1693 sheet: -1.63 (0.21), residues: 520 loop : -0.70 (0.16), residues: 1563 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP G 661 HIS 0.007 0.001 HIS G1697 PHE 0.022 0.002 PHE A 450 TYR 0.019 0.002 TYR A 417 ARG 0.008 0.000 ARG B 231 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7552 Ramachandran restraints generated. 3776 Oldfield, 0 Emsley, 3776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7552 Ramachandran restraints generated. 3776 Oldfield, 0 Emsley, 3776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 3252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 219 time to evaluate : 3.333 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 336 LYS cc_start: 0.9225 (mttm) cc_final: 0.8871 (mmtt) REVERT: A 342 GLN cc_start: 0.9220 (mt0) cc_final: 0.8883 (mp10) REVERT: A 529 MET cc_start: 0.9230 (mmp) cc_final: 0.8978 (mmp) REVERT: A 841 GLU cc_start: 0.9152 (mp0) cc_final: 0.8493 (tp30) REVERT: A 1123 GLN cc_start: 0.9271 (tm-30) cc_final: 0.8579 (tm-30) REVERT: A 1130 ASP cc_start: 0.9002 (m-30) cc_final: 0.8616 (m-30) REVERT: A 1167 LEU cc_start: 0.9000 (mt) cc_final: 0.8679 (mt) REVERT: A 1789 ARG cc_start: 0.8360 (tmt170) cc_final: 0.8061 (tpt90) REVERT: A 1821 LYS cc_start: 0.8551 (mppt) cc_final: 0.8310 (mttm) REVERT: B 149 LEU cc_start: 0.9207 (mp) cc_final: 0.8900 (pp) REVERT: G 618 GLU cc_start: 0.8673 (mt-10) cc_final: 0.8407 (mt-10) REVERT: G 1135 GLU cc_start: 0.9334 (pm20) cc_final: 0.8982 (mp0) REVERT: G 1136 GLU cc_start: 0.9229 (tp30) cc_final: 0.8920 (tp30) REVERT: G 1456 ASP cc_start: 0.9251 (m-30) cc_final: 0.8649 (p0) REVERT: G 1627 GLN cc_start: 0.8948 (mt0) cc_final: 0.8701 (mm-40) REVERT: G 1631 MET cc_start: 0.8865 (mmm) cc_final: 0.8209 (mmm) REVERT: G 1822 MET cc_start: 0.9076 (mtm) cc_final: 0.8785 (mtm) REVERT: G 1854 MET cc_start: 0.8441 (mmm) cc_final: 0.8097 (mmm) REVERT: G 1982 MET cc_start: 0.8980 (mmp) cc_final: 0.8753 (mmm) outliers start: 32 outliers final: 18 residues processed: 241 average time/residue: 0.4030 time to fit residues: 158.5521 Evaluate side-chains 214 residues out of total 3252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 196 time to evaluate : 3.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 485 ASP Chi-restraints excluded: chain A residue 1333 ASP Chi-restraints excluded: chain A residue 1483 ASN Chi-restraints excluded: chain A residue 1872 SER Chi-restraints excluded: chain B residue 157 HIS Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain G residue 80 PHE Chi-restraints excluded: chain G residue 141 SER Chi-restraints excluded: chain G residue 336 SER Chi-restraints excluded: chain G residue 775 ASP Chi-restraints excluded: chain G residue 1162 ASP Chi-restraints excluded: chain G residue 1380 SER Chi-restraints excluded: chain G residue 1467 GLU Chi-restraints excluded: chain G residue 1478 ASN Chi-restraints excluded: chain G residue 1641 GLU Chi-restraints excluded: chain G residue 1646 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 190 optimal weight: 7.9990 chunk 106 optimal weight: 3.9990 chunk 284 optimal weight: 40.0000 chunk 233 optimal weight: 0.9980 chunk 94 optimal weight: 6.9990 chunk 342 optimal weight: 2.9990 chunk 370 optimal weight: 20.0000 chunk 305 optimal weight: 5.9990 chunk 340 optimal weight: 7.9990 chunk 116 optimal weight: 6.9990 chunk 275 optimal weight: 1.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 506 ASN A 829 ASN ** A 987 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 989 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1690 ASN B 251 GLN ** B 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 38 ASN G 163 GLN ** G 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 640 GLN ** G 993 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G1697 HIS G1890 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.1718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 30314 Z= 0.209 Angle : 0.512 8.767 41060 Z= 0.264 Chirality : 0.041 0.211 4614 Planarity : 0.003 0.042 5299 Dihedral : 4.949 60.464 4055 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.12 % Favored : 96.85 % Rotamer: Outliers : 1.14 % Allowed : 10.43 % Favored : 88.43 % 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: -0.18 (0.14), residues: 3776 helix: 0.51 (0.13), residues: 1681 sheet: -1.18 (0.22), residues: 531 loop : -0.24 (0.16), residues: 1564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP G 661 HIS 0.006 0.001 HIS G1697 PHE 0.020 0.001 PHE A1820 TYR 0.019 0.001 TYR G 126 ARG 0.005 0.000 ARG B 247 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7552 Ramachandran restraints generated. 3776 Oldfield, 0 Emsley, 3776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7552 Ramachandran restraints generated. 3776 Oldfield, 0 Emsley, 3776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 3252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 217 time to evaluate : 3.408 Fit side-chains revert: symmetry clash REVERT: A 16 GLU cc_start: 0.9379 (mt-10) cc_final: 0.9124 (mm-30) REVERT: A 336 LYS cc_start: 0.9129 (mttm) cc_final: 0.8785 (mmtt) REVERT: A 342 GLN cc_start: 0.9254 (mt0) cc_final: 0.8915 (mp10) REVERT: A 431 GLU cc_start: 0.9421 (mm-30) cc_final: 0.9175 (tm-30) REVERT: A 529 MET cc_start: 0.9207 (mmp) cc_final: 0.8947 (mmp) REVERT: A 841 GLU cc_start: 0.9120 (mp0) cc_final: 0.8485 (tp30) REVERT: A 1017 ARG cc_start: 0.8962 (mmm-85) cc_final: 0.8711 (ttm-80) REVERT: A 1123 GLN cc_start: 0.9234 (tm-30) cc_final: 0.8515 (tm-30) REVERT: A 1130 ASP cc_start: 0.9131 (m-30) cc_final: 0.8753 (m-30) REVERT: A 1167 LEU cc_start: 0.8988 (mt) cc_final: 0.8600 (mt) REVERT: A 1461 ASP cc_start: 0.9316 (m-30) cc_final: 0.9054 (m-30) REVERT: A 1821 LYS cc_start: 0.8653 (mppt) cc_final: 0.8386 (mttm) REVERT: B 174 ASP cc_start: 0.8865 (t70) cc_final: 0.8492 (t0) REVERT: G 38 ASN cc_start: 0.2176 (OUTLIER) cc_final: 0.1654 (m110) REVERT: G 551 THR cc_start: 0.7240 (OUTLIER) cc_final: 0.6881 (p) REVERT: G 618 GLU cc_start: 0.8643 (mt-10) cc_final: 0.8324 (mt-10) REVERT: G 1456 ASP cc_start: 0.9182 (m-30) cc_final: 0.8612 (p0) REVERT: G 1658 GLU cc_start: 0.9134 (mt-10) cc_final: 0.8924 (mt-10) REVERT: G 1854 MET cc_start: 0.8562 (mmm) cc_final: 0.8186 (mmm) outliers start: 37 outliers final: 21 residues processed: 249 average time/residue: 0.3954 time to fit residues: 163.9834 Evaluate side-chains 221 residues out of total 3252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 198 time to evaluate : 3.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 802 MET Chi-restraints excluded: chain A residue 1333 ASP Chi-restraints excluded: chain A residue 1752 THR Chi-restraints excluded: chain A residue 1872 SER Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 157 HIS Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain G residue 38 ASN Chi-restraints excluded: chain G residue 336 SER Chi-restraints excluded: chain G residue 439 ILE Chi-restraints excluded: chain G residue 551 THR Chi-restraints excluded: chain G residue 626 SER Chi-restraints excluded: chain G residue 775 ASP Chi-restraints excluded: chain G residue 889 ASP Chi-restraints excluded: chain G residue 1094 GLU Chi-restraints excluded: chain G residue 1162 ASP Chi-restraints excluded: chain G residue 1343 VAL Chi-restraints excluded: chain G residue 1437 THR Chi-restraints excluded: chain G residue 1467 GLU Chi-restraints excluded: chain G residue 1478 ASN Chi-restraints excluded: chain G residue 1629 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 338 optimal weight: 5.9990 chunk 257 optimal weight: 0.1980 chunk 177 optimal weight: 6.9990 chunk 37 optimal weight: 0.3980 chunk 163 optimal weight: 0.8980 chunk 230 optimal weight: 0.5980 chunk 344 optimal weight: 1.9990 chunk 364 optimal weight: 20.0000 chunk 179 optimal weight: 20.0000 chunk 326 optimal weight: 8.9990 chunk 98 optimal weight: 3.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 829 ASN ** A 987 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 989 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1671 ASN ** A1689 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 251 GLN ** B 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 163 GLN ** G 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 993 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.1935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 30314 Z= 0.128 Angle : 0.472 7.481 41060 Z= 0.243 Chirality : 0.040 0.232 4614 Planarity : 0.003 0.042 5299 Dihedral : 4.479 58.933 4052 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 0.92 % Allowed : 11.63 % Favored : 87.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.32 (0.14), residues: 3776 helix: 0.94 (0.13), residues: 1664 sheet: -0.87 (0.22), residues: 530 loop : -0.01 (0.16), residues: 1582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP G 661 HIS 0.004 0.001 HIS B 152 PHE 0.019 0.001 PHE A 35 TYR 0.019 0.001 TYR B 294 ARG 0.004 0.000 ARG G 412 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7552 Ramachandran restraints generated. 3776 Oldfield, 0 Emsley, 3776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7552 Ramachandran restraints generated. 3776 Oldfield, 0 Emsley, 3776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 3252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 232 time to evaluate : 3.682 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 GLU cc_start: 0.9380 (mt-10) cc_final: 0.9091 (mm-30) REVERT: A 56 MET cc_start: 0.8309 (ttm) cc_final: 0.8068 (mtp) REVERT: A 336 LYS cc_start: 0.9095 (mttm) cc_final: 0.8715 (mmtt) REVERT: A 342 GLN cc_start: 0.9243 (mt0) cc_final: 0.8730 (mp10) REVERT: A 529 MET cc_start: 0.9186 (mmp) cc_final: 0.8931 (mmp) REVERT: A 841 GLU cc_start: 0.9033 (mp0) cc_final: 0.8407 (tp30) REVERT: A 923 MET cc_start: 0.9290 (ttm) cc_final: 0.9065 (tpp) REVERT: A 1017 ARG cc_start: 0.8929 (mmm-85) cc_final: 0.8691 (ttm-80) REVERT: A 1123 GLN cc_start: 0.9206 (tm-30) cc_final: 0.8433 (tm-30) REVERT: A 1130 ASP cc_start: 0.9053 (m-30) cc_final: 0.8664 (m-30) REVERT: A 1167 LEU cc_start: 0.8983 (mt) cc_final: 0.8604 (mt) REVERT: A 1396 MET cc_start: 0.9467 (mtm) cc_final: 0.9143 (mtp) REVERT: A 1461 ASP cc_start: 0.9292 (m-30) cc_final: 0.9056 (m-30) REVERT: A 1789 ARG cc_start: 0.8039 (tpt90) cc_final: 0.7249 (tpt90) REVERT: A 1821 LYS cc_start: 0.8647 (mppt) cc_final: 0.8362 (mttm) REVERT: B 174 ASP cc_start: 0.8714 (t70) cc_final: 0.8289 (t0) REVERT: B 211 GLU cc_start: 0.7487 (tm-30) cc_final: 0.6890 (tp30) REVERT: B 251 GLN cc_start: 0.7324 (OUTLIER) cc_final: 0.6585 (tp-100) REVERT: G 618 GLU cc_start: 0.8583 (mt-10) cc_final: 0.8275 (mt-10) REVERT: G 764 MET cc_start: 0.8678 (mpp) cc_final: 0.8430 (mpp) REVERT: G 1136 GLU cc_start: 0.9159 (tp30) cc_final: 0.8709 (tm-30) REVERT: G 1456 ASP cc_start: 0.9172 (m-30) cc_final: 0.8630 (p0) REVERT: G 1658 GLU cc_start: 0.9119 (mt-10) cc_final: 0.8880 (mt-10) REVERT: G 1854 MET cc_start: 0.8587 (mmm) cc_final: 0.8164 (mmm) outliers start: 30 outliers final: 19 residues processed: 258 average time/residue: 0.4205 time to fit residues: 178.9355 Evaluate side-chains 224 residues out of total 3252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 204 time to evaluate : 3.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 1871 ILE Chi-restraints excluded: chain A residue 1872 SER Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 251 GLN Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain G residue 141 SER Chi-restraints excluded: chain G residue 658 MET Chi-restraints excluded: chain G residue 1094 GLU Chi-restraints excluded: chain G residue 1156 CYS Chi-restraints excluded: chain G residue 1343 VAL Chi-restraints excluded: chain G residue 1380 SER Chi-restraints excluded: chain G residue 1467 GLU Chi-restraints excluded: chain G residue 1629 VAL Chi-restraints excluded: chain G residue 1641 GLU Chi-restraints excluded: chain G residue 1646 ASP Chi-restraints excluded: chain G residue 1777 THR Chi-restraints excluded: chain G residue 1862 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 303 optimal weight: 20.0000 chunk 206 optimal weight: 6.9990 chunk 5 optimal weight: 40.0000 chunk 271 optimal weight: 4.9990 chunk 150 optimal weight: 30.0000 chunk 310 optimal weight: 5.9990 chunk 251 optimal weight: 3.9990 chunk 0 optimal weight: 20.0000 chunk 186 optimal weight: 5.9990 chunk 327 optimal weight: 0.6980 chunk 91 optimal weight: 3.9990 overall best weight: 3.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 829 ASN ** A 987 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 989 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1671 ASN ** A1689 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 251 GLN ** B 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 275 GLN ** G 993 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.2007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 30314 Z= 0.247 Angle : 0.503 9.737 41060 Z= 0.257 Chirality : 0.041 0.230 4614 Planarity : 0.003 0.045 5299 Dihedral : 4.504 58.126 4052 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.54 % Allowed : 12.70 % Favored : 85.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.14), residues: 3776 helix: 1.04 (0.13), residues: 1664 sheet: -0.67 (0.23), residues: 519 loop : 0.02 (0.16), residues: 1593 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP G 661 HIS 0.010 0.001 HIS B 152 PHE 0.016 0.001 PHE A 35 TYR 0.017 0.001 TYR G 126 ARG 0.003 0.000 ARG G1150 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7552 Ramachandran restraints generated. 3776 Oldfield, 0 Emsley, 3776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7552 Ramachandran restraints generated. 3776 Oldfield, 0 Emsley, 3776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 3252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 204 time to evaluate : 3.551 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 16 GLU cc_start: 0.9371 (mt-10) cc_final: 0.9104 (mm-30) REVERT: A 336 LYS cc_start: 0.9126 (mttm) cc_final: 0.8725 (mmtt) REVERT: A 342 GLN cc_start: 0.9255 (mt0) cc_final: 0.8732 (mp10) REVERT: A 529 MET cc_start: 0.9184 (mmp) cc_final: 0.8908 (mmp) REVERT: A 841 GLU cc_start: 0.9082 (mp0) cc_final: 0.8446 (tp30) REVERT: A 923 MET cc_start: 0.9325 (ttm) cc_final: 0.9023 (tpp) REVERT: A 1016 GLU cc_start: 0.9346 (mt-10) cc_final: 0.8930 (mp0) REVERT: A 1017 ARG cc_start: 0.8948 (mmm-85) cc_final: 0.8737 (ttm-80) REVERT: A 1123 GLN cc_start: 0.9257 (tm-30) cc_final: 0.8534 (tm-30) REVERT: A 1129 GLU cc_start: 0.8458 (pp20) cc_final: 0.7912 (pp20) REVERT: A 1130 ASP cc_start: 0.9068 (m-30) cc_final: 0.8396 (m-30) REVERT: A 1167 LEU cc_start: 0.8910 (mt) cc_final: 0.8501 (mt) REVERT: A 1396 MET cc_start: 0.9484 (mtm) cc_final: 0.9159 (mtp) REVERT: A 1461 ASP cc_start: 0.9313 (m-30) cc_final: 0.9061 (m-30) REVERT: A 1789 ARG cc_start: 0.8040 (tpt90) cc_final: 0.7480 (tpt90) REVERT: A 1821 LYS cc_start: 0.8626 (mppt) cc_final: 0.8321 (mttm) REVERT: B 174 ASP cc_start: 0.8804 (t70) cc_final: 0.8351 (t0) REVERT: B 211 GLU cc_start: 0.7456 (tm-30) cc_final: 0.6930 (tp30) REVERT: G 81 ASP cc_start: 0.7316 (m-30) cc_final: 0.6811 (m-30) REVERT: G 534 ASP cc_start: 0.7106 (OUTLIER) cc_final: 0.6055 (m-30) REVERT: G 551 THR cc_start: 0.7562 (OUTLIER) cc_final: 0.7232 (p) REVERT: G 618 GLU cc_start: 0.8618 (mt-10) cc_final: 0.8347 (mt-10) REVERT: G 1136 GLU cc_start: 0.9172 (tp30) cc_final: 0.8728 (tm-30) REVERT: G 1175 LYS cc_start: 0.9434 (tttm) cc_final: 0.9051 (mmtt) REVERT: G 1658 GLU cc_start: 0.9114 (mt-10) cc_final: 0.8829 (mt-10) REVERT: G 2026 PHE cc_start: 0.9529 (m-80) cc_final: 0.9274 (m-80) outliers start: 50 outliers final: 37 residues processed: 245 average time/residue: 0.3970 time to fit residues: 162.2979 Evaluate side-chains 238 residues out of total 3252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 199 time to evaluate : 3.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 485 ASP Chi-restraints excluded: chain A residue 802 MET Chi-restraints excluded: chain A residue 1333 ASP Chi-restraints excluded: chain A residue 1872 SER Chi-restraints excluded: chain A residue 1879 VAL Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain G residue 6 THR Chi-restraints excluded: chain G residue 80 PHE Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain G residue 141 SER Chi-restraints excluded: chain G residue 176 LEU Chi-restraints excluded: chain G residue 439 ILE Chi-restraints excluded: chain G residue 468 LEU Chi-restraints excluded: chain G residue 534 ASP Chi-restraints excluded: chain G residue 551 THR Chi-restraints excluded: chain G residue 626 SER Chi-restraints excluded: chain G residue 658 MET Chi-restraints excluded: chain G residue 775 ASP Chi-restraints excluded: chain G residue 1094 GLU Chi-restraints excluded: chain G residue 1130 THR Chi-restraints excluded: chain G residue 1156 CYS Chi-restraints excluded: chain G residue 1162 ASP Chi-restraints excluded: chain G residue 1343 VAL Chi-restraints excluded: chain G residue 1380 SER Chi-restraints excluded: chain G residue 1437 THR Chi-restraints excluded: chain G residue 1467 GLU Chi-restraints excluded: chain G residue 1478 ASN Chi-restraints excluded: chain G residue 1580 THR Chi-restraints excluded: chain G residue 1616 VAL Chi-restraints excluded: chain G residue 1629 VAL Chi-restraints excluded: chain G residue 1641 GLU Chi-restraints excluded: chain G residue 1646 ASP Chi-restraints excluded: chain G residue 1676 MET Chi-restraints excluded: chain G residue 1777 THR Chi-restraints excluded: chain G residue 1862 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 122 optimal weight: 0.8980 chunk 328 optimal weight: 1.9990 chunk 72 optimal weight: 3.9990 chunk 213 optimal weight: 10.0000 chunk 89 optimal weight: 0.3980 chunk 364 optimal weight: 0.9980 chunk 302 optimal weight: 7.9990 chunk 168 optimal weight: 10.0000 chunk 30 optimal weight: 5.9990 chunk 120 optimal weight: 8.9990 chunk 191 optimal weight: 10.0000 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 829 ASN ** A 987 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 989 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1689 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 723 HIS ** G 993 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.2155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 30314 Z= 0.143 Angle : 0.467 8.765 41060 Z= 0.236 Chirality : 0.040 0.256 4614 Planarity : 0.003 0.043 5299 Dihedral : 4.286 57.694 4052 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 1.14 % Allowed : 13.35 % Favored : 85.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.64 (0.14), residues: 3776 helix: 1.19 (0.13), residues: 1663 sheet: -0.60 (0.22), residues: 532 loop : 0.13 (0.16), residues: 1581 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP G1138 HIS 0.009 0.001 HIS B 152 PHE 0.018 0.001 PHE A 35 TYR 0.014 0.001 TYR G 126 ARG 0.002 0.000 ARG A 340 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7552 Ramachandran restraints generated. 3776 Oldfield, 0 Emsley, 3776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7552 Ramachandran restraints generated. 3776 Oldfield, 0 Emsley, 3776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 3252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 213 time to evaluate : 3.406 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 16 GLU cc_start: 0.9363 (mt-10) cc_final: 0.9061 (mm-30) REVERT: A 336 LYS cc_start: 0.9070 (mttm) cc_final: 0.8682 (mmtt) REVERT: A 342 GLN cc_start: 0.9248 (mt0) cc_final: 0.8715 (mp10) REVERT: A 841 GLU cc_start: 0.9014 (mp0) cc_final: 0.8404 (tp30) REVERT: A 923 MET cc_start: 0.9264 (ttm) cc_final: 0.8977 (tpp) REVERT: A 1016 GLU cc_start: 0.9343 (mt-10) cc_final: 0.8938 (mp0) REVERT: A 1017 ARG cc_start: 0.8917 (mmm-85) cc_final: 0.8696 (ttm-80) REVERT: A 1123 GLN cc_start: 0.9181 (tm-30) cc_final: 0.8426 (tm-30) REVERT: A 1129 GLU cc_start: 0.8474 (pp20) cc_final: 0.7921 (pp20) REVERT: A 1130 ASP cc_start: 0.9048 (m-30) cc_final: 0.8369 (m-30) REVERT: A 1167 LEU cc_start: 0.8898 (mt) cc_final: 0.8520 (mt) REVERT: A 1396 MET cc_start: 0.9469 (mtm) cc_final: 0.9165 (mtp) REVERT: A 1813 TRP cc_start: 0.8676 (t-100) cc_final: 0.8451 (t-100) REVERT: A 1821 LYS cc_start: 0.8627 (mppt) cc_final: 0.8364 (mttm) REVERT: B 211 GLU cc_start: 0.7467 (tm-30) cc_final: 0.6942 (tp30) REVERT: G 534 ASP cc_start: 0.7340 (OUTLIER) cc_final: 0.6786 (m-30) REVERT: G 551 THR cc_start: 0.7385 (OUTLIER) cc_final: 0.7033 (p) REVERT: G 618 GLU cc_start: 0.8585 (mt-10) cc_final: 0.8324 (mt-10) REVERT: G 1136 GLU cc_start: 0.9138 (tp30) cc_final: 0.8699 (tm-30) REVERT: G 1175 LYS cc_start: 0.9421 (tttm) cc_final: 0.9056 (mmtt) REVERT: G 1223 MET cc_start: 0.7587 (tpp) cc_final: 0.7369 (tpp) REVERT: G 1627 GLN cc_start: 0.8420 (OUTLIER) cc_final: 0.7942 (mm-40) REVERT: G 1658 GLU cc_start: 0.9103 (mt-10) cc_final: 0.8848 (mt-10) REVERT: G 1678 MET cc_start: 0.9302 (mmp) cc_final: 0.9089 (mmp) REVERT: G 2026 PHE cc_start: 0.9536 (m-80) cc_final: 0.9246 (m-80) outliers start: 37 outliers final: 28 residues processed: 244 average time/residue: 0.4023 time to fit residues: 161.8691 Evaluate side-chains 233 residues out of total 3252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 202 time to evaluate : 3.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 802 MET Chi-restraints excluded: chain A residue 965 HIS Chi-restraints excluded: chain A residue 1333 ASP Chi-restraints excluded: chain A residue 1872 SER Chi-restraints excluded: chain A residue 1879 VAL Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain G residue 141 SER Chi-restraints excluded: chain G residue 176 LEU Chi-restraints excluded: chain G residue 534 ASP Chi-restraints excluded: chain G residue 551 THR Chi-restraints excluded: chain G residue 658 MET Chi-restraints excluded: chain G residue 889 ASP Chi-restraints excluded: chain G residue 1094 GLU Chi-restraints excluded: chain G residue 1156 CYS Chi-restraints excluded: chain G residue 1343 VAL Chi-restraints excluded: chain G residue 1380 SER Chi-restraints excluded: chain G residue 1467 GLU Chi-restraints excluded: chain G residue 1580 THR Chi-restraints excluded: chain G residue 1610 CYS Chi-restraints excluded: chain G residue 1627 GLN Chi-restraints excluded: chain G residue 1629 VAL Chi-restraints excluded: chain G residue 1641 GLU Chi-restraints excluded: chain G residue 1646 ASP Chi-restraints excluded: chain G residue 1676 MET Chi-restraints excluded: chain G residue 1777 THR Chi-restraints excluded: chain G residue 1862 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 71.7594 > 50: distance: 48 - 53: 34.896 distance: 53 - 54: 56.321 distance: 55 - 61: 3.813 distance: 58 - 59: 69.384 distance: 58 - 60: 69.004 distance: 61 - 62: 5.488 distance: 62 - 63: 70.043 distance: 63 - 64: 56.138 distance: 63 - 65: 17.773 distance: 65 - 66: 44.618 distance: 66 - 69: 39.762 distance: 69 - 70: 41.372 distance: 70 - 71: 56.944 distance: 70 - 72: 40.324 distance: 73 - 74: 40.621 distance: 74 - 77: 38.795 distance: 75 - 76: 39.640 distance: 78 - 80: 40.334 distance: 81 - 82: 55.892 distance: 83 - 84: 56.426 distance: 83 - 89: 39.214 distance: 86 - 87: 39.611 distance: 86 - 88: 56.771 distance: 90 - 91: 68.817 distance: 91 - 98: 56.478 distance: 93 - 94: 57.951 distance: 94 - 95: 38.470 distance: 96 - 97: 56.466 distance: 98 - 99: 39.931 distance: 99 - 100: 56.786 distance: 99 - 102: 39.616 distance: 100 - 106: 55.347 distance: 102 - 103: 40.817 distance: 103 - 105: 39.686 distance: 106 - 107: 12.530 distance: 107 - 108: 47.852 distance: 108 - 113: 56.627 distance: 110 - 111: 42.607 distance: 110 - 112: 11.691 distance: 114 - 115: 55.551 distance: 114 - 117: 40.699 distance: 115 - 116: 40.193 distance: 117 - 118: 38.552 distance: 118 - 119: 56.373 distance: 118 - 120: 40.804 distance: 120 - 122: 68.025 distance: 121 - 122: 56.815 distance: 123 - 124: 56.383 distance: 124 - 127: 13.270 distance: 125 - 131: 34.702 distance: 127 - 128: 12.691 distance: 128 - 129: 57.411 distance: 128 - 130: 39.245