Starting phenix.real_space_refine on Thu Mar 21 08:18:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8psk_17854/03_2024/8psk_17854_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8psk_17854/03_2024/8psk_17854.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8psk_17854/03_2024/8psk_17854.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8psk_17854/03_2024/8psk_17854.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8psk_17854/03_2024/8psk_17854_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8psk_17854/03_2024/8psk_17854_updated.pdb" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.002 sd= 0.012 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 106 5.16 5 C 18867 2.51 5 N 4954 2.21 5 O 5676 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 4": "OE1" <-> "OE2" Residue "A TYR 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 42": "OE1" <-> "OE2" Residue "A TYR 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 87": "OE1" <-> "OE2" Residue "A GLU 330": "OE1" <-> "OE2" Residue "A ASP 376": "OD1" <-> "OD2" Residue "A GLU 419": "OE1" <-> "OE2" Residue "A GLU 431": "OE1" <-> "OE2" Residue "A GLU 464": "OE1" <-> "OE2" Residue "A GLU 514": "OE1" <-> "OE2" Residue "A ASP 648": "OD1" <-> "OD2" Residue "A ASP 744": "OD1" <-> "OD2" Residue "A GLU 782": "OE1" <-> "OE2" Residue "A PHE 896": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 915": "OE1" <-> "OE2" Residue "A GLU 938": "OE1" <-> "OE2" Residue "A GLU 981": "OE1" <-> "OE2" Residue "A PHE 1024": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1082": "OE1" <-> "OE2" Residue "A ASP 1085": "OD1" <-> "OD2" Residue "A GLU 1139": "OE1" <-> "OE2" Residue "A ASP 1150": "OD1" <-> "OD2" Residue "A GLU 1162": "OE1" <-> "OE2" Residue "A ASP 1202": "OD1" <-> "OD2" Residue "A GLU 1310": "OE1" <-> "OE2" Residue "A TYR 1332": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1354": "OE1" <-> "OE2" Residue "A ASP 1391": "OD1" <-> "OD2" Residue "A TYR 1438": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1485": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1579": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1646": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1668": "OD1" <-> "OD2" Residue "A GLU 1672": "OE1" <-> "OE2" Residue "A GLU 1709": "OE1" <-> "OE2" Residue "A GLU 1711": "OE1" <-> "OE2" Residue "A GLU 1782": "OE1" <-> "OE2" Residue "A PHE 1786": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 202": "OE1" <-> "OE2" Residue "B ASP 288": "OD1" <-> "OD2" Residue "G GLU 73": "OE1" <-> "OE2" Residue "G PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 100": "OD1" <-> "OD2" Residue "G ASP 138": "OD1" <-> "OD2" Residue "G PHE 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 168": "OD1" <-> "OD2" Residue "G ASP 175": "OD1" <-> "OD2" Residue "G GLU 193": "OE1" <-> "OE2" Residue "G TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 285": "OE1" <-> "OE2" Residue "G PHE 292": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 311": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 329": "OE1" <-> "OE2" Residue "G TYR 387": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 403": "OD1" <-> "OD2" Residue "G GLU 491": "OE1" <-> "OE2" Residue "G PHE 578": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 618": "OE1" <-> "OE2" Residue "G PHE 657": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 767": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 1067": "OD1" <-> "OD2" Residue "G ASP 1075": "OD1" <-> "OD2" Residue "G GLU 1135": "OE1" <-> "OE2" Residue "G GLU 1222": "OE1" <-> "OE2" Residue "G TYR 1240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 1273": "OE1" <-> "OE2" Residue "G ASP 1278": "OD1" <-> "OD2" Residue "G GLU 1309": "OE1" <-> "OE2" Residue "G ASP 1346": "OD1" <-> "OD2" Residue "G GLU 1654": "OE1" <-> "OE2" Residue "G ASP 1689": "OD1" <-> "OD2" Residue "G GLU 1757": "OE1" <-> "OE2" Residue "G PHE 1804": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 1829": "OE1" <-> "OE2" Residue "G TYR 1873": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 1916": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 1976": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 1988": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 2019": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 29604 Number of models: 1 Model: "" Number of chains: 4 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: "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: 15.16, per 1000 atoms: 0.51 Number of scatterers: 29604 At special positions: 0 Unit cell: (183.57, 182.515, 176.185, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 106 16.00 P 1 15.00 O 5676 8.00 N 4954 7.00 C 18867 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=2.21 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=0, symmetry=0 Time building additional restraints: 11.02 Conformation dependent library (CDL) restraints added in 5.2 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: 168 helices and 26 sheets defined 44.5% alpha, 12.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 12.15 Creating SS restraints... Processing helix chain 'A' and resid 3 through 23 removed outlier: 3.729A pdb=" N PHE A 22 " --> pdb=" O LEU A 18 " (cutoff:3.500A) removed outlier: 4.486A 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: 4.086A pdb=" N LYS A 410 " --> pdb=" O TRP A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 442 removed outlier: 3.697A pdb=" N SER A 434 " --> pdb=" O GLU A 431 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N GLU A 435 " --> pdb=" O VAL A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 445 through 455 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 482 Processing helix chain 'A' and resid 522 through 531 Processing helix chain 'A' and resid 609 through 614 Processing helix chain 'A' and resid 653 through 669 Processing helix chain 'A' and resid 688 through 698 Processing helix chain 'A' and resid 712 through 725 Processing helix chain 'A' and resid 742 through 753 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: 4.092A pdb=" N GLU A 847 " --> pdb=" O LYS A 843 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N THR A 848 " --> pdb=" O LEU A 844 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N LEU A 849 " --> pdb=" O SER A 845 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N PHE A 850 " --> pdb=" O LEU A 846 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N ASN A 851 " --> pdb=" O GLU A 847 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N HIS A 854 " --> pdb=" O PHE A 850 " (cutoff:3.500A) Processing helix chain 'A' and resid 885 through 891 removed outlier: 3.882A pdb=" N MET A 891 " --> pdb=" O GLY A 887 " (cutoff:3.500A) Processing helix chain 'A' and resid 898 through 909 removed outlier: 3.571A pdb=" N LEU A 908 " --> pdb=" O ASN A 904 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N LEU A 909 " --> pdb=" O LEU A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 911 through 919 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 969 Processing helix chain 'A' and resid 998 through 1004 removed outlier: 3.839A pdb=" N GLN A1003 " --> pdb=" O LYS A 999 " (cutoff:3.500A) removed outlier: 3.859A 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 1033 through 1041 Processing helix chain 'A' and resid 1047 through 1056 Processing helix chain 'A' and resid 1086 through 1099 removed outlier: 4.447A pdb=" N LYS A1090 " --> pdb=" O ASP A1086 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N ALA A1091 " --> pdb=" O LYS A1087 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N THR A1095 " --> pdb=" O ALA A1091 " (cutoff:3.500A) removed outlier: 5.715A 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: 7.109A pdb=" N ASP A1150 " --> pdb=" O HIS A1146 " (cutoff:3.500A) removed outlier: 7.406A 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: 3.570A pdb=" N GLN A1207 " --> pdb=" O ASP A1203 " (cutoff:3.500A) Processing helix chain 'A' and resid 1210 through 1226 removed outlier: 3.591A 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 1276 through 1278 No H-bonds generated for 'chain 'A' and resid 1276 through 1278' Processing helix chain 'A' and resid 1280 through 1290 removed outlier: 3.949A pdb=" N MET A1283 " --> pdb=" O ILE A1280 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N SER A1284 " --> pdb=" O ASN A1281 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU A1290 " --> pdb=" O VAL A1287 " (cutoff:3.500A) Processing helix chain 'A' and resid 1304 through 1320 removed outlier: 4.651A pdb=" N SER A1308 " --> pdb=" O CYS A1305 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N SER A1311 " --> pdb=" O SER A1308 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ILE A1314 " --> pdb=" O SER A1311 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N VAL A1316 " --> pdb=" O ASP A1313 " (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 1474 Processing helix chain 'A' and resid 1479 through 1509 removed outlier: 4.321A pdb=" N ASN A1483 " --> pdb=" O SER A1479 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N GLU A1484 " --> pdb=" O GLU A1480 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLU A1492 " --> pdb=" O GLU A1488 " (cutoff:3.500A) Processing helix chain 'A' and resid 1521 through 1529 removed outlier: 3.538A pdb=" N LEU A1526 " --> pdb=" O LEU A1522 " (cutoff:3.500A) removed outlier: 4.554A 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: 3.769A pdb=" N LYS A1551 " --> pdb=" O LYS A1547 " (cutoff:3.500A) Processing helix chain 'A' and resid 1577 through 1581 removed outlier: 3.732A pdb=" N THR A1581 " --> pdb=" O LYS A1578 " (cutoff:3.500A) Processing helix chain 'A' and resid 1585 through 1600 removed outlier: 4.289A pdb=" N GLY A1589 " --> pdb=" O GLY A1586 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N MET A1593 " --> pdb=" O ALA A1590 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N LEU A1597 " --> pdb=" O ASN A1594 " (cutoff:3.500A) Processing helix chain 'A' and resid 1616 through 1620 removed outlier: 3.665A pdb=" N GLN A1620 " --> pdb=" O ILE A1617 " (cutoff:3.500A) Processing helix chain 'A' and resid 1658 through 1664 removed outlier: 3.573A pdb=" N TYR A1662 " --> pdb=" O ASP A1659 " (cutoff:3.500A) removed outlier: 4.195A 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 1757 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: 3.666A pdb=" N ALA A1801 " --> pdb=" O GLU A1797 " (cutoff:3.500A) Processing helix chain 'A' and resid 1805 through 1823 Processing helix chain 'A' and resid 1854 through 1861 removed outlier: 3.517A pdb=" N GLU A1860 " --> pdb=" O LYS A1856 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 159 Processing helix chain 'B' and resid 172 through 175 No H-bonds generated for 'chain 'B' and resid 172 through 175' Processing helix chain 'B' and resid 180 through 194 removed outlier: 3.690A pdb=" N ASN B 184 " --> pdb=" O SER B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 214 removed outlier: 3.503A pdb=" N GLU B 211 " --> pdb=" O GLU B 207 " (cutoff:3.500A) Processing helix chain 'B' and resid 224 through 236 Processing helix chain 'B' and resid 243 through 253 Processing helix chain 'B' and resid 258 through 270 Processing helix chain 'B' and resid 280 through 298 Processing helix chain 'G' and resid 24 through 40 removed outlier: 5.537A pdb=" N PHE G 28 " --> pdb=" O ALA G 25 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ILE G 29 " --> pdb=" O SER G 26 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N SER G 31 " --> pdb=" O PHE G 28 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LEU G 33 " --> pdb=" O ALA G 30 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N PHE G 37 " --> pdb=" O GLN G 34 " (cutoff:3.500A) Processing helix chain 'G' and resid 57 through 71 removed outlier: 3.753A pdb=" N LEU G 71 " --> pdb=" O TYR G 67 " (cutoff:3.500A) Processing helix chain 'G' and resid 81 through 94 Processing helix chain 'G' and resid 101 through 110 removed outlier: 3.611A 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 169 through 179 Processing helix chain 'G' and resid 181 through 201 removed outlier: 5.797A pdb=" N ASP G 186 " --> pdb=" O VAL G 182 " (cutoff:3.500A) removed outlier: 5.719A 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: 3.581A pdb=" N ALA G 280 " --> pdb=" O LEU G 277 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ILE G 283 " --> pdb=" O ALA G 280 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ALA G 284 " --> pdb=" O VAL G 281 " (cutoff:3.500A) Processing helix chain 'G' and resid 292 through 313 removed outlier: 3.930A pdb=" N ARG G 297 " --> pdb=" O PHE G 293 " (cutoff:3.500A) Processing helix chain 'G' and resid 321 through 329 Processing helix chain 'G' and resid 346 through 359 removed outlier: 4.072A 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: 3.539A pdb=" N THR G 392 " --> pdb=" O GLY G 388 " (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 444 Proline residue: G 434 - end of helix removed outlier: 4.468A pdb=" N ASP G 437 " --> pdb=" O PRO G 434 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ASN G 440 " --> pdb=" O ASP G 437 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU G 443 " --> pdb=" O ASN G 440 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N VAL G 444 " --> pdb=" O LYS G 441 " (cutoff:3.500A) Processing helix chain 'G' and resid 468 through 470 No H-bonds generated for 'chain 'G' and resid 468 through 470' 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 Processing helix chain 'G' and resid 544 through 548 Processing helix chain 'G' and resid 552 through 554 No H-bonds generated for 'chain 'G' and resid 552 through 554' 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: 3.777A pdb=" N LEU G 586 " --> pdb=" O LYS G 582 " (cutoff:3.500A) Processing helix chain 'G' and resid 604 through 611 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 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: 5.388A pdb=" N SER G 755 " --> pdb=" O LEU G 751 " (cutoff:3.500A) removed outlier: 5.469A 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 787 Processing helix chain 'G' and resid 803 through 807 removed outlier: 4.342A pdb=" N ILE G 807 " --> pdb=" O ARG G 804 " (cutoff:3.500A) Processing helix chain 'G' and resid 815 through 823 Processing helix chain 'G' and resid 832 through 836 Processing helix chain 'G' and resid 860 through 871 Processing helix chain 'G' and resid 877 through 898 removed outlier: 4.600A pdb=" N VAL G 881 " --> pdb=" O LYS G 877 " (cutoff:3.500A) Proline residue: G 882 - end of helix removed outlier: 5.206A pdb=" N ASP G 889 " --> pdb=" O GLU G 885 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N TYR G 890 " --> pdb=" O ALA G 886 " (cutoff:3.500A) 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 1006 Processing helix chain 'G' and resid 1025 through 1030 Processing helix chain 'G' and resid 1036 through 1038 No H-bonds generated for 'chain 'G' and resid 1036 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 1173 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 Processing helix chain 'G' and resid 1294 through 1304 Processing helix chain 'G' and resid 1324 through 1338 removed outlier: 3.523A pdb=" N GLY G1330 " --> pdb=" O ILE G1327 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N TRP G1331 " --> pdb=" O VAL G1328 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N ARG G1332 " --> pdb=" O VAL G1329 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N ILE G1335 " --> pdb=" O ARG G1332 " (cutoff:3.500A) Processing helix chain 'G' and resid 1347 through 1349 No H-bonds generated for 'chain 'G' and resid 1347 through 1349' 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 1438 through 1446 Processing helix chain 'G' and resid 1515 through 1523 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 1602 through 1604 No H-bonds generated for 'chain 'G' and resid 1602 through 1604' Processing helix chain 'G' and resid 1678 through 1682 Processing helix chain 'G' and resid 1685 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 1770 through 1772 No H-bonds generated for 'chain 'G' and resid 1770 through 1772' Processing helix chain 'G' and resid 1774 through 1795 Proline residue: G1779 - end of helix Processing helix chain 'G' and resid 1808 through 1817 removed outlier: 3.997A pdb=" N ALA G1816 " --> pdb=" O ALA G1813 " (cutoff:3.500A) Processing helix chain 'G' and resid 1824 through 1840 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 1881 Processing helix chain 'G' and resid 1904 through 1920 removed outlier: 3.593A pdb=" N ASP G1908 " --> pdb=" O LEU G1904 " (cutoff:3.500A) Processing helix chain 'G' and resid 1925 through 1929 removed outlier: 3.510A pdb=" N LYS G1929 " --> pdb=" O ILE G1925 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 1925 through 1929' Processing helix chain 'G' and resid 1936 through 1951 removed outlier: 3.987A pdb=" N GLU G1942 " --> pdb=" O GLY G1938 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ILE G1943 " --> pdb=" O HIS G1939 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ALA G1947 " --> pdb=" O ILE G1943 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LYS G1950 " --> pdb=" O GLU G1946 " (cutoff:3.500A) Processing helix chain 'G' and resid 1980 through 1982 No H-bonds generated for 'chain 'G' and resid 1980 through 1982' Processing helix chain 'G' and resid 1985 through 1994 removed outlier: 3.666A pdb=" N SER G1990 " --> pdb=" O LYS G1986 " (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 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 43 through 46 removed outlier: 6.688A pdb=" N GLU A 77 " --> pdb=" O VAL A 44 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N GLU A 46 " --> pdb=" O GLU A 77 " (cutoff:3.500A) removed outlier: 6.822A 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: 6.378A pdb=" N ALA A 767 " --> pdb=" O LEU A 679 " (cutoff:3.500A) removed outlier: 8.394A pdb=" N THR A 681 " --> pdb=" O ALA A 767 " (cutoff:3.500A) removed outlier: 6.711A 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: 4.253A pdb=" N MET A 923 " --> pdb=" O ARG A 641 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N ALA A 820 " --> pdb=" O THR A 863 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N CYS A 865 " --> pdb=" O ALA A 820 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N VAL A 822 " --> pdb=" O CYS A 865 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N ALA A 867 " --> pdb=" O VAL A 822 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N LEU A 824 " --> pdb=" O ALA A 867 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N ILE A 869 " --> pdb=" O LEU A 824 " (cutoff:3.500A) removed outlier: 6.527A 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: 6.395A pdb=" N ILE A1326 " --> pdb=" O GLY A1244 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLY A1023 " --> pdb=" O ILE A1386 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N MET A1388 " --> pdb=" O VAL A1021 " (cutoff:3.500A) removed outlier: 5.446A pdb=" N VAL A1021 " --> pdb=" O MET A1388 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N ILE A1019 " --> pdb=" O VAL A1404 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLY A1402 " --> pdb=" O VAL A1021 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N ILE A1654 " --> pdb=" O ALA A1405 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N ALA A1407 " --> pdb=" O GLN A1652 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N GLN A1652 " --> pdb=" O ALA A1407 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N THR A1409 " --> pdb=" O GLY A1650 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N GLY A1650 " --> pdb=" O THR A1409 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LYS A1649 " --> pdb=" O GLY A1645 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N VAL A1538 " --> pdb=" O SER A1640 " (cutoff:3.500A) removed outlier: 8.035A pdb=" N THR A1642 " --> pdb=" O VAL A1538 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N SER A1540 " --> pdb=" O THR A1642 " (cutoff:3.500A) removed outlier: 8.709A pdb=" N PHE A1644 " --> pdb=" O SER A1540 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N ILE A1573 " --> pdb=" O ALA A1539 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 1060 through 1067 removed outlier: 3.803A pdb=" N ARG A1070 " --> pdb=" O LEU A1067 " (cutoff:3.500A) 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 1119 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 1768 through 1775 removed outlier: 3.619A pdb=" N ASP A1866 " --> pdb=" O THR A1885 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'A' and resid 1837 through 1840 Processing sheet with id= L, first strand: chain 'G' and resid 6 through 13 removed outlier: 3.843A pdb=" N VAL G 22 " --> pdb=" O ARG G 7 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'G' and resid 458 through 460 removed outlier: 4.848A pdb=" N GLY G 272 " --> pdb=" O TYR G 460 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLY G 269 " --> pdb=" O LEU G 156 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N HIS G 500 " --> pdb=" O VAL G 157 " (cutoff:3.500A) removed outlier: 7.785A pdb=" N ILE G 159 " --> pdb=" O HIS G 500 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N LEU G 502 " --> pdb=" O ILE G 159 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N ARG G 526 " --> pdb=" O ILE G 501 " (cutoff:3.500A) removed outlier: 7.728A pdb=" N ASP G 503 " --> pdb=" O ARG G 526 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N ILE G 528 " --> pdb=" O ASP G 503 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'G' and resid 417 through 420 removed outlier: 6.081A pdb=" N SER G 380 " --> pdb=" O ILE G 368 " (cutoff:3.500A) removed outlier: 5.425A pdb=" N ILE G 368 " --> pdb=" O SER G 380 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'G' and resid 568 through 571 Processing sheet with id= P, first strand: chain 'G' and resid 618 through 620 removed outlier: 6.684A pdb=" N GLY G 648 " --> pdb=" O LEU G 619 " (cutoff:3.500A) removed outlier: 7.784A pdb=" N ILE G 649 " --> pdb=" O GLN G 677 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N LEU G 679 " --> pdb=" O ILE G 649 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N LEU G 651 " --> pdb=" O LEU G 679 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N ILE G 681 " --> pdb=" O LEU G 651 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N TYR G 702 " --> pdb=" O LEU G 679 " (cutoff:3.500A) removed outlier: 8.389A pdb=" N ILE G 681 " --> pdb=" O TYR G 702 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N GLY G 704 " --> pdb=" O ILE G 681 " (cutoff:3.500A) removed outlier: 8.088A pdb=" N LEU G 705 " --> pdb=" O PRO G 727 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N ALA G 729 " --> pdb=" O LEU G 705 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'G' and resid 843 through 847 Processing sheet with id= R, first strand: chain 'G' and resid 1126 through 1128 removed outlier: 6.406A pdb=" N GLU G1199 " --> pdb=" O PRO G1207 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N THR G1208 " --> pdb=" O ILE G1224 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N ILE G1218 " --> pdb=" O LEU G1214 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'G' and resid 1158 through 1161 Processing sheet with id= T, first strand: chain 'G' and resid 1284 through 1286 removed outlier: 6.748A pdb=" N ASP G1391 " --> pdb=" O GLU G1379 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N VAL G1381 " --> pdb=" O ILE G1389 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N ILE G1389 " --> pdb=" O VAL G1381 " (cutoff:3.500A) removed outlier: 4.905A pdb=" N ASN G1383 " --> pdb=" O GLY G1387 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N GLY G1387 " --> pdb=" O ASN G1383 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N ARG G1398 " --> pdb=" O PRO G1402 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N PHE G1411 " --> pdb=" O HIS G1352 " (cutoff:3.500A) removed outlier: 5.541A pdb=" N HIS G1352 " --> pdb=" O PHE G1411 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N ARG G1413 " --> pdb=" O LEU G1350 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N LEU G1350 " --> pdb=" O ARG G1413 " (cutoff:3.500A) removed outlier: 5.613A pdb=" N LEU G1353 " --> pdb=" O PHE G1612 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N ARG G1606 " --> pdb=" O MET G1359 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N GLU G1656 " --> pdb=" O ARG G1606 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N TYR G1608 " --> pdb=" O GLU G1654 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N GLU G1654 " --> pdb=" O TYR G1608 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N CYS G1610 " --> pdb=" O THR G1652 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N THR G1652 " --> pdb=" O CYS G1610 " (cutoff:3.500A) removed outlier: 5.206A pdb=" N PHE G1612 " --> pdb=" O VAL G1650 " (cutoff:3.500A) removed outlier: 7.845A pdb=" N VAL G1650 " --> pdb=" O PHE G1612 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N THR G1642 " --> pdb=" O VAL G1650 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N THR G1652 " --> pdb=" O PHE G1640 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N PHE G1640 " --> pdb=" O THR G1652 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N GLU G1654 " --> pdb=" O ILE G1638 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N ILE G1638 " --> pdb=" O GLU G1654 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N GLU G1656 " --> pdb=" O LYS G1636 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N LYS G1636 " --> pdb=" O GLU G1656 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N LYS G1639 " --> pdb=" O HIS G1628 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N HIS G1628 " --> pdb=" O LYS G1639 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N GLU G1641 " --> pdb=" O ILE G1626 " (cutoff:3.500A) removed outlier: 5.829A pdb=" N ILE G1626 " --> pdb=" O GLU G1641 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N ARG G1643 " --> pdb=" O THR G1624 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N THR G1624 " --> pdb=" O ARG G1643 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'G' and resid 1424 through 1427 removed outlier: 3.569A pdb=" N GLY G1487 " --> pdb=" O VAL G1504 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N VAL G1491 " --> pdb=" O GLU G1500 " (cutoff:3.500A) removed outlier: 5.667A pdb=" N GLU G1500 " --> pdb=" O VAL G1491 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'G' and resid 1431 through 1435 removed outlier: 3.934A pdb=" N LYS G1462 " --> pdb=" O ILE G1435 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'G' and resid 1663 through 1666 removed outlier: 6.988A pdb=" N THR G1803 " --> pdb=" O PHE G1664 " (cutoff:3.500A) removed outlier: 8.475A pdb=" N PHE G1666 " --> pdb=" O THR G1803 " (cutoff:3.500A) removed outlier: 7.104A 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: 6.371A pdb=" N ALA G1901 " --> pdb=" O ILE G1888 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N ILE G1888 " --> pdb=" O ALA G1901 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N ASP G1903 " --> pdb=" O VAL G1886 " (cutoff:3.500A) removed outlier: 5.886A pdb=" N VAL G1886 " --> pdb=" O ASP G1903 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'G' and resid 1537 through 1545 removed outlier: 6.913A pdb=" N ILE G1626 " --> pdb=" O ILE G1539 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N VAL G1541 " --> pdb=" O THR G1624 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N THR G1624 " --> pdb=" O VAL G1541 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N ASP G1543 " --> pdb=" O LEU G1622 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N LEU G1622 " --> pdb=" O ASP G1543 " (cutoff:3.500A) 1197 hydrogen bonds defined for protein. 3270 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 15.29 Time building geometry restraints manager: 12.06 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: 5070 1.31 - 1.44: 7640 1.44 - 1.58: 17324 1.58 - 1.72: 1 1.72 - 1.86: 187 Bond restraints: 30222 Sorted by residual: bond pdb=" C PRO A1627 " pdb=" O PRO A1627 " ideal model delta sigma weight residual 1.234 1.172 0.062 1.14e-02 7.69e+03 2.96e+01 bond pdb=" C PRO A1362 " pdb=" O PRO A1362 " ideal model delta sigma weight residual 1.237 1.171 0.067 1.26e-02 6.30e+03 2.80e+01 bond pdb=" C PRO A 736 " pdb=" O PRO A 736 " ideal model delta sigma weight residual 1.234 1.173 0.060 1.14e-02 7.69e+03 2.79e+01 bond pdb=" C PRO A1190 " pdb=" O PRO A1190 " ideal model delta sigma weight residual 1.233 1.173 0.060 1.16e-02 7.43e+03 2.63e+01 bond pdb=" C GLY A1248 " pdb=" O GLY A1248 " ideal model delta sigma weight residual 1.233 1.185 0.048 9.80e-03 1.04e+04 2.44e+01 ... (remaining 30217 not shown) Histogram of bond angle deviations from ideal: 91.11 - 100.04: 32 100.04 - 108.97: 3210 108.97 - 117.90: 20689 117.90 - 126.83: 16734 126.83 - 135.76: 271 Bond angle restraints: 40936 Sorted by residual: angle pdb=" C SER A1417 " pdb=" N VAL A1418 " pdb=" CA VAL A1418 " ideal model delta sigma weight residual 120.24 124.76 -4.52 6.30e-01 2.52e+00 5.15e+01 angle pdb=" N GLY B 240 " pdb=" CA GLY B 240 " pdb=" C GLY B 240 " ideal model delta sigma weight residual 114.69 106.29 8.40 1.19e+00 7.06e-01 4.99e+01 angle pdb=" C ILE A1189 " pdb=" CA ILE A1189 " pdb=" CB ILE A1189 " ideal model delta sigma weight residual 110.88 117.14 -6.26 9.80e-01 1.04e+00 4.08e+01 angle pdb=" C TRP G 661 " pdb=" N GLY G 662 " pdb=" CA GLY G 662 " ideal model delta sigma weight residual 119.94 126.78 -6.84 1.09e+00 8.42e-01 3.94e+01 angle pdb=" CB GLU G1309 " pdb=" CG GLU G1309 " pdb=" CD GLU G1309 " ideal model delta sigma weight residual 112.60 123.20 -10.60 1.70e+00 3.46e-01 3.89e+01 ... (remaining 40931 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.58: 16897 20.58 - 41.17: 1118 41.17 - 61.75: 160 61.75 - 82.34: 55 82.34 - 102.92: 16 Dihedral angle restraints: 18246 sinusoidal: 7337 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 17.54 75.46 1 1.00e+01 1.00e-02 7.19e+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 75.26 178.18 -102.92 1 2.00e+01 2.50e-03 2.94e+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 180.00 154.46 25.54 0 5.00e+00 4.00e-02 2.61e+01 ... (remaining 18243 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 2171 0.061 - 0.122: 1695 0.122 - 0.183: 611 0.183 - 0.244: 109 0.244 - 0.306: 16 Chirality restraints: 4602 Sorted by residual: chirality pdb=" CA SER B 235 " pdb=" N SER B 235 " pdb=" C SER B 235 " pdb=" CB SER B 235 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.34e+00 chirality pdb=" CA ILE G1751 " pdb=" N ILE G1751 " pdb=" C ILE G1751 " pdb=" CB ILE G1751 " both_signs ideal model delta sigma weight residual False 2.43 2.73 -0.29 2.00e-01 2.50e+01 2.14e+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 2.72 -0.29 2.00e-01 2.50e+01 2.13e+00 ... (remaining 4599 not shown) Planarity restraints: 5284 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' FMN G2101 " 0.013 2.00e-02 2.50e+03 3.61e-02 6.19e+01 pdb=" C10 FMN G2101 " 0.027 2.00e-02 2.50e+03 pdb=" C2 FMN G2101 " -0.048 2.00e-02 2.50e+03 pdb=" C4 FMN G2101 " -0.005 2.00e-02 2.50e+03 pdb=" C4A FMN G2101 " 0.045 2.00e-02 2.50e+03 pdb=" C5A FMN G2101 " 0.063 2.00e-02 2.50e+03 pdb=" C6 FMN G2101 " 0.029 2.00e-02 2.50e+03 pdb=" C7 FMN G2101 " -0.011 2.00e-02 2.50e+03 pdb=" C7M FMN G2101 " -0.065 2.00e-02 2.50e+03 pdb=" C8 FMN G2101 " -0.033 2.00e-02 2.50e+03 pdb=" C8M FMN G2101 " -0.031 2.00e-02 2.50e+03 pdb=" C9 FMN G2101 " -0.006 2.00e-02 2.50e+03 pdb=" C9A FMN G2101 " 0.041 2.00e-02 2.50e+03 pdb=" N1 FMN G2101 " -0.015 2.00e-02 2.50e+03 pdb=" N10 FMN G2101 " 0.037 2.00e-02 2.50e+03 pdb=" N3 FMN G2101 " -0.031 2.00e-02 2.50e+03 pdb=" N5 FMN G2101 " 0.049 2.00e-02 2.50e+03 pdb=" O2 FMN G2101 " -0.031 2.00e-02 2.50e+03 pdb=" O4 FMN G2101 " -0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 722 " 0.074 2.00e-02 2.50e+03 3.82e-02 2.92e+01 pdb=" CG TYR A 722 " -0.054 2.00e-02 2.50e+03 pdb=" CD1 TYR A 722 " -0.030 2.00e-02 2.50e+03 pdb=" CD2 TYR A 722 " -0.018 2.00e-02 2.50e+03 pdb=" CE1 TYR A 722 " -0.010 2.00e-02 2.50e+03 pdb=" CE2 TYR A 722 " -0.018 2.00e-02 2.50e+03 pdb=" CZ TYR A 722 " 0.024 2.00e-02 2.50e+03 pdb=" OH TYR A 722 " 0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A1529 " 0.068 2.00e-02 2.50e+03 3.52e-02 2.48e+01 pdb=" CG TYR A1529 " -0.047 2.00e-02 2.50e+03 pdb=" CD1 TYR A1529 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 TYR A1529 " -0.031 2.00e-02 2.50e+03 pdb=" CE1 TYR A1529 " -0.022 2.00e-02 2.50e+03 pdb=" CE2 TYR A1529 " -0.006 2.00e-02 2.50e+03 pdb=" CZ TYR A1529 " 0.016 2.00e-02 2.50e+03 pdb=" OH TYR A1529 " 0.035 2.00e-02 2.50e+03 ... (remaining 5281 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 721 2.69 - 3.25: 29147 3.25 - 3.80: 46642 3.80 - 4.35: 66113 4.35 - 4.90: 106485 Nonbonded interactions: 249108 Sorted by model distance: nonbonded pdb=" OD1 ASP G 287 " pdb=" OG SER G 291 " model vdw 2.142 2.440 nonbonded pdb=" O LEU B 221 " pdb=" OG SER B 225 " model vdw 2.213 2.440 nonbonded pdb=" OE1 GLU G1811 " pdb=" OH TYR G2010 " model vdw 2.223 2.440 nonbonded pdb=" OH TYR G 615 " pdb=" OD1 ASP G1075 " model vdw 2.240 2.440 nonbonded pdb=" O LYS G 355 " pdb=" OG SER G 358 " model vdw 2.248 2.440 ... (remaining 249103 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: 0.020 Extract box with map and model: 4.880 Check model and map are aligned: 0.470 Set scattering table: 0.260 Process input model: 82.260 Find NCS groups from input model: 0.780 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: 0.000 Load rotamer database and sin/cos tables:13.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 102.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8578 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 : 0.013 0.086 30222 Z= 0.889 Angle : 1.820 10.760 40936 Z= 1.339 Chirality : 0.088 0.306 4602 Planarity : 0.007 0.038 5284 Dihedral : 14.456 102.920 11217 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.27 % Allowed : 4.52 % Favored : 95.21 % Rotamer: Outliers : 0.25 % Allowed : 3.21 % Favored : 96.55 % 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: -2.78 (0.12), residues: 3760 helix: -2.33 (0.10), residues: 1664 sheet: -1.39 (0.20), residues: 500 loop : -1.19 (0.14), residues: 1596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.009 TRP G1449 HIS 0.015 0.004 HIS G1564 PHE 0.054 0.007 PHE G1300 TYR 0.074 0.008 TYR A 722 ARG 0.017 0.002 ARG A 396 *********************** 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 395 residues out of total 3245 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 387 time to evaluate : 3.431 Fit side-chains revert: symmetry clash REVERT: A 16 GLU cc_start: 0.8926 (tp30) cc_final: 0.8396 (tp30) REVERT: A 340 ARG cc_start: 0.6764 (mmt180) cc_final: 0.6233 (mpt180) REVERT: A 364 GLU cc_start: 0.5576 (tt0) cc_final: 0.5361 (tt0) REVERT: A 529 MET cc_start: 0.8806 (mmp) cc_final: 0.8236 (mmp) REVERT: A 537 LYS cc_start: 0.7557 (tptt) cc_final: 0.7336 (mttm) REVERT: A 612 GLU cc_start: 0.8289 (tp30) cc_final: 0.7978 (tp30) REVERT: A 944 ARG cc_start: 0.8605 (ttm110) cc_final: 0.8396 (ttp80) REVERT: A 1162 GLU cc_start: 0.7960 (mp0) cc_final: 0.7345 (mp0) REVERT: A 1180 ARG cc_start: 0.7269 (mpt180) cc_final: 0.6799 (mpt90) REVERT: A 1260 MET cc_start: 0.9154 (ptp) cc_final: 0.8913 (ptm) REVERT: A 1496 GLU cc_start: 0.6696 (tt0) cc_final: 0.6462 (tt0) REVERT: B 168 MET cc_start: 0.6459 (mmm) cc_final: 0.5996 (tpp) REVERT: B 179 LYS cc_start: 0.8313 (mppt) cc_final: 0.7740 (mptt) REVERT: B 183 GLN cc_start: 0.8311 (tp-100) cc_final: 0.7908 (tp40) REVERT: B 192 LYS cc_start: 0.8280 (pptt) cc_final: 0.8077 (ptmt) REVERT: B 237 MET cc_start: 0.7951 (OUTLIER) cc_final: 0.7454 (tpp) REVERT: B 261 GLN cc_start: 0.7962 (mt0) cc_final: 0.7541 (mt0) REVERT: B 271 ASN cc_start: 0.8370 (m110) cc_final: 0.8042 (m-40) REVERT: G 64 PHE cc_start: 0.8347 (t80) cc_final: 0.7985 (t80) REVERT: G 81 ASP cc_start: 0.7600 (m-30) cc_final: 0.7241 (m-30) REVERT: G 132 MET cc_start: 0.8609 (mmp) cc_final: 0.8216 (mpm) REVERT: G 217 GLU cc_start: 0.8342 (tp30) cc_final: 0.7861 (tp30) REVERT: G 221 ASN cc_start: 0.8470 (m110) cc_final: 0.7949 (m110) REVERT: G 325 GLU cc_start: 0.8530 (tp30) cc_final: 0.8076 (tp30) REVERT: G 329 GLU cc_start: 0.8147 (mt-10) cc_final: 0.7861 (mt-10) REVERT: G 387 TYR cc_start: 0.8318 (t80) cc_final: 0.7928 (t80) REVERT: G 447 ASN cc_start: 0.8350 (t0) cc_final: 0.7577 (p0) REVERT: G 553 ASN cc_start: 0.8168 (m110) cc_final: 0.7948 (m-40) REVERT: G 881 VAL cc_start: 0.8911 (t) cc_final: 0.8704 (t) REVERT: G 1309 GLU cc_start: 0.7011 (mm-30) cc_final: 0.6780 (mm-30) REVERT: G 1401 LYS cc_start: 0.8144 (pptt) cc_final: 0.7816 (pmtt) REVERT: G 1500 GLU cc_start: 0.8242 (tm-30) cc_final: 0.7965 (tm-30) REVERT: G 1673 GLU cc_start: 0.8094 (pm20) cc_final: 0.7864 (pm20) REVERT: G 1784 MET cc_start: 0.8730 (tmm) cc_final: 0.8292 (tmt) REVERT: G 1962 ARG cc_start: 0.6707 (tmt-80) cc_final: 0.6437 (tmt-80) REVERT: G 2015 THR cc_start: 0.8505 (m) cc_final: 0.8261 (p) outliers start: 8 outliers final: 4 residues processed: 393 average time/residue: 1.6892 time to fit residues: 757.5742 Evaluate side-chains 272 residues out of total 3245 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 267 time to evaluate : 3.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1022 THR Chi-restraints excluded: chain A residue 1096 SER Chi-restraints excluded: chain A residue 1327 CYS Chi-restraints excluded: chain B residue 237 MET Chi-restraints excluded: chain G residue 1381 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 317 optimal weight: 4.9990 chunk 284 optimal weight: 7.9990 chunk 158 optimal weight: 7.9990 chunk 97 optimal weight: 7.9990 chunk 192 optimal weight: 8.9990 chunk 152 optimal weight: 0.5980 chunk 294 optimal weight: 2.9990 chunk 114 optimal weight: 6.9990 chunk 179 optimal weight: 0.0070 chunk 219 optimal weight: 0.7980 chunk 341 optimal weight: 6.9990 overall best weight: 1.8802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 379 ASN A 524 GLN A 904 ASN A 989 GLN A1272 ASN A1380 GLN A1494 HIS A1495 ASN A1563 HIS A1780 ASN A1877 GLN G 102 HIS G 221 ASN G 346 GLN G 354 ASN G 440 ASN G 715 GLN G 718 ASN G 747 HIS G 908 ASN G 993 GLN G1088 GLN G1178 GLN G1217 ASN G1241 ASN G1355 ASN G1399 ASN G1595 ASN G1851 ASN G1890 ASN G1897 GLN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.1387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 30222 Z= 0.180 Angle : 0.538 10.724 40936 Z= 0.284 Chirality : 0.042 0.177 4602 Planarity : 0.004 0.032 5284 Dihedral : 5.149 102.290 4034 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.05 % Allowed : 1.73 % Favored : 98.22 % Rotamer: Outliers : 1.45 % Allowed : 8.82 % Favored : 89.73 % 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: -0.20 (0.13), residues: 3760 helix: 0.40 (0.12), residues: 1683 sheet: -0.81 (0.20), residues: 521 loop : -0.29 (0.16), residues: 1556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP G 661 HIS 0.008 0.001 HIS A1689 PHE 0.025 0.001 PHE A 35 TYR 0.018 0.002 TYR A 417 ARG 0.005 0.000 ARG A 59 *********************** 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 329 residues out of total 3245 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 282 time to evaluate : 3.486 Fit side-chains revert: symmetry clash REVERT: A 16 GLU cc_start: 0.8928 (tp30) cc_final: 0.8521 (tp30) REVERT: A 340 ARG cc_start: 0.6879 (mmt180) cc_final: 0.6423 (mmt180) REVERT: A 612 GLU cc_start: 0.8184 (tp30) cc_final: 0.7971 (tp30) REVERT: A 1044 GLU cc_start: 0.8543 (OUTLIER) cc_final: 0.8292 (pm20) REVERT: A 1162 GLU cc_start: 0.7885 (mp0) cc_final: 0.7571 (mp0) REVERT: A 1180 ARG cc_start: 0.7125 (mpt180) cc_final: 0.6365 (mpt90) REVERT: A 1260 MET cc_start: 0.9127 (ptp) cc_final: 0.8841 (ptm) REVERT: A 1491 ARG cc_start: 0.8566 (OUTLIER) cc_final: 0.8185 (tmt170) REVERT: A 1496 GLU cc_start: 0.6352 (tt0) cc_final: 0.5760 (tt0) REVERT: B 168 MET cc_start: 0.6443 (mmm) cc_final: 0.5819 (tpp) REVERT: B 193 GLU cc_start: 0.7942 (tp30) cc_final: 0.7552 (tm-30) REVERT: B 202 GLU cc_start: 0.7423 (pm20) cc_final: 0.6713 (pm20) REVERT: B 224 GLN cc_start: 0.8146 (tp40) cc_final: 0.7901 (mm-40) REVERT: B 261 GLN cc_start: 0.7908 (mt0) cc_final: 0.7520 (mt0) REVERT: B 271 ASN cc_start: 0.8069 (m110) cc_final: 0.7678 (m110) REVERT: G 64 PHE cc_start: 0.8305 (t80) cc_final: 0.7965 (t80) REVERT: G 81 ASP cc_start: 0.7610 (m-30) cc_final: 0.7280 (m-30) REVERT: G 97 GLU cc_start: 0.7918 (OUTLIER) cc_final: 0.7682 (pt0) REVERT: G 111 GLU cc_start: 0.8037 (mt-10) cc_final: 0.7822 (mt-10) REVERT: G 132 MET cc_start: 0.8464 (mmp) cc_final: 0.8081 (mpm) REVERT: G 167 ASP cc_start: 0.8346 (OUTLIER) cc_final: 0.7984 (p0) REVERT: G 217 GLU cc_start: 0.8303 (tp30) cc_final: 0.8082 (tp30) REVERT: G 229 ASP cc_start: 0.8558 (t70) cc_final: 0.8353 (t70) REVERT: G 325 GLU cc_start: 0.8545 (tp30) cc_final: 0.8050 (tp30) REVERT: G 387 TYR cc_start: 0.8211 (t80) cc_final: 0.7820 (t80) REVERT: G 447 ASN cc_start: 0.8459 (t0) cc_final: 0.7742 (p0) REVERT: G 497 LYS cc_start: 0.8105 (mmtm) cc_final: 0.7863 (mmmt) REVERT: G 553 ASN cc_start: 0.8016 (m110) cc_final: 0.7802 (m-40) REVERT: G 764 MET cc_start: 0.9010 (mtm) cc_final: 0.8691 (mtm) REVERT: G 910 GLN cc_start: 0.8621 (tt0) cc_final: 0.8194 (mp10) REVERT: G 1401 LYS cc_start: 0.8043 (pptt) cc_final: 0.7771 (pptt) REVERT: G 1673 GLU cc_start: 0.8040 (pm20) cc_final: 0.7761 (pm20) REVERT: G 1956 ARG cc_start: 0.6340 (mmp80) cc_final: 0.5889 (mmp80) outliers start: 47 outliers final: 14 residues processed: 313 average time/residue: 1.5985 time to fit residues: 579.4677 Evaluate side-chains 268 residues out of total 3245 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 250 time to evaluate : 3.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain A residue 674 LYS Chi-restraints excluded: chain A residue 946 GLU Chi-restraints excluded: chain A residue 1044 GLU Chi-restraints excluded: chain A residue 1096 SER Chi-restraints excluded: chain A residue 1179 LEU Chi-restraints excluded: chain A residue 1203 ASP Chi-restraints excluded: chain A residue 1284 SER Chi-restraints excluded: chain A residue 1333 ASP Chi-restraints excluded: chain A residue 1395 LYS Chi-restraints excluded: chain A residue 1491 ARG Chi-restraints excluded: chain G residue 97 GLU Chi-restraints excluded: chain G residue 167 ASP Chi-restraints excluded: chain G residue 328 LEU Chi-restraints excluded: chain G residue 827 VAL Chi-restraints excluded: chain G residue 850 MET Chi-restraints excluded: chain G residue 1381 VAL Chi-restraints excluded: chain G residue 1904 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: 4.9990 chunk 284 optimal weight: 20.0000 chunk 232 optimal weight: 3.9990 chunk 94 optimal weight: 1.9990 chunk 342 optimal weight: 3.9990 chunk 369 optimal weight: 20.0000 chunk 304 optimal weight: 8.9990 chunk 339 optimal weight: 10.0000 chunk 116 optimal weight: 0.9990 chunk 274 optimal weight: 9.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 475 GLN A 758 ASN A 904 ASN A1063 HIS A1207 GLN A1494 HIS A1549 ASN A1806 GLN G 93 ASN G 181 HIS G 221 ASN G1341 ASN G1399 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 moved from start: 0.1575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 30222 Z= 0.246 Angle : 0.527 9.712 40936 Z= 0.275 Chirality : 0.043 0.178 4602 Planarity : 0.004 0.035 5284 Dihedral : 4.849 100.663 4029 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.50 % Favored : 97.47 % Rotamer: Outliers : 1.82 % Allowed : 9.96 % Favored : 88.22 % 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: 0.50 (0.14), residues: 3760 helix: 1.14 (0.13), residues: 1670 sheet: -0.54 (0.21), residues: 515 loop : -0.10 (0.16), residues: 1575 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP G 865 HIS 0.008 0.001 HIS A1689 PHE 0.023 0.002 PHE A 35 TYR 0.018 0.002 TYR A 722 ARG 0.006 0.000 ARG A 709 *********************** 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 320 residues out of total 3245 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 261 time to evaluate : 3.587 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.7757 (tpt) cc_final: 0.7194 (tpt) REVERT: A 16 GLU cc_start: 0.8905 (tp30) cc_final: 0.8471 (tp30) REVERT: A 340 ARG cc_start: 0.6916 (mmt180) cc_final: 0.6487 (mmt180) REVERT: A 529 MET cc_start: 0.8861 (mmp) cc_final: 0.8413 (mmp) REVERT: A 944 ARG cc_start: 0.8656 (OUTLIER) cc_final: 0.8423 (ttp80) REVERT: A 1159 GLU cc_start: 0.8065 (mp0) cc_final: 0.7667 (pm20) REVERT: A 1162 GLU cc_start: 0.7828 (mp0) cc_final: 0.7504 (mp0) REVERT: A 1180 ARG cc_start: 0.7176 (mpt180) cc_final: 0.6404 (mpt90) REVERT: A 1260 MET cc_start: 0.9189 (ptp) cc_final: 0.8928 (ptm) REVERT: A 1498 GLU cc_start: 0.8474 (OUTLIER) cc_final: 0.8137 (tm-30) REVERT: A 1712 GLU cc_start: 0.8449 (mt-10) cc_final: 0.8182 (mt-10) REVERT: A 1806 GLN cc_start: 0.7456 (OUTLIER) cc_final: 0.7137 (tt0) REVERT: B 168 MET cc_start: 0.6436 (mmm) cc_final: 0.5937 (tpp) REVERT: B 193 GLU cc_start: 0.7870 (tp30) cc_final: 0.7554 (tm-30) REVERT: B 202 GLU cc_start: 0.7298 (pm20) cc_final: 0.6569 (pm20) REVERT: B 261 GLN cc_start: 0.7933 (mt0) cc_final: 0.7555 (mt0) REVERT: G 81 ASP cc_start: 0.7630 (m-30) cc_final: 0.7304 (m-30) REVERT: G 97 GLU cc_start: 0.7873 (OUTLIER) cc_final: 0.7590 (pt0) REVERT: G 111 GLU cc_start: 0.8062 (mt-10) cc_final: 0.7860 (mt-10) REVERT: G 132 MET cc_start: 0.8375 (mmp) cc_final: 0.8031 (mpm) REVERT: G 167 ASP cc_start: 0.8275 (OUTLIER) cc_final: 0.7804 (p0) REVERT: G 325 GLU cc_start: 0.8556 (tp30) cc_final: 0.8095 (tp30) REVERT: G 387 TYR cc_start: 0.8265 (t80) cc_final: 0.7873 (t80) REVERT: G 447 ASN cc_start: 0.8475 (t0) cc_final: 0.7737 (p0) REVERT: G 497 LYS cc_start: 0.8099 (mmtm) cc_final: 0.7858 (mmmt) REVERT: G 764 MET cc_start: 0.8986 (mtm) cc_final: 0.8694 (mtm) REVERT: G 1467 GLU cc_start: 0.8673 (OUTLIER) cc_final: 0.8449 (mp0) REVERT: G 1784 MET cc_start: 0.8977 (OUTLIER) cc_final: 0.8703 (tmt) REVERT: G 1838 MET cc_start: 0.8662 (OUTLIER) cc_final: 0.8458 (mmp) outliers start: 59 outliers final: 22 residues processed: 299 average time/residue: 1.6623 time to fit residues: 577.0454 Evaluate side-chains 274 residues out of total 3245 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 244 time to evaluate : 3.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain A residue 487 ASP Chi-restraints excluded: chain A residue 658 LEU Chi-restraints excluded: chain A residue 674 LYS Chi-restraints excluded: chain A residue 944 ARG Chi-restraints excluded: chain A residue 946 GLU Chi-restraints excluded: chain A residue 1179 LEU Chi-restraints excluded: chain A residue 1203 ASP Chi-restraints excluded: chain A residue 1284 SER Chi-restraints excluded: chain A residue 1333 ASP Chi-restraints excluded: chain A residue 1395 LYS Chi-restraints excluded: chain A residue 1498 GLU Chi-restraints excluded: chain A residue 1677 VAL Chi-restraints excluded: chain A residue 1806 GLN Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 174 ASP Chi-restraints excluded: chain G residue 97 GLU Chi-restraints excluded: chain G residue 104 LEU Chi-restraints excluded: chain G residue 167 ASP Chi-restraints excluded: chain G residue 328 LEU Chi-restraints excluded: chain G residue 334 VAL Chi-restraints excluded: chain G residue 510 SER Chi-restraints excluded: chain G residue 658 MET Chi-restraints excluded: chain G residue 827 VAL Chi-restraints excluded: chain G residue 880 LEU Chi-restraints excluded: chain G residue 1381 VAL Chi-restraints excluded: chain G residue 1467 GLU Chi-restraints excluded: chain G residue 1753 LYS Chi-restraints excluded: chain G residue 1784 MET Chi-restraints excluded: chain G residue 1838 MET 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: 5.9990 chunk 177 optimal weight: 5.9990 chunk 37 optimal weight: 0.9980 chunk 163 optimal weight: 7.9990 chunk 229 optimal weight: 7.9990 chunk 343 optimal weight: 9.9990 chunk 363 optimal weight: 20.0000 chunk 179 optimal weight: 9.9990 chunk 325 optimal weight: 10.0000 chunk 97 optimal weight: 7.9990 overall best weight: 5.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1494 HIS A1495 ASN ** A1806 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 430 HIS G 650 ASN G1367 GLN G1399 ASN G1421 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8541 moved from start: 0.1730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.084 30222 Z= 0.375 Angle : 0.575 10.814 40936 Z= 0.299 Chirality : 0.045 0.188 4602 Planarity : 0.004 0.038 5284 Dihedral : 5.015 102.979 4028 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.53 % Favored : 97.45 % Rotamer: Outliers : 2.44 % Allowed : 10.85 % Favored : 86.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.14), residues: 3760 helix: 1.09 (0.13), residues: 1675 sheet: -0.55 (0.21), residues: 512 loop : -0.07 (0.16), residues: 1573 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP G 865 HIS 0.009 0.001 HIS A1689 PHE 0.023 0.002 PHE A1376 TYR 0.021 0.002 TYR A 722 ARG 0.006 0.001 ARG A1489 *********************** 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 329 residues out of total 3245 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 250 time to evaluate : 3.587 Fit side-chains revert: symmetry clash REVERT: A 16 GLU cc_start: 0.8836 (tp30) cc_final: 0.8395 (tp30) REVERT: A 340 ARG cc_start: 0.6721 (mmt180) cc_final: 0.5888 (mpt180) REVERT: A 517 GLU cc_start: 0.7505 (OUTLIER) cc_final: 0.7160 (mm-30) REVERT: A 529 MET cc_start: 0.8854 (mmp) cc_final: 0.8529 (mmp) REVERT: A 881 ASN cc_start: 0.8396 (OUTLIER) cc_final: 0.8163 (p0) REVERT: A 944 ARG cc_start: 0.8671 (OUTLIER) cc_final: 0.8425 (ttp80) REVERT: A 1162 GLU cc_start: 0.7900 (mp0) cc_final: 0.7553 (mp0) REVERT: A 1180 ARG cc_start: 0.7169 (mpt180) cc_final: 0.6428 (mpt90) REVERT: A 1298 ILE cc_start: 0.9043 (OUTLIER) cc_final: 0.8636 (tp) REVERT: A 1498 GLU cc_start: 0.8471 (OUTLIER) cc_final: 0.8176 (tm-30) REVERT: B 168 MET cc_start: 0.6509 (mmm) cc_final: 0.5784 (tpp) REVERT: B 193 GLU cc_start: 0.7872 (tp30) cc_final: 0.7598 (tm-30) REVERT: B 202 GLU cc_start: 0.7422 (pm20) cc_final: 0.6644 (pm20) REVERT: B 224 GLN cc_start: 0.8410 (tp40) cc_final: 0.8193 (mm-40) REVERT: G 81 ASP cc_start: 0.7701 (m-30) cc_final: 0.7383 (m-30) REVERT: G 97 GLU cc_start: 0.7874 (OUTLIER) cc_final: 0.7562 (pt0) REVERT: G 114 THR cc_start: 0.6763 (m) cc_final: 0.6372 (t) REVERT: G 132 MET cc_start: 0.8338 (mmp) cc_final: 0.7983 (mpm) REVERT: G 167 ASP cc_start: 0.8307 (p0) cc_final: 0.7920 (p0) REVERT: G 387 TYR cc_start: 0.8358 (t80) cc_final: 0.7987 (t80) REVERT: G 696 GLU cc_start: 0.8353 (OUTLIER) cc_final: 0.8127 (mp0) REVERT: G 1467 GLU cc_start: 0.8668 (OUTLIER) cc_final: 0.8445 (mp0) REVERT: G 1784 MET cc_start: 0.9084 (OUTLIER) cc_final: 0.8816 (tmt) REVERT: G 1801 ASP cc_start: 0.7915 (OUTLIER) cc_final: 0.7603 (p0) outliers start: 79 outliers final: 35 residues processed: 306 average time/residue: 1.5115 time to fit residues: 539.9173 Evaluate side-chains 284 residues out of total 3245 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 239 time to evaluate : 3.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 487 ASP Chi-restraints excluded: chain A residue 517 GLU Chi-restraints excluded: chain A residue 674 LYS Chi-restraints excluded: chain A residue 757 LYS Chi-restraints excluded: chain A residue 881 ASN Chi-restraints excluded: chain A residue 944 ARG Chi-restraints excluded: chain A residue 946 GLU Chi-restraints excluded: chain A residue 1127 VAL Chi-restraints excluded: chain A residue 1179 LEU Chi-restraints excluded: chain A residue 1203 ASP Chi-restraints excluded: chain A residue 1284 SER Chi-restraints excluded: chain A residue 1298 ILE Chi-restraints excluded: chain A residue 1305 CYS Chi-restraints excluded: chain A residue 1333 ASP Chi-restraints excluded: chain A residue 1395 LYS Chi-restraints excluded: chain A residue 1498 GLU Chi-restraints excluded: chain A residue 1677 VAL Chi-restraints excluded: chain A residue 1776 ILE Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 174 ASP Chi-restraints excluded: chain G residue 22 VAL Chi-restraints excluded: chain G residue 97 GLU Chi-restraints excluded: chain G residue 281 VAL Chi-restraints excluded: chain G residue 328 LEU Chi-restraints excluded: chain G residue 334 VAL Chi-restraints excluded: chain G residue 510 SER Chi-restraints excluded: chain G residue 616 THR Chi-restraints excluded: chain G residue 630 MET Chi-restraints excluded: chain G residue 658 MET Chi-restraints excluded: chain G residue 696 GLU Chi-restraints excluded: chain G residue 827 VAL Chi-restraints excluded: chain G residue 850 MET Chi-restraints excluded: chain G residue 880 LEU Chi-restraints excluded: chain G residue 1348 LEU Chi-restraints excluded: chain G residue 1381 VAL Chi-restraints excluded: chain G residue 1467 GLU Chi-restraints excluded: chain G residue 1586 SER Chi-restraints excluded: chain G residue 1616 VAL Chi-restraints excluded: chain G residue 1753 LYS Chi-restraints excluded: chain G residue 1784 MET Chi-restraints excluded: chain G residue 1801 ASP Chi-restraints excluded: chain G residue 1904 LEU Chi-restraints excluded: chain G residue 1936 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 302 optimal weight: 5.9990 chunk 206 optimal weight: 0.9990 chunk 5 optimal weight: 5.9990 chunk 270 optimal weight: 9.9990 chunk 149 optimal weight: 20.0000 chunk 310 optimal weight: 10.0000 chunk 251 optimal weight: 4.9990 chunk 0 optimal weight: 20.0000 chunk 185 optimal weight: 0.4980 chunk 326 optimal weight: 6.9990 chunk 91 optimal weight: 3.9990 overall best weight: 3.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 904 ASN A1494 HIS A1806 GLN B 261 GLN G 418 ASN G1399 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.1812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 30222 Z= 0.253 Angle : 0.520 9.982 40936 Z= 0.270 Chirality : 0.043 0.160 4602 Planarity : 0.004 0.034 5284 Dihedral : 4.859 103.157 4028 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.61 % Favored : 97.37 % Rotamer: Outliers : 2.28 % Allowed : 11.81 % Favored : 85.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.65 (0.14), residues: 3760 helix: 1.25 (0.13), residues: 1677 sheet: -0.50 (0.22), residues: 502 loop : 0.01 (0.16), residues: 1581 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP G 661 HIS 0.007 0.001 HIS A1689 PHE 0.023 0.002 PHE A 35 TYR 0.016 0.002 TYR A 722 ARG 0.005 0.000 ARG A 709 *********************** 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 328 residues out of total 3245 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 254 time to evaluate : 3.750 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 16 GLU cc_start: 0.8837 (tp30) cc_final: 0.8393 (tp30) REVERT: A 340 ARG cc_start: 0.6717 (mmt180) cc_final: 0.5896 (mpt180) REVERT: A 517 GLU cc_start: 0.7503 (OUTLIER) cc_final: 0.7164 (mm-30) REVERT: A 529 MET cc_start: 0.8841 (mmp) cc_final: 0.8577 (mmp) REVERT: A 881 ASN cc_start: 0.8352 (OUTLIER) cc_final: 0.8133 (p0) REVERT: A 944 ARG cc_start: 0.8678 (OUTLIER) cc_final: 0.8439 (ttp80) REVERT: A 958 SER cc_start: 0.8223 (OUTLIER) cc_final: 0.7918 (m) REVERT: A 1159 GLU cc_start: 0.8038 (mp0) cc_final: 0.7667 (pm20) REVERT: A 1162 GLU cc_start: 0.7901 (mp0) cc_final: 0.7540 (mp0) REVERT: A 1180 ARG cc_start: 0.7261 (mpt180) cc_final: 0.6542 (mpt90) REVERT: A 1298 ILE cc_start: 0.8992 (OUTLIER) cc_final: 0.8595 (tp) REVERT: A 1491 ARG cc_start: 0.8490 (tpt90) cc_final: 0.8063 (tpp80) REVERT: A 1498 GLU cc_start: 0.8446 (OUTLIER) cc_final: 0.8133 (tm-30) REVERT: B 168 MET cc_start: 0.6518 (mmm) cc_final: 0.5988 (tpp) REVERT: B 193 GLU cc_start: 0.7879 (tp30) cc_final: 0.7510 (tm-30) REVERT: B 202 GLU cc_start: 0.7502 (pm20) cc_final: 0.6695 (pm20) REVERT: G 67 TYR cc_start: 0.8195 (t80) cc_final: 0.7714 (t80) REVERT: G 81 ASP cc_start: 0.7609 (m-30) cc_final: 0.7298 (m-30) REVERT: G 97 GLU cc_start: 0.7864 (OUTLIER) cc_final: 0.7544 (pt0) REVERT: G 114 THR cc_start: 0.6764 (m) cc_final: 0.6391 (t) REVERT: G 132 MET cc_start: 0.8317 (mmp) cc_final: 0.7911 (mpm) REVERT: G 167 ASP cc_start: 0.8283 (p0) cc_final: 0.7798 (p0) REVERT: G 387 TYR cc_start: 0.8357 (t80) cc_final: 0.7911 (t80) REVERT: G 831 LYS cc_start: 0.8734 (OUTLIER) cc_final: 0.8519 (mtmm) REVERT: G 1650 VAL cc_start: 0.9230 (OUTLIER) cc_final: 0.9023 (m) REVERT: G 1784 MET cc_start: 0.9058 (OUTLIER) cc_final: 0.8785 (tmt) REVERT: G 1838 MET cc_start: 0.8728 (OUTLIER) cc_final: 0.8310 (mtp) REVERT: G 1849 ARG cc_start: 0.6103 (ttp80) cc_final: 0.5817 (ptm160) REVERT: G 2045 TRP cc_start: 0.7891 (t-100) cc_final: 0.7006 (t-100) outliers start: 74 outliers final: 37 residues processed: 308 average time/residue: 1.5854 time to fit residues: 571.6165 Evaluate side-chains 294 residues out of total 3245 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 246 time to evaluate : 3.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 487 ASP Chi-restraints excluded: chain A residue 517 GLU Chi-restraints excluded: chain A residue 674 LYS Chi-restraints excluded: chain A residue 881 ASN Chi-restraints excluded: chain A residue 944 ARG Chi-restraints excluded: chain A residue 946 GLU Chi-restraints excluded: chain A residue 958 SER Chi-restraints excluded: chain A residue 1022 THR Chi-restraints excluded: chain A residue 1127 VAL Chi-restraints excluded: chain A residue 1173 LEU Chi-restraints excluded: chain A residue 1179 LEU Chi-restraints excluded: chain A residue 1203 ASP Chi-restraints excluded: chain A residue 1284 SER Chi-restraints excluded: chain A residue 1298 ILE Chi-restraints excluded: chain A residue 1305 CYS Chi-restraints excluded: chain A residue 1333 ASP Chi-restraints excluded: chain A residue 1395 LYS Chi-restraints excluded: chain A residue 1498 GLU Chi-restraints excluded: chain A residue 1677 VAL Chi-restraints excluded: chain A residue 1776 ILE Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 174 ASP Chi-restraints excluded: chain G residue 22 VAL Chi-restraints excluded: chain G residue 97 GLU Chi-restraints excluded: chain G residue 104 LEU Chi-restraints excluded: chain G residue 281 VAL Chi-restraints excluded: chain G residue 328 LEU Chi-restraints excluded: chain G residue 334 VAL Chi-restraints excluded: chain G residue 418 ASN Chi-restraints excluded: chain G residue 447 ASN Chi-restraints excluded: chain G residue 510 SER Chi-restraints excluded: chain G residue 553 ASN Chi-restraints excluded: chain G residue 630 MET Chi-restraints excluded: chain G residue 658 MET Chi-restraints excluded: chain G residue 827 VAL Chi-restraints excluded: chain G residue 831 LYS Chi-restraints excluded: chain G residue 880 LEU Chi-restraints excluded: chain G residue 1348 LEU Chi-restraints excluded: chain G residue 1381 VAL Chi-restraints excluded: chain G residue 1382 VAL Chi-restraints excluded: chain G residue 1616 VAL Chi-restraints excluded: chain G residue 1650 VAL Chi-restraints excluded: chain G residue 1753 LYS Chi-restraints excluded: chain G residue 1784 MET Chi-restraints excluded: chain G residue 1838 MET Chi-restraints excluded: chain G residue 1904 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 122 optimal weight: 3.9990 chunk 327 optimal weight: 9.9990 chunk 71 optimal weight: 1.9990 chunk 213 optimal weight: 20.0000 chunk 89 optimal weight: 0.0970 chunk 363 optimal weight: 20.0000 chunk 301 optimal weight: 2.9990 chunk 168 optimal weight: 3.9990 chunk 30 optimal weight: 8.9990 chunk 120 optimal weight: 0.9980 chunk 190 optimal weight: 9.9990 overall best weight: 2.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 904 ASN A1148 HIS A1494 HIS A1783 ASN A1806 GLN G 418 ASN G 715 GLN G 752 GLN G1399 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.1906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 30222 Z= 0.182 Angle : 0.495 9.208 40936 Z= 0.256 Chirality : 0.042 0.155 4602 Planarity : 0.003 0.038 5284 Dihedral : 4.693 101.147 4028 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.53 % Favored : 97.45 % Rotamer: Outliers : 2.00 % Allowed : 12.48 % 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: 0.76 (0.14), residues: 3760 helix: 1.32 (0.13), residues: 1683 sheet: -0.37 (0.22), residues: 508 loop : 0.05 (0.16), residues: 1569 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP G 661 HIS 0.006 0.001 HIS A1689 PHE 0.024 0.001 PHE A 35 TYR 0.017 0.001 TYR B 294 ARG 0.008 0.000 ARG A 709 *********************** 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 323 residues out of total 3245 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 258 time to evaluate : 3.569 Fit side-chains revert: symmetry clash REVERT: A 16 GLU cc_start: 0.8863 (tp30) cc_final: 0.8402 (tp30) REVERT: A 340 ARG cc_start: 0.6697 (mmt180) cc_final: 0.6088 (mpt180) REVERT: A 517 GLU cc_start: 0.7506 (OUTLIER) cc_final: 0.7179 (mm-30) REVERT: A 529 MET cc_start: 0.8853 (mmp) cc_final: 0.8548 (mmp) REVERT: A 958 SER cc_start: 0.8222 (OUTLIER) cc_final: 0.7922 (m) REVERT: A 1159 GLU cc_start: 0.8076 (mp0) cc_final: 0.7749 (pm20) REVERT: A 1162 GLU cc_start: 0.7873 (mp0) cc_final: 0.7510 (mp0) REVERT: A 1180 ARG cc_start: 0.7291 (mpt180) cc_final: 0.6557 (mpt90) REVERT: A 1498 GLU cc_start: 0.8436 (OUTLIER) cc_final: 0.8112 (tm-30) REVERT: B 168 MET cc_start: 0.6455 (mmm) cc_final: 0.5875 (tpp) REVERT: B 192 LYS cc_start: 0.8465 (OUTLIER) cc_final: 0.8253 (ttpp) REVERT: B 193 GLU cc_start: 0.7820 (tp30) cc_final: 0.7555 (tm-30) REVERT: B 202 GLU cc_start: 0.7352 (pm20) cc_final: 0.6598 (pm20) REVERT: G 67 TYR cc_start: 0.8147 (t80) cc_final: 0.7678 (t80) REVERT: G 81 ASP cc_start: 0.7589 (m-30) cc_final: 0.7285 (m-30) REVERT: G 97 GLU cc_start: 0.7809 (OUTLIER) cc_final: 0.7469 (pt0) REVERT: G 114 THR cc_start: 0.6764 (m) cc_final: 0.6400 (t) REVERT: G 132 MET cc_start: 0.8304 (mmp) cc_final: 0.7856 (mpm) REVERT: G 167 ASP cc_start: 0.8255 (OUTLIER) cc_final: 0.7808 (p0) REVERT: G 387 TYR cc_start: 0.8342 (t80) cc_final: 0.7973 (t80) REVERT: G 696 GLU cc_start: 0.8322 (OUTLIER) cc_final: 0.7987 (mp0) REVERT: G 1650 VAL cc_start: 0.9230 (OUTLIER) cc_final: 0.9023 (m) REVERT: G 1784 MET cc_start: 0.9002 (OUTLIER) cc_final: 0.8742 (tmt) REVERT: G 1849 ARG cc_start: 0.6040 (ttp80) cc_final: 0.5778 (ptm160) REVERT: G 2045 TRP cc_start: 0.7871 (t-100) cc_final: 0.7059 (t-100) outliers start: 65 outliers final: 31 residues processed: 306 average time/residue: 1.5667 time to fit residues: 559.1878 Evaluate side-chains 284 residues out of total 3245 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 244 time to evaluate : 3.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain A residue 487 ASP Chi-restraints excluded: chain A residue 517 GLU Chi-restraints excluded: chain A residue 658 LEU Chi-restraints excluded: chain A residue 674 LYS Chi-restraints excluded: chain A residue 944 ARG Chi-restraints excluded: chain A residue 946 GLU Chi-restraints excluded: chain A residue 958 SER Chi-restraints excluded: chain A residue 1127 VAL Chi-restraints excluded: chain A residue 1179 LEU Chi-restraints excluded: chain A residue 1203 ASP Chi-restraints excluded: chain A residue 1284 SER Chi-restraints excluded: chain A residue 1305 CYS Chi-restraints excluded: chain A residue 1333 ASP Chi-restraints excluded: chain A residue 1395 LYS Chi-restraints excluded: chain A residue 1498 GLU Chi-restraints excluded: chain A residue 1677 VAL Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 174 ASP Chi-restraints excluded: chain B residue 192 LYS Chi-restraints excluded: chain G residue 22 VAL Chi-restraints excluded: chain G residue 97 GLU Chi-restraints excluded: chain G residue 167 ASP Chi-restraints excluded: chain G residue 328 LEU Chi-restraints excluded: chain G residue 334 VAL Chi-restraints excluded: chain G residue 447 ASN Chi-restraints excluded: chain G residue 510 SER Chi-restraints excluded: chain G residue 630 MET Chi-restraints excluded: chain G residue 658 MET Chi-restraints excluded: chain G residue 696 GLU Chi-restraints excluded: chain G residue 827 VAL Chi-restraints excluded: chain G residue 880 LEU Chi-restraints excluded: chain G residue 1348 LEU Chi-restraints excluded: chain G residue 1381 VAL Chi-restraints excluded: chain G residue 1382 VAL Chi-restraints excluded: chain G residue 1616 VAL Chi-restraints excluded: chain G residue 1650 VAL Chi-restraints excluded: chain G residue 1753 LYS Chi-restraints excluded: chain G residue 1784 MET Chi-restraints excluded: chain G residue 1936 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 350 optimal weight: 9.9990 chunk 41 optimal weight: 2.9990 chunk 207 optimal weight: 9.9990 chunk 265 optimal weight: 6.9990 chunk 205 optimal weight: 6.9990 chunk 306 optimal weight: 9.9990 chunk 203 optimal weight: 9.9990 chunk 362 optimal weight: 5.9990 chunk 226 optimal weight: 9.9990 chunk 220 optimal weight: 0.9990 chunk 167 optimal weight: 4.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 758 ASN A1494 HIS ** A1806 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 330 ASN G1399 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.1952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 30222 Z= 0.316 Angle : 0.549 10.385 40936 Z= 0.284 Chirality : 0.044 0.173 4602 Planarity : 0.004 0.036 5284 Dihedral : 4.869 102.096 4028 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.79 % Favored : 97.18 % Rotamer: Outliers : 2.19 % Allowed : 12.98 % Favored : 84.83 % 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: 0.67 (0.14), residues: 3760 helix: 1.22 (0.13), residues: 1677 sheet: -0.40 (0.22), residues: 489 loop : 0.03 (0.16), residues: 1594 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP G 865 HIS 0.008 0.001 HIS A1689 PHE 0.026 0.002 PHE A 22 TYR 0.019 0.002 TYR A 722 ARG 0.011 0.001 ARG A 520 *********************** 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 319 residues out of total 3245 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 248 time to evaluate : 3.977 Fit side-chains revert: symmetry clash REVERT: A 16 GLU cc_start: 0.8798 (tp30) cc_final: 0.8319 (tp30) REVERT: A 340 ARG cc_start: 0.6732 (mmt180) cc_final: 0.6156 (mpt180) REVERT: A 517 GLU cc_start: 0.7508 (OUTLIER) cc_final: 0.7189 (mm-30) REVERT: A 529 MET cc_start: 0.8846 (mmp) cc_final: 0.8519 (mmp) REVERT: A 537 LYS cc_start: 0.7369 (tptt) cc_final: 0.7136 (mttm) REVERT: A 958 SER cc_start: 0.8230 (OUTLIER) cc_final: 0.7913 (m) REVERT: A 1162 GLU cc_start: 0.7850 (mp0) cc_final: 0.7451 (mp0) REVERT: A 1180 ARG cc_start: 0.7291 (mpt180) cc_final: 0.6558 (mpt90) REVERT: A 1209 ASP cc_start: 0.8571 (t70) cc_final: 0.8316 (t70) REVERT: A 1298 ILE cc_start: 0.9004 (OUTLIER) cc_final: 0.8610 (tp) REVERT: A 1498 GLU cc_start: 0.8452 (OUTLIER) cc_final: 0.8152 (tm-30) REVERT: B 168 MET cc_start: 0.6477 (mmm) cc_final: 0.5841 (tpp) REVERT: B 192 LYS cc_start: 0.8467 (OUTLIER) cc_final: 0.8248 (ttpp) REVERT: B 193 GLU cc_start: 0.7823 (tp30) cc_final: 0.7582 (tm-30) REVERT: B 202 GLU cc_start: 0.7337 (pm20) cc_final: 0.6554 (pm20) REVERT: G 67 TYR cc_start: 0.8235 (t80) cc_final: 0.7705 (t80) REVERT: G 97 GLU cc_start: 0.7839 (OUTLIER) cc_final: 0.7498 (pt0) REVERT: G 114 THR cc_start: 0.6735 (m) cc_final: 0.6349 (t) REVERT: G 132 MET cc_start: 0.8136 (mmp) cc_final: 0.7763 (mpm) REVERT: G 167 ASP cc_start: 0.8300 (OUTLIER) cc_final: 0.7916 (p0) REVERT: G 387 TYR cc_start: 0.8399 (t80) cc_final: 0.7975 (t80) REVERT: G 696 GLU cc_start: 0.8397 (OUTLIER) cc_final: 0.8060 (mp0) REVERT: G 831 LYS cc_start: 0.8729 (OUTLIER) cc_final: 0.8508 (mtmm) REVERT: G 1741 ILE cc_start: 0.2616 (OUTLIER) cc_final: 0.2212 (mm) REVERT: G 1784 MET cc_start: 0.9074 (OUTLIER) cc_final: 0.8805 (tmt) REVERT: G 1849 ARG cc_start: 0.6092 (ttp80) cc_final: 0.5787 (ptm160) REVERT: G 2045 TRP cc_start: 0.7825 (t-100) cc_final: 0.6951 (t-100) outliers start: 71 outliers final: 38 residues processed: 303 average time/residue: 1.5609 time to fit residues: 556.0096 Evaluate side-chains 291 residues out of total 3245 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 242 time to evaluate : 3.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 487 ASP Chi-restraints excluded: chain A residue 517 GLU Chi-restraints excluded: chain A residue 658 LEU Chi-restraints excluded: chain A residue 674 LYS Chi-restraints excluded: chain A residue 944 ARG Chi-restraints excluded: chain A residue 946 GLU Chi-restraints excluded: chain A residue 958 SER Chi-restraints excluded: chain A residue 1096 SER Chi-restraints excluded: chain A residue 1127 VAL Chi-restraints excluded: chain A residue 1179 LEU Chi-restraints excluded: chain A residue 1203 ASP Chi-restraints excluded: chain A residue 1284 SER Chi-restraints excluded: chain A residue 1298 ILE Chi-restraints excluded: chain A residue 1305 CYS Chi-restraints excluded: chain A residue 1333 ASP Chi-restraints excluded: chain A residue 1395 LYS Chi-restraints excluded: chain A residue 1498 GLU Chi-restraints excluded: chain A residue 1677 VAL Chi-restraints excluded: chain A residue 1776 ILE Chi-restraints excluded: chain A residue 1806 GLN Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 174 ASP Chi-restraints excluded: chain B residue 192 LYS Chi-restraints excluded: chain G residue 22 VAL Chi-restraints excluded: chain G residue 97 GLU Chi-restraints excluded: chain G residue 167 ASP Chi-restraints excluded: chain G residue 328 LEU Chi-restraints excluded: chain G residue 334 VAL Chi-restraints excluded: chain G residue 423 VAL Chi-restraints excluded: chain G residue 447 ASN Chi-restraints excluded: chain G residue 510 SER Chi-restraints excluded: chain G residue 630 MET Chi-restraints excluded: chain G residue 658 MET Chi-restraints excluded: chain G residue 696 GLU Chi-restraints excluded: chain G residue 827 VAL Chi-restraints excluded: chain G residue 831 LYS Chi-restraints excluded: chain G residue 880 LEU Chi-restraints excluded: chain G residue 1348 LEU Chi-restraints excluded: chain G residue 1381 VAL Chi-restraints excluded: chain G residue 1382 VAL Chi-restraints excluded: chain G residue 1472 VAL Chi-restraints excluded: chain G residue 1586 SER Chi-restraints excluded: chain G residue 1616 VAL Chi-restraints excluded: chain G residue 1741 ILE Chi-restraints excluded: chain G residue 1753 LYS Chi-restraints excluded: chain G residue 1784 MET Chi-restraints excluded: chain G residue 1936 VAL 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: 9.9990 chunk 216 optimal weight: 3.9990 chunk 109 optimal weight: 0.6980 chunk 71 optimal weight: 0.9980 chunk 70 optimal weight: 20.0000 chunk 230 optimal weight: 7.9990 chunk 246 optimal weight: 10.0000 chunk 179 optimal weight: 9.9990 chunk 33 optimal weight: 8.9990 chunk 284 optimal weight: 9.9990 overall best weight: 4.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 904 ASN A1494 HIS A1601 ASN ** A1806 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 418 ASN G1399 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 moved from start: 0.2026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 30222 Z= 0.323 Angle : 0.553 10.634 40936 Z= 0.287 Chirality : 0.044 0.174 4602 Planarity : 0.004 0.035 5284 Dihedral : 4.914 104.044 4028 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.71 % Favored : 97.23 % Rotamer: Outliers : 1.97 % Allowed : 13.53 % Favored : 84.49 % 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: 0.63 (0.14), residues: 3760 helix: 1.19 (0.13), residues: 1673 sheet: -0.45 (0.22), residues: 489 loop : 0.02 (0.16), residues: 1598 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP G 865 HIS 0.008 0.001 HIS A1689 PHE 0.027 0.002 PHE A 22 TYR 0.022 0.002 TYR B 294 ARG 0.006 0.001 ARG A 709 *********************** 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 313 residues out of total 3245 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 249 time to evaluate : 3.586 Fit side-chains revert: symmetry clash REVERT: A 16 GLU cc_start: 0.8825 (tp30) cc_final: 0.8372 (tp30) REVERT: A 340 ARG cc_start: 0.6749 (mmt180) cc_final: 0.6143 (mpt180) REVERT: A 517 GLU cc_start: 0.7503 (OUTLIER) cc_final: 0.7156 (mm-30) REVERT: A 529 MET cc_start: 0.8853 (mmp) cc_final: 0.8532 (mmp) REVERT: A 537 LYS cc_start: 0.7347 (tptt) cc_final: 0.7135 (mttm) REVERT: A 944 ARG cc_start: 0.8688 (OUTLIER) cc_final: 0.8447 (ttp80) REVERT: A 958 SER cc_start: 0.8229 (OUTLIER) cc_final: 0.7918 (m) REVERT: A 1142 GLU cc_start: 0.8760 (mt-10) cc_final: 0.8490 (mt-10) REVERT: A 1159 GLU cc_start: 0.8047 (mp0) cc_final: 0.7769 (pm20) REVERT: A 1162 GLU cc_start: 0.7872 (mp0) cc_final: 0.7450 (mp0) REVERT: A 1180 ARG cc_start: 0.7282 (mpt180) cc_final: 0.6543 (mpt90) REVERT: A 1209 ASP cc_start: 0.8582 (t70) cc_final: 0.8321 (t70) REVERT: A 1298 ILE cc_start: 0.9006 (OUTLIER) cc_final: 0.8610 (tp) REVERT: A 1498 GLU cc_start: 0.8460 (OUTLIER) cc_final: 0.8161 (tm-30) REVERT: B 168 MET cc_start: 0.6489 (mmm) cc_final: 0.5789 (tpp) REVERT: B 192 LYS cc_start: 0.8491 (OUTLIER) cc_final: 0.8290 (ttpp) REVERT: G 67 TYR cc_start: 0.8241 (t80) cc_final: 0.7636 (t80) REVERT: G 97 GLU cc_start: 0.7820 (OUTLIER) cc_final: 0.7453 (pt0) REVERT: G 114 THR cc_start: 0.6781 (m) cc_final: 0.6393 (t) REVERT: G 132 MET cc_start: 0.8259 (mmp) cc_final: 0.7923 (mpm) REVERT: G 167 ASP cc_start: 0.8331 (p0) cc_final: 0.7947 (p0) REVERT: G 387 TYR cc_start: 0.8413 (t80) cc_final: 0.7977 (t80) REVERT: G 696 GLU cc_start: 0.8419 (OUTLIER) cc_final: 0.8055 (mp0) REVERT: G 831 LYS cc_start: 0.8729 (OUTLIER) cc_final: 0.8512 (mtmm) REVERT: G 1741 ILE cc_start: 0.2119 (OUTLIER) cc_final: 0.1620 (mm) REVERT: G 1784 MET cc_start: 0.9111 (OUTLIER) cc_final: 0.8826 (tmt) REVERT: G 1801 ASP cc_start: 0.7896 (OUTLIER) cc_final: 0.7593 (p0) REVERT: G 1849 ARG cc_start: 0.6139 (ttp80) cc_final: 0.5812 (ptm-80) REVERT: G 2045 TRP cc_start: 0.7806 (t-100) cc_final: 0.6971 (t-100) outliers start: 64 outliers final: 39 residues processed: 298 average time/residue: 1.6054 time to fit residues: 559.8259 Evaluate side-chains 292 residues out of total 3245 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 241 time to evaluate : 3.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 487 ASP Chi-restraints excluded: chain A residue 517 GLU Chi-restraints excluded: chain A residue 658 LEU Chi-restraints excluded: chain A residue 674 LYS Chi-restraints excluded: chain A residue 944 ARG Chi-restraints excluded: chain A residue 946 GLU Chi-restraints excluded: chain A residue 958 SER Chi-restraints excluded: chain A residue 1127 VAL Chi-restraints excluded: chain A residue 1179 LEU Chi-restraints excluded: chain A residue 1203 ASP Chi-restraints excluded: chain A residue 1284 SER Chi-restraints excluded: chain A residue 1298 ILE Chi-restraints excluded: chain A residue 1305 CYS Chi-restraints excluded: chain A residue 1333 ASP Chi-restraints excluded: chain A residue 1395 LYS Chi-restraints excluded: chain A residue 1498 GLU Chi-restraints excluded: chain A residue 1677 VAL Chi-restraints excluded: chain A residue 1776 ILE Chi-restraints excluded: chain A residue 1806 GLN Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 174 ASP Chi-restraints excluded: chain B residue 192 LYS Chi-restraints excluded: chain G residue 22 VAL Chi-restraints excluded: chain G residue 97 GLU Chi-restraints excluded: chain G residue 328 LEU Chi-restraints excluded: chain G residue 334 VAL Chi-restraints excluded: chain G residue 418 ASN Chi-restraints excluded: chain G residue 423 VAL Chi-restraints excluded: chain G residue 447 ASN Chi-restraints excluded: chain G residue 510 SER Chi-restraints excluded: chain G residue 630 MET Chi-restraints excluded: chain G residue 658 MET Chi-restraints excluded: chain G residue 688 LEU Chi-restraints excluded: chain G residue 696 GLU Chi-restraints excluded: chain G residue 827 VAL Chi-restraints excluded: chain G residue 831 LYS Chi-restraints excluded: chain G residue 880 LEU Chi-restraints excluded: chain G residue 1190 SER Chi-restraints excluded: chain G residue 1348 LEU Chi-restraints excluded: chain G residue 1381 VAL Chi-restraints excluded: chain G residue 1382 VAL Chi-restraints excluded: chain G residue 1472 VAL Chi-restraints excluded: chain G residue 1586 SER Chi-restraints excluded: chain G residue 1632 ILE Chi-restraints excluded: chain G residue 1741 ILE Chi-restraints excluded: chain G residue 1753 LYS Chi-restraints excluded: chain G residue 1784 MET Chi-restraints excluded: chain G residue 1801 ASP Chi-restraints excluded: chain G residue 1936 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 329 optimal weight: 5.9990 chunk 347 optimal weight: 3.9990 chunk 316 optimal weight: 4.9990 chunk 337 optimal weight: 4.9990 chunk 203 optimal weight: 5.9990 chunk 147 optimal weight: 20.0000 chunk 265 optimal weight: 0.9990 chunk 103 optimal weight: 8.9990 chunk 305 optimal weight: 5.9990 chunk 319 optimal weight: 9.9990 chunk 336 optimal weight: 10.0000 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 904 ASN A1494 HIS ** A1806 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G1399 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.2054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 30222 Z= 0.307 Angle : 0.551 10.569 40936 Z= 0.285 Chirality : 0.044 0.183 4602 Planarity : 0.004 0.040 5284 Dihedral : 4.905 104.855 4028 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.87 % Favored : 97.07 % Rotamer: Outliers : 2.10 % Allowed : 13.72 % Favored : 84.19 % 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: 0.67 (0.14), residues: 3760 helix: 1.22 (0.13), residues: 1665 sheet: -0.37 (0.22), residues: 483 loop : 0.03 (0.16), residues: 1612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP G 865 HIS 0.008 0.001 HIS A1689 PHE 0.026 0.002 PHE A 22 TYR 0.024 0.002 TYR B 294 ARG 0.010 0.001 ARG G 419 *********************** 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 311 residues out of total 3245 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 243 time to evaluate : 3.265 Fit side-chains revert: symmetry clash REVERT: A 16 GLU cc_start: 0.8822 (tp30) cc_final: 0.8353 (tp30) REVERT: A 340 ARG cc_start: 0.6730 (mmt180) cc_final: 0.6134 (mpt180) REVERT: A 517 GLU cc_start: 0.7503 (OUTLIER) cc_final: 0.7159 (mm-30) REVERT: A 529 MET cc_start: 0.8850 (mmp) cc_final: 0.8530 (mmp) REVERT: A 537 LYS cc_start: 0.7382 (tptt) cc_final: 0.7137 (mttm) REVERT: A 944 ARG cc_start: 0.8688 (OUTLIER) cc_final: 0.8449 (ttp80) REVERT: A 958 SER cc_start: 0.8227 (OUTLIER) cc_final: 0.7916 (m) REVERT: A 1142 GLU cc_start: 0.8765 (mt-10) cc_final: 0.8466 (mt-10) REVERT: A 1159 GLU cc_start: 0.8049 (mp0) cc_final: 0.7685 (pm20) REVERT: A 1162 GLU cc_start: 0.7883 (mp0) cc_final: 0.7440 (mp0) REVERT: A 1180 ARG cc_start: 0.7269 (mpt180) cc_final: 0.6529 (mpt90) REVERT: A 1209 ASP cc_start: 0.8567 (t70) cc_final: 0.8300 (t70) REVERT: A 1298 ILE cc_start: 0.9002 (OUTLIER) cc_final: 0.8608 (tp) REVERT: A 1498 GLU cc_start: 0.8458 (OUTLIER) cc_final: 0.8161 (tm-30) REVERT: B 168 MET cc_start: 0.6503 (mmm) cc_final: 0.5822 (tpp) REVERT: B 192 LYS cc_start: 0.8448 (OUTLIER) cc_final: 0.8245 (ttpp) REVERT: G 67 TYR cc_start: 0.8232 (t80) cc_final: 0.7554 (t80) REVERT: G 97 GLU cc_start: 0.7812 (OUTLIER) cc_final: 0.7449 (pt0) REVERT: G 114 THR cc_start: 0.6835 (m) cc_final: 0.6455 (t) REVERT: G 132 MET cc_start: 0.8249 (mmp) cc_final: 0.7913 (mpm) REVERT: G 167 ASP cc_start: 0.8333 (p0) cc_final: 0.7913 (p0) REVERT: G 387 TYR cc_start: 0.8408 (t80) cc_final: 0.7966 (t80) REVERT: G 696 GLU cc_start: 0.8417 (OUTLIER) cc_final: 0.8052 (mp0) REVERT: G 831 LYS cc_start: 0.8729 (OUTLIER) cc_final: 0.8505 (mtmm) REVERT: G 1741 ILE cc_start: 0.2130 (OUTLIER) cc_final: 0.1643 (mm) REVERT: G 1784 MET cc_start: 0.9110 (OUTLIER) cc_final: 0.8825 (tmt) REVERT: G 1801 ASP cc_start: 0.7856 (OUTLIER) cc_final: 0.7543 (p0) REVERT: G 1849 ARG cc_start: 0.6114 (ttp80) cc_final: 0.5818 (ptm-80) REVERT: G 2045 TRP cc_start: 0.7812 (t-100) cc_final: 0.6957 (t-100) outliers start: 68 outliers final: 42 residues processed: 292 average time/residue: 1.5810 time to fit residues: 540.9464 Evaluate side-chains 295 residues out of total 3245 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 241 time to evaluate : 3.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 487 ASP Chi-restraints excluded: chain A residue 517 GLU Chi-restraints excluded: chain A residue 658 LEU Chi-restraints excluded: chain A residue 674 LYS Chi-restraints excluded: chain A residue 944 ARG Chi-restraints excluded: chain A residue 946 GLU Chi-restraints excluded: chain A residue 958 SER Chi-restraints excluded: chain A residue 1096 SER Chi-restraints excluded: chain A residue 1127 VAL Chi-restraints excluded: chain A residue 1179 LEU Chi-restraints excluded: chain A residue 1203 ASP Chi-restraints excluded: chain A residue 1260 MET Chi-restraints excluded: chain A residue 1284 SER Chi-restraints excluded: chain A residue 1298 ILE Chi-restraints excluded: chain A residue 1305 CYS Chi-restraints excluded: chain A residue 1333 ASP Chi-restraints excluded: chain A residue 1395 LYS Chi-restraints excluded: chain A residue 1498 GLU Chi-restraints excluded: chain A residue 1677 VAL Chi-restraints excluded: chain A residue 1776 ILE Chi-restraints excluded: chain A residue 1806 GLN Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 174 ASP Chi-restraints excluded: chain B residue 192 LYS Chi-restraints excluded: chain G residue 22 VAL Chi-restraints excluded: chain G residue 97 GLU Chi-restraints excluded: chain G residue 324 LEU Chi-restraints excluded: chain G residue 328 LEU Chi-restraints excluded: chain G residue 334 VAL Chi-restraints excluded: chain G residue 423 VAL Chi-restraints excluded: chain G residue 447 ASN Chi-restraints excluded: chain G residue 510 SER Chi-restraints excluded: chain G residue 630 MET Chi-restraints excluded: chain G residue 658 MET Chi-restraints excluded: chain G residue 688 LEU Chi-restraints excluded: chain G residue 696 GLU Chi-restraints excluded: chain G residue 827 VAL Chi-restraints excluded: chain G residue 831 LYS Chi-restraints excluded: chain G residue 850 MET Chi-restraints excluded: chain G residue 880 LEU Chi-restraints excluded: chain G residue 1190 SER Chi-restraints excluded: chain G residue 1348 LEU Chi-restraints excluded: chain G residue 1381 VAL Chi-restraints excluded: chain G residue 1382 VAL Chi-restraints excluded: chain G residue 1472 VAL Chi-restraints excluded: chain G residue 1586 SER Chi-restraints excluded: chain G residue 1632 ILE Chi-restraints excluded: chain G residue 1741 ILE Chi-restraints excluded: chain G residue 1753 LYS Chi-restraints excluded: chain G residue 1784 MET Chi-restraints excluded: chain G residue 1801 ASP Chi-restraints excluded: chain G residue 1936 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 221 optimal weight: 10.0000 chunk 357 optimal weight: 20.0000 chunk 217 optimal weight: 3.9990 chunk 169 optimal weight: 20.0000 chunk 248 optimal weight: 10.0000 chunk 374 optimal weight: 8.9990 chunk 344 optimal weight: 2.9990 chunk 298 optimal weight: 0.9980 chunk 30 optimal weight: 20.0000 chunk 230 optimal weight: 8.9990 chunk 182 optimal weight: 7.9990 overall best weight: 4.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1494 HIS ** A1806 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 418 ASN G 500 HIS G1399 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 moved from start: 0.2093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 30222 Z= 0.355 Angle : 0.577 10.862 40936 Z= 0.298 Chirality : 0.045 0.188 4602 Planarity : 0.004 0.036 5284 Dihedral : 4.993 106.701 4028 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.03 % Favored : 96.91 % Rotamer: Outliers : 1.94 % Allowed : 14.09 % Favored : 83.97 % 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: 0.60 (0.14), residues: 3760 helix: 1.14 (0.13), residues: 1665 sheet: -0.40 (0.22), residues: 483 loop : 0.01 (0.16), residues: 1612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP G 865 HIS 0.008 0.001 HIS A1689 PHE 0.027 0.002 PHE A 22 TYR 0.026 0.002 TYR B 294 ARG 0.006 0.001 ARG G1962 ********************** 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 312 residues out of total 3245 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 249 time to evaluate : 3.397 Fit side-chains revert: symmetry clash REVERT: A 16 GLU cc_start: 0.8833 (tp30) cc_final: 0.8363 (tp30) REVERT: A 340 ARG cc_start: 0.6737 (mmt180) cc_final: 0.6187 (mpt180) REVERT: A 517 GLU cc_start: 0.7506 (OUTLIER) cc_final: 0.7160 (mm-30) REVERT: A 529 MET cc_start: 0.8834 (mmp) cc_final: 0.8506 (mmp) REVERT: A 537 LYS cc_start: 0.7348 (tptt) cc_final: 0.7117 (mttm) REVERT: A 816 GLU cc_start: 0.8250 (mp0) cc_final: 0.7938 (mt-10) REVERT: A 944 ARG cc_start: 0.8689 (OUTLIER) cc_final: 0.8457 (ttp80) REVERT: A 958 SER cc_start: 0.8240 (OUTLIER) cc_final: 0.7933 (m) REVERT: A 1142 GLU cc_start: 0.8769 (mt-10) cc_final: 0.8482 (mt-10) REVERT: A 1159 GLU cc_start: 0.8151 (mp0) cc_final: 0.7800 (pm20) REVERT: A 1162 GLU cc_start: 0.7897 (mp0) cc_final: 0.7501 (mp0) REVERT: A 1180 ARG cc_start: 0.7273 (mpt180) cc_final: 0.6529 (mpt90) REVERT: A 1209 ASP cc_start: 0.8599 (t70) cc_final: 0.8340 (t70) REVERT: A 1298 ILE cc_start: 0.9014 (OUTLIER) cc_final: 0.8618 (tp) REVERT: A 1491 ARG cc_start: 0.8465 (tpt90) cc_final: 0.7912 (tpp80) REVERT: A 1498 GLU cc_start: 0.8464 (OUTLIER) cc_final: 0.8165 (tm-30) REVERT: B 168 MET cc_start: 0.6436 (mmm) cc_final: 0.5733 (tpp) REVERT: B 192 LYS cc_start: 0.8445 (OUTLIER) cc_final: 0.8234 (ttpp) REVERT: G 67 TYR cc_start: 0.8188 (t80) cc_final: 0.7553 (t80) REVERT: G 97 GLU cc_start: 0.7840 (OUTLIER) cc_final: 0.7484 (pt0) REVERT: G 114 THR cc_start: 0.6868 (m) cc_final: 0.6499 (t) REVERT: G 132 MET cc_start: 0.8068 (mmp) cc_final: 0.7765 (mpm) REVERT: G 167 ASP cc_start: 0.8305 (p0) cc_final: 0.8001 (p0) REVERT: G 387 TYR cc_start: 0.8406 (t80) cc_final: 0.7939 (t80) REVERT: G 696 GLU cc_start: 0.8420 (OUTLIER) cc_final: 0.8054 (mp0) REVERT: G 831 LYS cc_start: 0.8724 (OUTLIER) cc_final: 0.8506 (mtmm) REVERT: G 1741 ILE cc_start: 0.2180 (OUTLIER) cc_final: 0.1679 (mm) REVERT: G 1784 MET cc_start: 0.9115 (OUTLIER) cc_final: 0.8833 (tmt) REVERT: G 1801 ASP cc_start: 0.7860 (OUTLIER) cc_final: 0.7548 (p0) REVERT: G 1849 ARG cc_start: 0.6116 (ttp80) cc_final: 0.5813 (ptm-80) REVERT: G 2045 TRP cc_start: 0.7817 (t-100) cc_final: 0.6921 (t-100) outliers start: 63 outliers final: 43 residues processed: 297 average time/residue: 1.5884 time to fit residues: 550.7688 Evaluate side-chains 299 residues out of total 3245 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 244 time to evaluate : 3.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 487 ASP Chi-restraints excluded: chain A residue 517 GLU Chi-restraints excluded: chain A residue 658 LEU Chi-restraints excluded: chain A residue 674 LYS Chi-restraints excluded: chain A residue 944 ARG Chi-restraints excluded: chain A residue 946 GLU Chi-restraints excluded: chain A residue 958 SER Chi-restraints excluded: chain A residue 1096 SER Chi-restraints excluded: chain A residue 1127 VAL Chi-restraints excluded: chain A residue 1179 LEU Chi-restraints excluded: chain A residue 1203 ASP Chi-restraints excluded: chain A residue 1260 MET Chi-restraints excluded: chain A residue 1284 SER Chi-restraints excluded: chain A residue 1298 ILE Chi-restraints excluded: chain A residue 1305 CYS Chi-restraints excluded: chain A residue 1333 ASP Chi-restraints excluded: chain A residue 1395 LYS Chi-restraints excluded: chain A residue 1498 GLU Chi-restraints excluded: chain A residue 1677 VAL Chi-restraints excluded: chain A residue 1776 ILE Chi-restraints excluded: chain A residue 1806 GLN Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 174 ASP Chi-restraints excluded: chain B residue 192 LYS Chi-restraints excluded: chain G residue 22 VAL Chi-restraints excluded: chain G residue 97 GLU Chi-restraints excluded: chain G residue 324 LEU Chi-restraints excluded: chain G residue 328 LEU Chi-restraints excluded: chain G residue 334 VAL Chi-restraints excluded: chain G residue 418 ASN Chi-restraints excluded: chain G residue 423 VAL Chi-restraints excluded: chain G residue 447 ASN Chi-restraints excluded: chain G residue 510 SER Chi-restraints excluded: chain G residue 630 MET Chi-restraints excluded: chain G residue 658 MET Chi-restraints excluded: chain G residue 688 LEU Chi-restraints excluded: chain G residue 696 GLU Chi-restraints excluded: chain G residue 827 VAL Chi-restraints excluded: chain G residue 831 LYS Chi-restraints excluded: chain G residue 850 MET Chi-restraints excluded: chain G residue 880 LEU Chi-restraints excluded: chain G residue 1190 SER Chi-restraints excluded: chain G residue 1348 LEU Chi-restraints excluded: chain G residue 1381 VAL Chi-restraints excluded: chain G residue 1382 VAL Chi-restraints excluded: chain G residue 1472 VAL Chi-restraints excluded: chain G residue 1586 SER Chi-restraints excluded: chain G residue 1632 ILE Chi-restraints excluded: chain G residue 1741 ILE Chi-restraints excluded: chain G residue 1753 LYS Chi-restraints excluded: chain G residue 1784 MET Chi-restraints excluded: chain G residue 1801 ASP Chi-restraints excluded: chain G residue 1936 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 236 optimal weight: 6.9990 chunk 317 optimal weight: 7.9990 chunk 91 optimal weight: 0.8980 chunk 275 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 chunk 82 optimal weight: 0.9990 chunk 298 optimal weight: 0.9980 chunk 125 optimal weight: 3.9990 chunk 306 optimal weight: 8.9990 chunk 37 optimal weight: 0.9990 chunk 55 optimal weight: 3.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1494 HIS ** A1806 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 418 ASN G1399 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.109800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.081112 restraints weight = 52504.610| |-----------------------------------------------------------------------------| r_work (start): 0.3016 rms_B_bonded: 1.99 r_work: 0.2886 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2769 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.2140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 30222 Z= 0.158 Angle : 0.502 9.728 40936 Z= 0.259 Chirality : 0.042 0.181 4602 Planarity : 0.003 0.035 5284 Dihedral : 4.700 104.363 4028 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.58 % Favored : 97.37 % Rotamer: Outliers : 1.39 % Allowed : 14.83 % Favored : 83.79 % 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: 0.76 (0.14), residues: 3760 helix: 1.25 (0.13), residues: 1690 sheet: -0.34 (0.22), residues: 492 loop : 0.11 (0.16), residues: 1578 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP G 661 HIS 0.006 0.001 HIS A1689 PHE 0.026 0.001 PHE G 28 TYR 0.025 0.001 TYR B 294 ARG 0.008 0.000 ARG A 709 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10759.34 seconds wall clock time: 191 minutes 13.29 seconds (11473.29 seconds total)