Starting phenix.real_space_refine on Thu Mar 21 08:18:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8psl_17855/03_2024/8psl_17855_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8psl_17855/03_2024/8psl_17855.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8psl_17855/03_2024/8psl_17855.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8psl_17855/03_2024/8psl_17855.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8psl_17855/03_2024/8psl_17855_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8psl_17855/03_2024/8psl_17855_updated.pdb" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 106 5.16 5 C 18870 2.51 5 N 4955 2.21 5 O 5678 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 349": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 384": "OE1" <-> "OE2" Residue "A ASP 403": "OD1" <-> "OD2" Residue "A GLU 419": "OE1" <-> "OE2" Residue "A GLU 435": "OE1" <-> "OE2" Residue "A GLU 514": "OE1" <-> "OE2" Residue "A TYR 525": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 612": "OE1" <-> "OE2" Residue "A GLU 633": "OE1" <-> "OE2" Residue "A ASP 648": "OD1" <-> "OD2" Residue "A ASP 716": "OD1" <-> "OD2" Residue "A GLU 750": "OE1" <-> "OE2" Residue "A PHE 771": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 780": "OE1" <-> "OE2" Residue "A ASP 785": "OD1" <-> "OD2" Residue "A PHE 790": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 896": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 912": "OE1" <-> "OE2" Residue "A GLU 915": "OE1" <-> "OE2" Residue "A GLU 935": "OE1" <-> "OE2" Residue "A GLU 981": "OE1" <-> "OE2" Residue "A GLU 1016": "OE1" <-> "OE2" Residue "A GLU 1026": "OE1" <-> "OE2" Residue "A GLU 1038": "OE1" <-> "OE2" Residue "A GLU 1052": "OE1" <-> "OE2" Residue "A GLU 1117": "OE1" <-> "OE2" Residue "A GLU 1132": "OE1" <-> "OE2" Residue "A GLU 1135": "OE1" <-> "OE2" Residue "A GLU 1156": "OE1" <-> "OE2" Residue "A ASP 1313": "OD1" <-> "OD2" Residue "A GLU 1317": "OE1" <-> "OE2" Residue "A TYR 1332": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1337": "OE1" <-> "OE2" Residue "A GLU 1354": "OE1" <-> "OE2" Residue "A PHE 1376": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1391": "OD1" <-> "OD2" Residue "A TYR 1401": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1498": "OE1" <-> "OE2" Residue "A GLU 1568": "OE1" <-> "OE2" Residue "A GLU 1681": "OE1" <-> "OE2" Residue "A PHE 1786": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1817": "OE1" <-> "OE2" Residue "B GLU 143": "OE1" <-> "OE2" Residue "B ASP 164": "OD1" <-> "OD2" Residue "B GLU 185": "OE1" <-> "OE2" Residue "B GLU 199": "OE1" <-> "OE2" Residue "B GLU 202": "OE1" <-> "OE2" Residue "B PHE 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 286": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 43": "OE1" <-> "OE2" Residue "G ASP 81": "OD1" <-> "OD2" Residue "G ASP 138": "OD1" <-> "OD2" Residue "G PHE 304": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 347": "OE1" <-> "OE2" Residue "G PHE 427": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 437": "OD1" <-> "OD2" Residue "G ASP 481": "OD1" <-> "OD2" Residue "G ASP 538": "OD1" <-> "OD2" Residue "G ASP 549": "OD1" <-> "OD2" Residue "G PHE 578": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 580": "OE1" <-> "OE2" Residue "G PHE 796": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 919": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 920": "OE1" <-> "OE2" Residue "G GLU 955": "OE1" <-> "OE2" Residue "G GLU 992": "OE1" <-> "OE2" Residue "G PHE 1003": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 1102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 1106": "OE1" <-> "OE2" Residue "G PHE 1154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 1183": "OE1" <-> "OE2" Residue "G PHE 1325": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 1423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 1471": "OE1" <-> "OE2" Residue "G PHE 1486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 1497": "OE1" <-> "OE2" Residue "G TYR 1545": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 1646": "OD1" <-> "OD2" Residue "G GLU 1767": "OE1" <-> "OE2" Residue "G GLU 1790": "OE1" <-> "OE2" Residue "G TYR 1833": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 29610 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: 16010 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2035, 16010 Classifications: {'peptide': 2035} Link IDs: {'PCIS': 1, 'PTRANS': 108, 'TRANS': 1925} 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: 15.56, per 1000 atoms: 0.53 Number of scatterers: 29610 At special positions: 0 Unit cell: (181.46, 181.46, 174.075, 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 5678 8.00 N 4955 7.00 C 18870 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=2.10 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 11.29 Conformation dependent library (CDL) restraints added in 5.8 seconds 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7028 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 167 helices and 31 sheets defined 43.5% alpha, 10.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 9.85 Creating SS restraints... Processing helix chain 'A' and resid 3 through 19 Processing helix chain 'A' and resid 21 through 23 No H-bonds generated for 'chain 'A' and resid 21 through 23' Processing helix chain 'A' and resid 29 through 35 removed outlier: 4.657A pdb=" N VAL A 34 " --> pdb=" O GLU A 30 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 63 removed outlier: 4.389A pdb=" N ARG A 59 " --> pdb=" O GLY A 55 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N THR A 60 " --> pdb=" O MET A 56 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LEU A 61 " --> pdb=" O ALA A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 66 through 72 Processing helix chain 'A' and resid 85 through 89 Processing helix chain 'A' and resid 330 through 350 Processing helix chain 'A' and resid 356 through 381 removed outlier: 4.281A pdb=" N PHE A 361 " --> pdb=" O GLY A 357 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N GLU A 364 " --> pdb=" O LYS A 360 " (cutoff:3.500A) 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: 4.722A pdb=" N LYS A 410 " --> pdb=" O TRP A 406 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ILE A 421 " --> pdb=" O TYR A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 441 removed outlier: 3.852A pdb=" N ASN A 438 " --> pdb=" O SER A 434 " (cutoff:3.500A) Processing helix chain 'A' and resid 445 through 455 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 615 removed outlier: 3.536A pdb=" N ALA A 614 " --> pdb=" O THR A 610 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N SER A 615 " --> pdb=" O LYS A 611 " (cutoff:3.500A) Processing helix chain 'A' and resid 653 through 668 Processing helix chain 'A' and resid 688 through 699 Processing helix chain 'A' and resid 712 through 724 Processing helix chain 'A' and resid 742 through 753 Processing helix chain 'A' and resid 756 through 758 No H-bonds generated for 'chain 'A' and resid 756 through 758' Processing helix chain 'A' and resid 781 through 783 No H-bonds generated for 'chain 'A' and resid 781 through 783' Processing helix chain 'A' and resid 786 through 795 Processing helix chain 'A' and resid 797 through 812 Processing helix chain 'A' and resid 840 through 850 removed outlier: 3.988A pdb=" N LEU A 846 " --> pdb=" O SER A 842 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N GLU A 847 " --> pdb=" O LYS A 843 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N THR A 848 " --> pdb=" O LEU A 844 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N LEU A 849 " --> pdb=" O SER A 845 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N PHE A 850 " --> pdb=" O LEU A 846 " (cutoff:3.500A) Processing helix chain 'A' and resid 858 through 860 No H-bonds generated for 'chain 'A' and resid 858 through 860' Processing helix chain 'A' and resid 883 through 891 removed outlier: 3.957A pdb=" N GLU A 886 " --> pdb=" O ILE A 883 " (cutoff:3.500A) Processing helix chain 'A' and resid 898 through 908 removed outlier: 3.654A pdb=" N LEU A 908 " --> pdb=" O ASN A 904 " (cutoff:3.500A) Processing helix chain 'A' and resid 911 through 917 Processing helix chain 'A' and resid 936 through 955 removed outlier: 4.350A pdb=" N THR A 950 " --> pdb=" O GLU A 946 " (cutoff:3.500A) Processing helix chain 'A' and resid 959 through 969 removed outlier: 4.066A pdb=" N GLU A 964 " --> pdb=" O GLU A 960 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N VAL A 968 " --> pdb=" O GLU A 964 " (cutoff:3.500A) Processing helix chain 'A' and resid 998 through 1004 removed outlier: 3.751A pdb=" N GLN A1003 " --> pdb=" O LYS A 999 " (cutoff:3.500A) removed outlier: 3.921A 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 removed outlier: 3.574A pdb=" N TRP A1037 " --> pdb=" O ALA A1033 " (cutoff:3.500A) Processing helix chain 'A' and resid 1047 through 1056 Processing helix chain 'A' and resid 1086 through 1100 removed outlier: 4.431A pdb=" N LYS A1090 " --> pdb=" O ASP A1086 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N ALA A1091 " --> pdb=" O LYS A1087 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N THR A1095 " --> pdb=" O ALA A1091 " (cutoff:3.500A) removed outlier: 5.848A 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 1116 through 1118 No H-bonds generated for 'chain 'A' and resid 1116 through 1118' Processing helix chain 'A' and resid 1138 through 1151 removed outlier: 3.719A pdb=" N GLN A1147 " --> pdb=" O GLN A1143 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N ASP A1150 " --> pdb=" O HIS A1146 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N LYS A1151 " --> pdb=" O GLN A1147 " (cutoff:3.500A) Processing helix chain 'A' and resid 1202 through 1205 No H-bonds generated for 'chain 'A' and resid 1202 through 1205' Processing helix chain 'A' and resid 1210 through 1224 Processing helix chain 'A' and resid 1233 through 1236 Processing helix chain 'A' and resid 1240 through 1242 No H-bonds generated for 'chain 'A' and resid 1240 through 1242' Processing helix chain 'A' and resid 1254 through 1261 Processing helix chain 'A' and resid 1274 through 1278 Processing helix chain 'A' and resid 1280 through 1290 removed outlier: 3.570A pdb=" N MET A1283 " --> pdb=" O ILE A1280 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N SER A1284 " --> pdb=" O ASN A1281 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N MET A1289 " --> pdb=" O TRP A1286 " (cutoff:3.500A) Processing helix chain 'A' and resid 1307 through 1320 Processing helix chain 'A' and resid 1337 through 1346 Processing helix chain 'A' and resid 1352 through 1357 removed outlier: 3.540A pdb=" N GLU A1357 " --> pdb=" O LEU A1353 " (cutoff:3.500A) Processing helix chain 'A' and resid 1362 through 1364 No H-bonds generated for 'chain 'A' and resid 1362 through 1364' Processing helix chain 'A' and resid 1390 through 1396 Processing helix chain 'A' and resid 1425 through 1429 removed outlier: 3.622A pdb=" N ALA A1429 " --> pdb=" O LEU A1426 " (cutoff:3.500A) Processing helix chain 'A' and resid 1441 through 1443 No H-bonds generated for 'chain 'A' and resid 1441 through 1443' Processing helix chain 'A' and resid 1445 through 1474 removed outlier: 3.599A pdb=" N LYS A1471 " --> pdb=" O LEU A1467 " (cutoff:3.500A) Processing helix chain 'A' and resid 1479 through 1509 removed outlier: 4.048A pdb=" N ASN A1483 " --> pdb=" O SER A1479 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N GLU A1484 " --> pdb=" O GLU A1480 " (cutoff:3.500A) Processing helix chain 'A' and resid 1521 through 1529 removed outlier: 4.552A pdb=" N TYR A1529 " --> pdb=" O ALA A1525 " (cutoff:3.500A) Processing helix chain 'A' and resid 1547 through 1564 removed outlier: 4.136A pdb=" N LYS A1551 " --> pdb=" O LYS A1547 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU A1564 " --> pdb=" O MET A1560 " (cutoff:3.500A) Processing helix chain 'A' and resid 1578 through 1581 No H-bonds generated for 'chain 'A' and resid 1578 through 1581' Processing helix chain 'A' and resid 1585 through 1602 removed outlier: 4.279A pdb=" N GLY A1589 " --> pdb=" O GLY A1586 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ALA A1590 " --> pdb=" O ALA A1587 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N MET A1592 " --> pdb=" O GLY A1589 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N MET A1593 " --> pdb=" O ALA A1590 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N LEU A1600 " --> pdb=" O LEU A1597 " (cutoff:3.500A) Processing helix chain 'A' and resid 1616 through 1620 Processing helix chain 'A' and resid 1658 through 1664 removed outlier: 4.360A pdb=" N GLY A1663 " --> pdb=" O TYR A1660 " (cutoff:3.500A) Processing helix chain 'A' and resid 1667 through 1693 Processing helix chain 'A' and resid 1711 through 1716 Processing helix chain 'A' and resid 1735 through 1737 No H-bonds generated for 'chain 'A' and resid 1735 through 1737' Processing helix chain 'A' and resid 1741 through 1744 No H-bonds generated for 'chain 'A' and resid 1741 through 1744' Processing helix chain 'A' and resid 1747 through 1759 removed outlier: 3.622A pdb=" N MET A1759 " --> pdb=" O MET A1755 " (cutoff:3.500A) 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 removed outlier: 3.644A pdb=" N ARG A1789 " --> pdb=" O THR A1785 " (cutoff:3.500A) Processing helix chain 'A' and resid 1795 through 1801 removed outlier: 3.607A 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 1834 through 1836 No H-bonds generated for 'chain 'A' and resid 1834 through 1836' Processing helix chain 'A' and resid 1854 through 1861 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 193 Processing helix chain 'B' and resid 206 through 214 removed outlier: 4.028A pdb=" N GLU B 211 " --> pdb=" O GLU B 207 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N THR B 212 " --> pdb=" O GLU B 208 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 235 Processing helix chain 'B' and resid 243 through 253 Processing helix chain 'B' and resid 258 through 271 removed outlier: 3.592A pdb=" N GLY B 263 " --> pdb=" O GLY B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 298 Processing helix chain 'G' and resid 24 through 40 removed outlier: 3.566A pdb=" N PHE G 27 " --> pdb=" O THR G 24 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N PHE G 28 " --> pdb=" O ALA G 25 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N ILE G 29 " --> pdb=" O SER G 26 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N SER G 31 " --> pdb=" O PHE G 28 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLN G 32 " --> pdb=" O ILE G 29 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LEU G 33 " --> pdb=" O ALA G 30 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N GLN G 34 " --> pdb=" O SER G 31 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLN G 36 " --> pdb=" O LEU G 33 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N PHE G 37 " --> pdb=" O GLN G 34 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ASN G 38 " --> pdb=" O GLU G 35 " (cutoff:3.500A) Processing helix chain 'G' and resid 59 through 71 removed outlier: 3.888A pdb=" N LEU G 71 " --> pdb=" O TYR G 67 " (cutoff:3.500A) Processing helix chain 'G' and resid 80 through 95 Processing helix chain 'G' and resid 101 through 111 Processing helix chain 'G' and resid 116 through 132 removed outlier: 3.667A pdb=" N LYS G 120 " --> pdb=" O LEU G 116 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N LEU G 122 " --> pdb=" O LYS G 118 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LYS G 124 " --> pdb=" O LYS G 120 " (cutoff:3.500A) 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: 6.807A pdb=" N ASP G 186 " --> pdb=" O VAL G 182 " (cutoff:3.500A) removed outlier: 5.372A pdb=" N LEU G 187 " --> pdb=" O LEU G 183 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ARG G 200 " --> pdb=" O SER G 196 " (cutoff:3.500A) Processing helix chain 'G' and resid 205 through 208 No H-bonds generated for 'chain 'G' and resid 205 through 208' Processing helix chain 'G' and resid 215 through 220 Processing helix chain 'G' and resid 228 through 232 Processing helix chain 'G' and resid 234 through 255 Proline residue: G 239 - end of helix Processing helix chain 'G' and resid 260 through 266 Processing helix chain 'G' and resid 276 through 285 removed outlier: 3.560A pdb=" N ALA G 280 " --> pdb=" O LEU G 277 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N VAL G 281 " --> pdb=" O VAL G 278 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ILE G 283 " --> pdb=" O ALA G 280 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ALA G 284 " --> pdb=" O VAL G 281 " (cutoff:3.500A) Processing helix chain 'G' and resid 295 through 313 Processing helix chain 'G' and resid 321 through 329 Processing helix chain 'G' and resid 346 through 359 removed outlier: 3.923A 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: 3.689A 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 445 Proline residue: G 434 - end of helix removed outlier: 4.157A pdb=" N ASP G 437 " --> pdb=" O PRO G 434 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LEU G 443 " --> pdb=" O ASN G 440 " (cutoff:3.500A) Processing helix chain 'G' and resid 475 through 484 Processing helix chain 'G' and resid 490 through 493 No H-bonds generated for 'chain 'G' and resid 490 through 493' Processing helix chain 'G' and resid 508 through 510 No H-bonds generated for 'chain 'G' and resid 508 through 510' Processing helix chain 'G' and resid 512 through 519 Processing helix chain 'G' and resid 544 through 548 removed outlier: 3.779A pdb=" N PHE G 548 " --> pdb=" O LYS G 544 " (cutoff:3.500A) No H-bonds generated for '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: 3.531A pdb=" N LEU G 586 " --> pdb=" O LYS G 582 " (cutoff:3.500A) Processing helix chain 'G' and resid 604 through 613 removed outlier: 3.622A pdb=" N ALA G 609 " --> pdb=" O ASP G 605 " (cutoff:3.500A) Processing helix chain 'G' and resid 621 through 623 No H-bonds generated for 'chain 'G' and resid 621 through 623' Processing helix chain 'G' and resid 627 through 638 Processing helix chain 'G' and resid 656 through 671 removed outlier: 3.825A pdb=" N TRP G 661 " --> pdb=" O PHE G 657 " (cutoff:3.500A) Proline residue: G 664 - end of helix Processing helix chain 'G' and resid 688 through 697 removed outlier: 3.582A pdb=" N GLU G 693 " --> pdb=" O GLU G 689 " (cutoff:3.500A) Processing helix chain 'G' and resid 710 through 722 Processing helix chain 'G' and resid 748 through 758 removed outlier: 5.458A pdb=" N SER G 755 " --> pdb=" O LEU G 751 " (cutoff:3.500A) removed outlier: 5.657A pdb=" N LYS G 756 " --> pdb=" O GLN G 752 " (cutoff:3.500A) Processing helix chain 'G' and resid 775 through 782 Proline residue: G 779 - end of helix Processing helix chain 'G' and resid 786 through 789 Processing helix chain 'G' and resid 803 through 805 No H-bonds generated for 'chain 'G' and resid 803 through 805' Processing helix chain 'G' and resid 815 through 823 Processing helix chain 'G' and resid 832 through 834 No H-bonds generated for 'chain 'G' and resid 832 through 834' Processing helix chain 'G' and resid 860 through 871 removed outlier: 4.026A pdb=" N TRP G 865 " --> pdb=" O GLY G 861 " (cutoff:3.500A) Processing helix chain 'G' and resid 877 through 886 removed outlier: 4.191A pdb=" N VAL G 881 " --> pdb=" O LYS G 877 " (cutoff:3.500A) Proline residue: G 882 - end of helix Processing helix chain 'G' and resid 888 through 898 Processing helix chain 'G' and resid 914 through 916 No H-bonds generated for 'chain 'G' and resid 914 through 916' Processing helix chain 'G' and resid 919 through 930 Processing helix chain 'G' and resid 941 through 958 Processing helix chain 'G' and resid 970 through 974 Processing helix chain 'G' and resid 976 through 986 removed outlier: 4.501A pdb=" N ILE G 980 " --> pdb=" O ASP G 977 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N GLU G 981 " --> pdb=" O GLU G 978 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LYS G 982 " --> pdb=" O ALA G 979 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N PHE G 984 " --> pdb=" O GLU G 981 " (cutoff:3.500A) Processing helix chain 'G' and resid 988 through 991 Processing helix chain 'G' and resid 997 through 1008 removed outlier: 3.809A pdb=" N GLN G1008 " --> pdb=" O LEU G1004 " (cutoff:3.500A) Processing helix chain 'G' and resid 1023 through 1030 removed outlier: 3.610A pdb=" N GLU G1026 " --> pdb=" O ARG G1023 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N PHE G1029 " --> pdb=" O GLU G1026 " (cutoff:3.500A) Processing helix chain 'G' and resid 1035 through 1038 Processing helix chain 'G' and resid 1048 through 1050 No H-bonds generated for 'chain 'G' and resid 1048 through 1050' Processing helix chain 'G' and resid 1059 through 1062 Processing helix chain 'G' and resid 1070 through 1088 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 removed outlier: 3.543A pdb=" N PHE G1154 " --> pdb=" O ARG G1150 " (cutoff:3.500A) Processing helix chain 'G' and resid 1169 through 1173 Processing helix chain 'G' and resid 1258 through 1270 removed outlier: 3.558A pdb=" N LYS G1268 " --> pdb=" O GLU G1264 " (cutoff:3.500A) Processing helix chain 'G' and resid 1294 through 1303 Processing helix chain 'G' and resid 1309 through 1311 No H-bonds generated for 'chain 'G' and resid 1309 through 1311' Processing helix chain 'G' and resid 1325 through 1339 removed outlier: 3.806A pdb=" N GLY G1330 " --> pdb=" O ILE G1327 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N ARG G1332 " --> pdb=" O VAL G1329 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N ILE G1335 " --> pdb=" O ARG G1332 " (cutoff:3.500A) Processing helix chain 'G' and resid 1438 through 1446 Processing helix chain 'G' and resid 1515 through 1522 Processing helix chain 'G' and resid 1551 through 1557 removed outlier: 3.814A pdb=" N VAL G1556 " --> pdb=" O PRO G1552 " (cutoff:3.500A) Processing helix chain 'G' and resid 1562 through 1564 No H-bonds generated for 'chain 'G' and resid 1562 through 1564' Processing helix chain 'G' and resid 1567 through 1572 Processing helix chain 'G' and resid 1582 through 1596 Processing helix chain 'G' and resid 1678 through 1683 removed outlier: 3.636A pdb=" N THR G1683 " --> pdb=" O ASP G1679 " (cutoff:3.500A) Processing helix chain 'G' and resid 1686 through 1701 removed outlier: 3.581A pdb=" N VAL G1690 " --> pdb=" O ALA G1686 " (cutoff:3.500A) Processing helix chain 'G' and resid 1706 through 1711 Processing helix chain 'G' and resid 1724 through 1735 removed outlier: 3.588A pdb=" N ARG G1728 " --> pdb=" O GLU G1724 " (cutoff:3.500A) 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 1794 Proline residue: G1779 - end of helix Processing helix chain 'G' and resid 1810 through 1818 Processing helix chain 'G' and resid 1824 through 1840 removed outlier: 3.695A pdb=" N GLU G1829 " --> pdb=" O GLU G1825 " (cutoff:3.500A) Processing helix chain 'G' and resid 1859 through 1862 No H-bonds generated for 'chain 'G' and resid 1859 through 1862' Processing helix chain 'G' and resid 1868 through 1882 removed outlier: 3.523A pdb=" N TYR G1873 " --> pdb=" O GLU G1869 " (cutoff:3.500A) Processing helix chain 'G' and resid 1906 through 1920 removed outlier: 3.830A pdb=" N LYS G1918 " --> pdb=" O LEU G1914 " (cutoff:3.500A) Processing helix chain 'G' and resid 1924 through 1929 removed outlier: 3.654A pdb=" N LYS G1929 " --> pdb=" O ILE G1925 " (cutoff:3.500A) Processing helix chain 'G' and resid 1935 through 1948 removed outlier: 4.009A pdb=" N ILE G1943 " --> pdb=" O HIS G1939 " (cutoff:3.500A) Processing helix chain 'G' and resid 1979 through 1995 removed outlier: 4.664A pdb=" N ASN G1983 " --> pdb=" O TYR G1980 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N LYS G1986 " --> pdb=" O ASN G1983 " (cutoff:3.500A) Proline residue: G1987 - end of helix removed outlier: 3.602A pdb=" N LEU G1992 " --> pdb=" O LYS G1989 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LYS G1993 " --> pdb=" O SER G1990 " (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 2037 through 2046 removed outlier: 5.483A pdb=" N GLU G2046 " --> pdb=" O ILE G2042 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 43 through 46 removed outlier: 6.821A pdb=" N GLU A 77 " --> pdb=" O VAL A 44 " (cutoff:3.500A) removed outlier: 7.783A pdb=" N GLU A 46 " --> pdb=" O GLU A 77 " (cutoff:3.500A) removed outlier: 6.741A 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: 7.033A pdb=" N VAL A 678 " --> pdb=" O VAL A 704 " (cutoff:3.500A) removed outlier: 8.049A pdb=" N THR A 706 " --> pdb=" O VAL A 678 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N ILE A 680 " --> pdb=" O THR A 706 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N ALA A 767 " --> pdb=" O LEU A 679 " (cutoff:3.500A) removed outlier: 8.486A pdb=" N THR A 681 " --> pdb=" O ALA A 767 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N ILE A 769 " --> pdb=" O THR A 681 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 500 through 503 Processing sheet with id= D, first strand: chain 'A' and resid 641 through 643 Processing sheet with id= E, first strand: chain 'A' and resid 820 through 822 Processing sheet with id= F, first strand: chain 'A' and resid 1060 through 1066 Processing sheet with id= G, first strand: chain 'A' and resid 1119 through 1126 removed outlier: 3.982A pdb=" N MET A1121 " --> pdb=" O LYS A1177 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 1134 through 1136 Processing sheet with id= I, first strand: chain 'A' and resid 1243 through 1245 removed outlier: 6.709A pdb=" N ILE A1326 " --> pdb=" O GLY A1244 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLY A1023 " --> pdb=" O ILE A1386 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N MET A1388 " --> pdb=" O VAL A1021 " (cutoff:3.500A) removed outlier: 5.234A pdb=" N VAL A1021 " --> pdb=" O MET A1388 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'A' and resid 1403 through 1410 removed outlier: 6.671A pdb=" N ILE A1654 " --> pdb=" O ALA A1405 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N ALA A1407 " --> pdb=" O GLN A1652 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N GLN A1652 " --> pdb=" O ALA A1407 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N THR A1409 " --> pdb=" O GLY A1650 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N GLY A1650 " --> pdb=" O THR A1409 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N VAL A1538 " --> pdb=" O SER A1640 " (cutoff:3.500A) removed outlier: 8.350A pdb=" N THR A1642 " --> pdb=" O VAL A1538 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N SER A1540 " --> pdb=" O THR A1642 " (cutoff:3.500A) removed outlier: 8.680A pdb=" N PHE A1644 " --> pdb=" O SER A1540 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N ILE A1573 " --> pdb=" O ALA A1539 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'A' and resid 1768 through 1775 Processing sheet with id= L, first strand: chain 'A' and resid 1837 through 1840 Processing sheet with id= M, first strand: chain 'G' and resid 6 through 13 removed outlier: 3.586A pdb=" N LEU G 16 " --> pdb=" O HIS G 13 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'G' and resid 458 through 460 removed outlier: 4.862A pdb=" N GLY G 272 " --> pdb=" O TYR G 460 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N GLY G 269 " --> pdb=" O LEU G 156 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N HIS G 500 " --> pdb=" O VAL G 157 " (cutoff:3.500A) removed outlier: 7.953A pdb=" N ILE G 159 " --> pdb=" O HIS G 500 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N LEU G 502 " --> pdb=" O ILE G 159 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N ARG G 526 " --> pdb=" O ILE G 501 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N ASP G 503 " --> pdb=" O ARG G 526 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N ILE G 528 " --> pdb=" O ASP G 503 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'G' and resid 418 through 420 removed outlier: 6.400A pdb=" N SER G 380 " --> pdb=" O ILE G 368 " (cutoff:3.500A) removed outlier: 5.493A pdb=" N ILE G 368 " --> pdb=" O SER G 380 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'G' and resid 618 through 620 removed outlier: 6.776A pdb=" N GLY G 648 " --> pdb=" O LEU G 619 " (cutoff:3.500A) removed outlier: 7.898A pdb=" N ILE G 649 " --> pdb=" O GLN G 677 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N LEU G 679 " --> pdb=" O ILE G 649 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N LEU G 651 " --> pdb=" O LEU G 679 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N ILE G 681 " --> pdb=" O LEU G 651 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N TYR G 702 " --> pdb=" O LEU G 679 " (cutoff:3.500A) removed outlier: 8.991A pdb=" N ILE G 681 " --> pdb=" O TYR G 702 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N GLY G 704 " --> pdb=" O ILE G 681 " (cutoff:3.500A) removed outlier: 8.118A pdb=" N LEU G 705 " --> pdb=" O PRO G 727 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N ALA G 729 " --> pdb=" O LEU G 705 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'G' and resid 731 through 733 removed outlier: 6.109A pdb=" N ILE G 766 " --> pdb=" O TRP G 732 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N GLY G 798 " --> pdb=" O PHE G 767 " (cutoff:3.500A) No H-bonds generated for sheet with id= Q Processing sheet with id= R, first strand: chain 'G' and resid 843 through 847 Processing sheet with id= S, first strand: chain 'G' and resid 1126 through 1128 Processing sheet with id= T, first strand: chain 'G' and resid 1158 through 1160 Processing sheet with id= U, first strand: chain 'G' and resid 1198 through 1200 Processing sheet with id= V, first strand: chain 'G' and resid 1218 through 1225 Processing sheet with id= W, first strand: chain 'G' and resid 1285 through 1287 removed outlier: 3.740A pdb=" N THR G1374 " --> pdb=" O GLY G1287 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N MET G1404 " --> pdb=" O LEU G1396 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N ARG G1398 " --> pdb=" O PRO G1402 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N SER G1354 " --> pdb=" O SER G1409 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N PHE G1411 " --> pdb=" O HIS G1352 " (cutoff:3.500A) removed outlier: 5.897A pdb=" N HIS G1352 " --> pdb=" O PHE G1411 " (cutoff:3.500A) removed outlier: 7.640A pdb=" N ARG G1413 " --> pdb=" O LEU G1350 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N LEU G1350 " --> pdb=" O ARG G1413 " (cutoff:3.500A) removed outlier: 5.964A pdb=" N LEU G1353 " --> pdb=" O PHE G1612 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N THR G1642 " --> pdb=" O VAL G1650 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N THR G1652 " --> pdb=" O PHE G1640 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N PHE G1640 " --> pdb=" O THR G1652 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N GLU G1654 " --> pdb=" O ILE G1638 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N ILE G1638 " --> pdb=" O GLU G1654 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N GLU G1656 " --> pdb=" O LYS G1636 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N LYS G1636 " --> pdb=" O GLU G1656 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N LYS G1639 " --> pdb=" O HIS G1628 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N HIS G1628 " --> pdb=" O LYS G1639 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N GLU G1641 " --> pdb=" O ILE G1626 " (cutoff:3.500A) removed outlier: 5.532A pdb=" N ILE G1626 " --> pdb=" O GLU G1641 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N ARG G1643 " --> pdb=" O THR G1624 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N THR G1624 " --> pdb=" O ARG G1643 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'G' and resid 1423 through 1427 Processing sheet with id= Y, first strand: chain 'G' and resid 1432 through 1435 removed outlier: 3.514A pdb=" N ILE G1435 " --> pdb=" O LYS G1462 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N LYS G1462 " --> pdb=" O ILE G1435 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'G' and resid 1450 through 1452 Processing sheet with id= AA, first strand: chain 'G' and resid 1716 through 1720 Processing sheet with id= AB, first strand: chain 'G' and resid 1737 through 1741 Processing sheet with id= AC, first strand: chain 'G' and resid 1852 through 1857 removed outlier: 6.497A pdb=" N ALA G1901 " --> pdb=" O ILE G1888 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N ILE G1888 " --> pdb=" O ALA G1901 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N ASP G1903 " --> pdb=" O VAL G1886 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N VAL G1886 " --> pdb=" O ASP G1903 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'G' and resid 1377 through 1382 removed outlier: 6.660A pdb=" N ASP G1391 " --> pdb=" O GLU G1379 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N VAL G1381 " --> pdb=" O ILE G1389 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N ILE G1389 " --> pdb=" O VAL G1381 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'G' and resid 1537 through 1542 removed outlier: 6.964A pdb=" N ILE G1626 " --> pdb=" O ILE G1539 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N VAL G1541 " --> pdb=" O THR G1624 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N THR G1624 " --> pdb=" O VAL G1541 " (cutoff:3.500A) 1090 hydrogen bonds defined for protein. 3003 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: 14.99 Time building geometry restraints manager: 12.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.33: 6547 1.33 - 1.49: 8383 1.49 - 1.64: 15111 1.64 - 1.79: 70 1.79 - 1.95: 117 Bond restraints: 30228 Sorted by residual: bond pdb=" CG MET A1121 " pdb=" SD MET A1121 " ideal model delta sigma weight residual 1.803 1.948 -0.145 2.50e-02 1.60e+03 3.38e+01 bond pdb=" N THR G 56 " pdb=" CA THR G 56 " ideal model delta sigma weight residual 1.455 1.495 -0.040 7.00e-03 2.04e+04 3.32e+01 bond pdb=" N ILE G1798 " pdb=" CA ILE G1798 " ideal model delta sigma weight residual 1.458 1.496 -0.038 7.70e-03 1.69e+04 2.46e+01 bond pdb=" N VAL A 957 " pdb=" CA VAL A 957 " ideal model delta sigma weight residual 1.460 1.502 -0.042 8.60e-03 1.35e+04 2.34e+01 bond pdb=" C TYR A 725 " pdb=" O TYR A 725 " ideal model delta sigma weight residual 1.235 1.288 -0.053 1.10e-02 8.26e+03 2.32e+01 ... (remaining 30223 not shown) Histogram of bond angle deviations from ideal: 94.80 - 103.22: 237 103.22 - 111.64: 11452 111.64 - 120.07: 17978 120.07 - 128.49: 11115 128.49 - 136.91: 162 Bond angle restraints: 40944 Sorted by residual: angle pdb=" CB GLU A 381 " pdb=" CG GLU A 381 " pdb=" CD GLU A 381 " ideal model delta sigma weight residual 112.60 130.57 -17.97 1.70e+00 3.46e-01 1.12e+02 angle pdb=" CB GLU A1317 " pdb=" CG GLU A1317 " pdb=" CD GLU A1317 " ideal model delta sigma weight residual 112.60 124.21 -11.61 1.70e+00 3.46e-01 4.67e+01 angle pdb=" CB GLU A 780 " pdb=" CG GLU A 780 " pdb=" CD GLU A 780 " ideal model delta sigma weight residual 112.60 124.00 -11.40 1.70e+00 3.46e-01 4.50e+01 angle pdb=" CA GLY A1582 " pdb=" C GLY A1582 " pdb=" O GLY A1582 " ideal model delta sigma weight residual 122.52 117.24 5.28 7.90e-01 1.60e+00 4.46e+01 angle pdb=" C GLU B 272 " pdb=" N PRO B 273 " pdb=" CA PRO B 273 " ideal model delta sigma weight residual 119.87 113.04 6.83 1.04e+00 9.25e-01 4.32e+01 ... (remaining 40939 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.09: 16499 18.09 - 36.18: 1403 36.18 - 54.26: 240 54.26 - 72.35: 76 72.35 - 90.44: 32 Dihedral angle restraints: 18250 sinusoidal: 7338 harmonic: 10912 Sorted by residual: dihedral pdb=" CA ALA G 897 " pdb=" C ALA G 897 " pdb=" N ASP G 898 " pdb=" CA ASP G 898 " ideal model delta harmonic sigma weight residual -180.00 -153.23 -26.77 0 5.00e+00 4.00e-02 2.87e+01 dihedral pdb=" CA ILE G1503 " pdb=" C ILE G1503 " pdb=" N VAL G1504 " pdb=" CA VAL G1504 " ideal model delta harmonic sigma weight residual 180.00 155.25 24.75 0 5.00e+00 4.00e-02 2.45e+01 dihedral pdb=" CA GLY A1565 " pdb=" C GLY A1565 " pdb=" N ARG A1566 " pdb=" CA ARG A1566 " ideal model delta harmonic sigma weight residual 180.00 156.16 23.84 0 5.00e+00 4.00e-02 2.27e+01 ... (remaining 18247 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 2092 0.060 - 0.120: 1744 0.120 - 0.181: 648 0.181 - 0.241: 113 0.241 - 0.301: 6 Chirality restraints: 4603 Sorted by residual: chirality pdb=" CA ILE A1326 " pdb=" N ILE A1326 " pdb=" C ILE A1326 " pdb=" CB ILE A1326 " both_signs ideal model delta sigma weight residual False 2.43 2.73 -0.30 2.00e-01 2.50e+01 2.26e+00 chirality pdb=" CA ILE G 652 " pdb=" N ILE G 652 " pdb=" C ILE G 652 " pdb=" CB ILE G 652 " both_signs ideal model delta sigma weight residual False 2.43 2.70 -0.27 2.00e-01 2.50e+01 1.83e+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 2.69 -0.26 2.00e-01 2.50e+01 1.71e+00 ... (remaining 4600 not shown) Planarity restraints: 5285 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A1401 " -0.059 2.00e-02 2.50e+03 2.98e-02 1.77e+01 pdb=" CG TYR A1401 " 0.042 2.00e-02 2.50e+03 pdb=" CD1 TYR A1401 " 0.020 2.00e-02 2.50e+03 pdb=" CD2 TYR A1401 " 0.026 2.00e-02 2.50e+03 pdb=" CE1 TYR A1401 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 TYR A1401 " 0.001 2.00e-02 2.50e+03 pdb=" CZ TYR A1401 " -0.013 2.00e-02 2.50e+03 pdb=" OH TYR A1401 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A1376 " 0.035 2.00e-02 2.50e+03 2.41e-02 1.02e+01 pdb=" CG PHE A1376 " -0.050 2.00e-02 2.50e+03 pdb=" CD1 PHE A1376 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 PHE A1376 " -0.007 2.00e-02 2.50e+03 pdb=" CE1 PHE A1376 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE A1376 " 0.008 2.00e-02 2.50e+03 pdb=" CZ PHE A1376 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 718 " -0.043 2.00e-02 2.50e+03 2.15e-02 9.28e+00 pdb=" CG TYR A 718 " 0.027 2.00e-02 2.50e+03 pdb=" CD1 TYR A 718 " 0.020 2.00e-02 2.50e+03 pdb=" CD2 TYR A 718 " 0.016 2.00e-02 2.50e+03 pdb=" CE1 TYR A 718 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR A 718 " 0.006 2.00e-02 2.50e+03 pdb=" CZ TYR A 718 " -0.005 2.00e-02 2.50e+03 pdb=" OH TYR A 718 " -0.021 2.00e-02 2.50e+03 ... (remaining 5282 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 667 2.68 - 3.23: 28919 3.23 - 3.79: 46336 3.79 - 4.34: 65241 4.34 - 4.90: 104638 Nonbonded interactions: 245801 Sorted by model distance: nonbonded pdb=" O GLY B 222 " pdb=" OG SER B 226 " model vdw 2.124 2.440 nonbonded pdb=" O VAL G1443 " pdb=" OG SER G1446 " model vdw 2.202 2.440 nonbonded pdb=" O GLN G 456 " pdb=" NH1 ARG G 469 " model vdw 2.204 2.520 nonbonded pdb=" O PHE G1419 " pdb=" OG1 THR G1422 " model vdw 2.205 2.440 nonbonded pdb=" OE1 GLU A1107 " pdb=" OG1 THR A1191 " model vdw 2.207 2.440 ... (remaining 245796 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 group one per residue 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: 0.600 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: 4.950 Check model and map are aligned: 0.470 Set scattering table: 0.270 Process input model: 83.200 Find NCS groups from input model: 1.010 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 93.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.014 0.145 30228 Z= 0.915 Angle : 1.890 17.974 40944 Z= 1.379 Chirality : 0.086 0.301 4603 Planarity : 0.006 0.030 5285 Dihedral : 14.721 90.442 11219 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.48 % Allowed : 7.29 % Favored : 92.24 % Rotamer: Outliers : 0.22 % Allowed : 3.70 % Favored : 96.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.55 (0.11), residues: 3761 helix: -2.57 (0.10), residues: 1628 sheet: -2.36 (0.21), residues: 460 loop : -1.93 (0.14), residues: 1673 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.006 TRP A1286 HIS 0.015 0.003 HIS G1697 PHE 0.050 0.004 PHE A1376 TYR 0.059 0.005 TYR A1401 ARG 0.010 0.001 ARG A1430 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 3246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 309 time to evaluate : 3.779 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 352 MET cc_start: 0.8767 (ttm) cc_final: 0.8557 (tpp) REVERT: A 384 GLU cc_start: 0.9175 (mt-10) cc_final: 0.8936 (pt0) REVERT: A 419 GLU cc_start: 0.9347 (mt-10) cc_final: 0.8952 (mt-10) REVERT: A 440 MET cc_start: 0.9522 (mmm) cc_final: 0.9283 (mmm) REVERT: A 847 GLU cc_start: 0.9146 (mp0) cc_final: 0.8873 (mp0) REVERT: A 952 GLU cc_start: 0.9043 (pp20) cc_final: 0.8837 (pp20) REVERT: A 991 ASP cc_start: 0.9180 (t0) cc_final: 0.8961 (t0) REVERT: A 1268 GLU cc_start: 0.9191 (mm-30) cc_final: 0.8830 (tt0) REVERT: A 1273 ASP cc_start: 0.9187 (p0) cc_final: 0.8895 (p0) REVERT: A 1338 GLU cc_start: 0.8694 (mp0) cc_final: 0.8070 (mt-10) REVERT: A 1430 ARG cc_start: 0.4923 (tmt-80) cc_final: 0.4315 (tpt170) REVERT: A 1646 PHE cc_start: 0.9128 (m-10) cc_final: 0.8925 (m-10) REVERT: A 1649 LYS cc_start: 0.4656 (mmtt) cc_final: 0.4039 (mmtt) REVERT: A 1690 ASN cc_start: 0.9580 (t0) cc_final: 0.9330 (t0) REVERT: A 1819 VAL cc_start: 0.8493 (t) cc_final: 0.8267 (m) REVERT: B 185 GLU cc_start: 0.9078 (mt-10) cc_final: 0.8750 (mt-10) REVERT: B 211 GLU cc_start: 0.8926 (mp0) cc_final: 0.8685 (mp0) REVERT: B 292 GLN cc_start: 0.9198 (mp10) cc_final: 0.8834 (mp10) REVERT: B 301 ASP cc_start: 0.8556 (t0) cc_final: 0.8201 (t0) REVERT: G 764 MET cc_start: 0.9038 (ttm) cc_final: 0.8834 (ttm) REVERT: G 863 MET cc_start: 0.9164 (mmm) cc_final: 0.8832 (mmm) REVERT: G 870 GLU cc_start: 0.9327 (mt-10) cc_final: 0.9088 (pt0) REVERT: G 1221 MET cc_start: 0.8830 (tmm) cc_final: 0.8557 (tmm) REVERT: G 1229 MET cc_start: 0.4974 (tpt) cc_final: 0.4685 (tpt) REVERT: G 1323 MET cc_start: 0.6898 (ptp) cc_final: 0.6463 (ptp) REVERT: G 1359 MET cc_start: 0.6497 (tpp) cc_final: 0.5625 (tpt) REVERT: G 1784 MET cc_start: 0.8140 (tmm) cc_final: 0.7308 (tmm) REVERT: G 1829 GLU cc_start: 0.9153 (mt-10) cc_final: 0.8950 (mm-30) REVERT: G 1838 MET cc_start: 0.9001 (tmm) cc_final: 0.8736 (tmm) REVERT: G 1876 GLU cc_start: 0.7583 (tp30) cc_final: 0.7318 (tp30) REVERT: G 2005 ARG cc_start: 0.8291 (mtp85) cc_final: 0.7982 (mtp180) outliers start: 7 outliers final: 0 residues processed: 311 average time/residue: 0.4306 time to fit residues: 212.6779 Evaluate side-chains 218 residues out of total 3246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 218 time to evaluate : 3.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 317 optimal weight: 6.9990 chunk 284 optimal weight: 8.9990 chunk 158 optimal weight: 6.9990 chunk 97 optimal weight: 5.9990 chunk 192 optimal weight: 9.9990 chunk 152 optimal weight: 4.9990 chunk 294 optimal weight: 0.8980 chunk 114 optimal weight: 5.9990 chunk 179 optimal weight: 30.0000 chunk 219 optimal weight: 6.9990 chunk 341 optimal weight: 7.9990 overall best weight: 4.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 GLN A 341 GLN A 344 GLN A 374 GLN A 379 ASN ** A 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 506 ASN A 527 GLN A 777 GLN A 821 GLN A 983 GLN A 987 ASN A 989 GLN A1000 GLN A1207 GLN A1380 GLN A1542 HIS A1648 GLN A1652 GLN ** A1845 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1854 ASN ** B 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 271 ASN G 79 GLN ** G 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 163 GLN G 181 HIS G 330 ASN G 354 ASN G 390 ASN G 440 ASN G 747 HIS ** G1055 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G1061 GLN G1078 HIS G1217 ASN G1355 ASN G1595 ASN G1619 ASN G1659 GLN G1697 HIS ** G1896 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G1912 ASN Total number of N/Q/H flips: 37 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.1481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 30228 Z= 0.288 Angle : 0.582 8.561 40944 Z= 0.302 Chirality : 0.042 0.178 4603 Planarity : 0.004 0.040 5285 Dihedral : 5.004 83.142 4028 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.30 % Favored : 96.57 % Rotamer: Outliers : 0.83 % Allowed : 7.67 % Favored : 91.49 % 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: -1.24 (0.13), residues: 3761 helix: -0.25 (0.12), residues: 1651 sheet: -1.72 (0.22), residues: 515 loop : -0.96 (0.15), residues: 1595 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP G1449 HIS 0.013 0.001 HIS G 102 PHE 0.020 0.002 PHE B 241 TYR 0.014 0.002 TYR A 511 ARG 0.006 0.000 ARG G1956 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 3246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 242 time to evaluate : 3.480 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ILE cc_start: 0.8624 (mm) cc_final: 0.8139 (tp) REVERT: A 384 GLU cc_start: 0.9178 (mt-10) cc_final: 0.8904 (pt0) REVERT: A 847 GLU cc_start: 0.9128 (mp0) cc_final: 0.8748 (tm-30) REVERT: A 923 MET cc_start: 0.8066 (ttp) cc_final: 0.7803 (ttp) REVERT: A 946 GLU cc_start: 0.9218 (mp0) cc_final: 0.8880 (pp20) REVERT: A 1128 GLU cc_start: 0.8677 (mt-10) cc_final: 0.7938 (mp0) REVERT: A 1268 GLU cc_start: 0.9130 (mm-30) cc_final: 0.8701 (tt0) REVERT: A 1273 ASP cc_start: 0.8936 (p0) cc_final: 0.8592 (p0) REVERT: A 1338 GLU cc_start: 0.8677 (mp0) cc_final: 0.7974 (mt-10) REVERT: A 1498 GLU cc_start: 0.8900 (tt0) cc_final: 0.8517 (tp30) REVERT: A 1646 PHE cc_start: 0.9017 (m-10) cc_final: 0.8808 (m-10) REVERT: A 1649 LYS cc_start: 0.4271 (mmtt) cc_final: 0.3826 (mmtt) REVERT: A 1759 MET cc_start: 0.7634 (tmm) cc_final: 0.7168 (tmm) REVERT: B 185 GLU cc_start: 0.8743 (mt-10) cc_final: 0.8417 (mt-10) REVERT: B 211 GLU cc_start: 0.9035 (mp0) cc_final: 0.8820 (mp0) REVERT: B 237 MET cc_start: 0.8846 (mmm) cc_final: 0.8607 (tpp) REVERT: B 290 MET cc_start: 0.9138 (mmt) cc_final: 0.8924 (mmt) REVERT: B 301 ASP cc_start: 0.8581 (t0) cc_final: 0.8325 (t0) REVERT: G 132 MET cc_start: 0.8728 (mpp) cc_final: 0.8506 (mpp) REVERT: G 331 ASN cc_start: 0.9285 (m110) cc_final: 0.9071 (m-40) REVERT: G 447 ASN cc_start: 0.9049 (m-40) cc_final: 0.8391 (p0) REVERT: G 764 MET cc_start: 0.8822 (ttm) cc_final: 0.8598 (ttm) REVERT: G 794 MET cc_start: 0.9212 (tpp) cc_final: 0.8622 (mmt) REVERT: G 870 GLU cc_start: 0.9265 (mt-10) cc_final: 0.8951 (pt0) REVERT: G 1221 MET cc_start: 0.8595 (tmm) cc_final: 0.8348 (tmm) REVERT: G 1265 MET cc_start: 0.9389 (tmm) cc_final: 0.9184 (tmm) REVERT: G 1359 MET cc_start: 0.5914 (tpp) cc_final: 0.5097 (tpt) REVERT: G 1784 MET cc_start: 0.8459 (tmm) cc_final: 0.7865 (tmm) REVERT: G 1822 MET cc_start: 0.8508 (ptp) cc_final: 0.8152 (ptp) REVERT: G 1838 MET cc_start: 0.9056 (tmm) cc_final: 0.8818 (tmm) REVERT: G 1876 GLU cc_start: 0.7390 (tp30) cc_final: 0.7119 (tp30) REVERT: G 2005 ARG cc_start: 0.8355 (mtp85) cc_final: 0.7844 (tpp-160) outliers start: 27 outliers final: 13 residues processed: 259 average time/residue: 0.4105 time to fit residues: 172.1824 Evaluate side-chains 222 residues out of total 3246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 209 time to evaluate : 3.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1168 LEU Chi-restraints excluded: chain A residue 1270 VAL Chi-restraints excluded: chain A residue 1732 THR Chi-restraints excluded: chain A residue 1873 HIS Chi-restraints excluded: chain B residue 171 THR Chi-restraints excluded: chain G residue 329 GLU Chi-restraints excluded: chain G residue 389 LEU Chi-restraints excluded: chain G residue 417 SER Chi-restraints excluded: chain G residue 1245 ASP Chi-restraints excluded: chain G residue 1486 PHE Chi-restraints excluded: chain G residue 1511 SER Chi-restraints excluded: chain G residue 1939 HIS Chi-restraints excluded: chain G residue 1983 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 189 optimal weight: 20.0000 chunk 105 optimal weight: 7.9990 chunk 284 optimal weight: 8.9990 chunk 232 optimal weight: 6.9990 chunk 94 optimal weight: 3.9990 chunk 342 optimal weight: 0.2980 chunk 369 optimal weight: 6.9990 chunk 304 optimal weight: 0.7980 chunk 339 optimal weight: 5.9990 chunk 116 optimal weight: 6.9990 chunk 274 optimal weight: 4.9990 overall best weight: 3.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 713 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1380 GLN A1482 GLN A1845 ASN ** B 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 163 GLN ** G1055 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G1619 ASN ** G1896 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.1709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 30228 Z= 0.199 Angle : 0.510 8.677 40944 Z= 0.261 Chirality : 0.041 0.154 4603 Planarity : 0.003 0.036 5285 Dihedral : 4.597 76.369 4028 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.40 % Favored : 96.46 % Rotamer: Outliers : 0.89 % Allowed : 9.03 % Favored : 90.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.14), residues: 3761 helix: 0.67 (0.13), residues: 1645 sheet: -1.45 (0.22), residues: 523 loop : -0.55 (0.16), residues: 1593 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1030 HIS 0.010 0.001 HIS G 102 PHE 0.014 0.001 PHE A 450 TYR 0.012 0.001 TYR A 511 ARG 0.004 0.000 ARG A 709 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 3246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 245 time to evaluate : 3.152 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ILE cc_start: 0.8623 (mm) cc_final: 0.8111 (tp) REVERT: A 384 GLU cc_start: 0.9172 (mt-10) cc_final: 0.8901 (pt0) REVERT: A 435 GLU cc_start: 0.9133 (tt0) cc_final: 0.8861 (tt0) REVERT: A 826 MET cc_start: 0.9134 (mmm) cc_final: 0.8659 (mtp) REVERT: A 847 GLU cc_start: 0.9145 (mp0) cc_final: 0.8743 (tm-30) REVERT: A 946 GLU cc_start: 0.9175 (OUTLIER) cc_final: 0.8874 (pp20) REVERT: A 1128 GLU cc_start: 0.8631 (mt-10) cc_final: 0.7883 (mp0) REVERT: A 1273 ASP cc_start: 0.9026 (p0) cc_final: 0.8613 (p0) REVERT: A 1338 GLU cc_start: 0.8659 (mp0) cc_final: 0.7934 (mt-10) REVERT: A 1498 GLU cc_start: 0.8886 (tt0) cc_final: 0.8459 (tp30) REVERT: A 1646 PHE cc_start: 0.8999 (m-10) cc_final: 0.8790 (m-10) REVERT: A 1649 LYS cc_start: 0.4308 (mmtt) cc_final: 0.3828 (mmtt) REVERT: B 185 GLU cc_start: 0.8829 (mt-10) cc_final: 0.8493 (mt-10) REVERT: B 211 GLU cc_start: 0.9037 (mp0) cc_final: 0.8806 (mp0) REVERT: B 237 MET cc_start: 0.8718 (mmm) cc_final: 0.8410 (tpp) REVERT: B 301 ASP cc_start: 0.8519 (t0) cc_final: 0.8231 (t0) REVERT: G 132 MET cc_start: 0.8669 (mpp) cc_final: 0.8218 (mmt) REVERT: G 167 ASP cc_start: 0.8411 (p0) cc_final: 0.8120 (p0) REVERT: G 245 GLN cc_start: 0.8863 (OUTLIER) cc_final: 0.8514 (mm-40) REVERT: G 447 ASN cc_start: 0.9028 (m-40) cc_final: 0.8337 (p0) REVERT: G 794 MET cc_start: 0.9176 (tpp) cc_final: 0.8557 (mmt) REVERT: G 870 GLU cc_start: 0.9269 (mt-10) cc_final: 0.8998 (pt0) REVERT: G 1164 MET cc_start: 0.8238 (mmm) cc_final: 0.7830 (tpp) REVERT: G 1221 MET cc_start: 0.8625 (tmm) cc_final: 0.8367 (tmm) REVERT: G 1265 MET cc_start: 0.9424 (tmm) cc_final: 0.9198 (tmm) REVERT: G 1359 MET cc_start: 0.5832 (tpp) cc_final: 0.4994 (tpt) REVERT: G 1631 MET cc_start: 0.8370 (mmm) cc_final: 0.7595 (mmm) REVERT: G 1784 MET cc_start: 0.8499 (tmm) cc_final: 0.7889 (tmm) REVERT: G 1822 MET cc_start: 0.8479 (ptp) cc_final: 0.8108 (ptp) REVERT: G 1838 MET cc_start: 0.9067 (tmm) cc_final: 0.8815 (tmm) REVERT: G 1876 GLU cc_start: 0.7388 (tp30) cc_final: 0.7109 (tp30) REVERT: G 2005 ARG cc_start: 0.8319 (mtp85) cc_final: 0.7826 (tpp-160) outliers start: 29 outliers final: 15 residues processed: 264 average time/residue: 0.4241 time to fit residues: 182.1146 Evaluate side-chains 228 residues out of total 3246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 211 time to evaluate : 4.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 946 GLU Chi-restraints excluded: chain A residue 1168 LEU Chi-restraints excluded: chain A residue 1189 ILE Chi-restraints excluded: chain A residue 1270 VAL Chi-restraints excluded: chain A residue 1730 SER Chi-restraints excluded: chain A residue 1732 THR Chi-restraints excluded: chain A residue 1746 ASN Chi-restraints excluded: chain A residue 1873 HIS Chi-restraints excluded: chain B residue 292 GLN Chi-restraints excluded: chain G residue 145 LEU Chi-restraints excluded: chain G residue 245 GLN Chi-restraints excluded: chain G residue 329 GLU Chi-restraints excluded: chain G residue 351 ASP Chi-restraints excluded: chain G residue 389 LEU Chi-restraints excluded: chain G residue 1417 THR Chi-restraints excluded: chain G residue 1511 SER Chi-restraints excluded: chain G residue 1939 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 337 optimal weight: 40.0000 chunk 257 optimal weight: 3.9990 chunk 177 optimal weight: 0.7980 chunk 37 optimal weight: 7.9990 chunk 163 optimal weight: 4.9990 chunk 229 optimal weight: 8.9990 chunk 343 optimal weight: 20.0000 chunk 363 optimal weight: 30.0000 chunk 179 optimal weight: 7.9990 chunk 325 optimal weight: 7.9990 chunk 97 optimal weight: 4.9990 overall best weight: 4.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 713 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1380 GLN A1433 HIS A1794 GLN ** B 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 165 ASN ** G1055 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G1226 ASN G1619 ASN ** G1896 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1897 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.1934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 30228 Z= 0.258 Angle : 0.535 10.246 40944 Z= 0.272 Chirality : 0.041 0.156 4603 Planarity : 0.003 0.036 5285 Dihedral : 4.556 69.076 4028 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.40 % Favored : 96.52 % Rotamer: Outliers : 1.48 % Allowed : 10.45 % Favored : 88.07 % 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: -0.07 (0.14), residues: 3761 helix: 0.81 (0.13), residues: 1659 sheet: -1.31 (0.22), residues: 515 loop : -0.38 (0.16), residues: 1587 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1030 HIS 0.010 0.001 HIS G 102 PHE 0.019 0.001 PHE A 35 TYR 0.015 0.001 TYR G 67 ARG 0.004 0.000 ARG B 247 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 3246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 224 time to evaluate : 2.939 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ILE cc_start: 0.8622 (mm) cc_final: 0.8024 (tp) REVERT: A 384 GLU cc_start: 0.9176 (mt-10) cc_final: 0.8905 (pt0) REVERT: A 826 MET cc_start: 0.9098 (mmm) cc_final: 0.8663 (mtp) REVERT: A 847 GLU cc_start: 0.9190 (mp0) cc_final: 0.8982 (mp0) REVERT: A 946 GLU cc_start: 0.9185 (OUTLIER) cc_final: 0.8873 (pp20) REVERT: A 1124 GLU cc_start: 0.9263 (tt0) cc_final: 0.8972 (tt0) REVERT: A 1128 GLU cc_start: 0.8637 (mt-10) cc_final: 0.7866 (mp0) REVERT: A 1273 ASP cc_start: 0.8976 (p0) cc_final: 0.8592 (p0) REVERT: A 1333 ASP cc_start: 0.9115 (OUTLIER) cc_final: 0.8607 (m-30) REVERT: A 1338 GLU cc_start: 0.8659 (mp0) cc_final: 0.7887 (mt-10) REVERT: A 1498 GLU cc_start: 0.8883 (tt0) cc_final: 0.8453 (tp30) REVERT: A 1649 LYS cc_start: 0.3548 (mmtt) cc_final: 0.3069 (mmtt) REVERT: A 1759 MET cc_start: 0.7665 (tmm) cc_final: 0.7287 (tmm) REVERT: B 185 GLU cc_start: 0.8835 (mt-10) cc_final: 0.8482 (mt-10) REVERT: B 301 ASP cc_start: 0.8528 (t0) cc_final: 0.8272 (t0) REVERT: G 132 MET cc_start: 0.8543 (mpp) cc_final: 0.8335 (mmt) REVERT: G 167 ASP cc_start: 0.8445 (p0) cc_final: 0.8166 (p0) REVERT: G 447 ASN cc_start: 0.9037 (m-40) cc_final: 0.8312 (p0) REVERT: G 794 MET cc_start: 0.9143 (tpp) cc_final: 0.8513 (mmt) REVERT: G 870 GLU cc_start: 0.9259 (mt-10) cc_final: 0.8990 (pt0) REVERT: G 1074 MET cc_start: 0.9213 (mmm) cc_final: 0.8316 (mmm) REVERT: G 1164 MET cc_start: 0.8190 (mmm) cc_final: 0.7952 (tpp) REVERT: G 1221 MET cc_start: 0.8603 (tmm) cc_final: 0.8341 (tmm) REVERT: G 1265 MET cc_start: 0.9426 (tmm) cc_final: 0.9173 (tmm) REVERT: G 1359 MET cc_start: 0.5865 (tpp) cc_final: 0.5051 (tpt) REVERT: G 1413 ARG cc_start: 0.9112 (mtp85) cc_final: 0.8721 (mmm-85) REVERT: G 1784 MET cc_start: 0.8525 (tmm) cc_final: 0.7912 (tmm) REVERT: G 1822 MET cc_start: 0.8494 (ptp) cc_final: 0.8124 (ptp) REVERT: G 1838 MET cc_start: 0.9088 (tmm) cc_final: 0.8806 (tmm) REVERT: G 1876 GLU cc_start: 0.7453 (tp30) cc_final: 0.7193 (tp30) REVERT: G 2005 ARG cc_start: 0.8258 (mtp85) cc_final: 0.7935 (tpp-160) outliers start: 48 outliers final: 26 residues processed: 256 average time/residue: 0.4312 time to fit residues: 179.5577 Evaluate side-chains 235 residues out of total 3246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 207 time to evaluate : 3.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 485 ASP Chi-restraints excluded: chain A residue 707 THR Chi-restraints excluded: chain A residue 946 GLU Chi-restraints excluded: chain A residue 1112 ASN Chi-restraints excluded: chain A residue 1168 LEU Chi-restraints excluded: chain A residue 1189 ILE Chi-restraints excluded: chain A residue 1260 MET Chi-restraints excluded: chain A residue 1270 VAL Chi-restraints excluded: chain A residue 1294 SER Chi-restraints excluded: chain A residue 1333 ASP Chi-restraints excluded: chain A residue 1730 SER Chi-restraints excluded: chain A residue 1732 THR Chi-restraints excluded: chain A residue 1746 ASN Chi-restraints excluded: chain A residue 1873 HIS Chi-restraints excluded: chain G residue 119 THR Chi-restraints excluded: chain G residue 329 GLU Chi-restraints excluded: chain G residue 351 ASP Chi-restraints excluded: chain G residue 389 LEU Chi-restraints excluded: chain G residue 417 SER Chi-restraints excluded: chain G residue 1223 MET Chi-restraints excluded: chain G residue 1245 ASP Chi-restraints excluded: chain G residue 1381 VAL Chi-restraints excluded: chain G residue 1417 THR Chi-restraints excluded: chain G residue 1511 SER Chi-restraints excluded: chain G residue 1516 VAL Chi-restraints excluded: chain G residue 1646 ASP Chi-restraints excluded: chain G residue 1760 THR Chi-restraints excluded: chain G residue 1939 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 302 optimal weight: 8.9990 chunk 206 optimal weight: 20.0000 chunk 5 optimal weight: 8.9990 chunk 270 optimal weight: 8.9990 chunk 149 optimal weight: 10.0000 chunk 310 optimal weight: 1.9990 chunk 251 optimal weight: 0.9980 chunk 0 optimal weight: 30.0000 chunk 185 optimal weight: 6.9990 chunk 326 optimal weight: 40.0000 chunk 91 optimal weight: 1.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 713 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1549 ASN ** B 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 677 GLN ** G1055 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G1619 ASN ** G1896 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1897 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.2074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 30228 Z= 0.240 Angle : 0.515 9.638 40944 Z= 0.262 Chirality : 0.041 0.158 4603 Planarity : 0.003 0.036 5285 Dihedral : 4.480 62.018 4028 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.62 % Favored : 96.36 % Rotamer: Outliers : 1.60 % Allowed : 11.16 % Favored : 87.24 % 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: 0.10 (0.14), residues: 3761 helix: 0.94 (0.13), residues: 1657 sheet: -1.24 (0.22), residues: 524 loop : -0.26 (0.16), residues: 1580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1030 HIS 0.009 0.001 HIS G 102 PHE 0.017 0.001 PHE A 35 TYR 0.016 0.001 TYR G 67 ARG 0.006 0.000 ARG A 709 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 3246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 220 time to evaluate : 3.430 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 384 GLU cc_start: 0.9170 (mt-10) cc_final: 0.8904 (pt0) REVERT: A 419 GLU cc_start: 0.9300 (mt-10) cc_final: 0.9089 (mt-10) REVERT: A 826 MET cc_start: 0.9041 (mmm) cc_final: 0.8661 (mtp) REVERT: A 847 GLU cc_start: 0.9243 (mp0) cc_final: 0.9013 (mp0) REVERT: A 946 GLU cc_start: 0.9174 (OUTLIER) cc_final: 0.8873 (pp20) REVERT: A 1124 GLU cc_start: 0.9256 (tt0) cc_final: 0.8960 (tt0) REVERT: A 1128 GLU cc_start: 0.8623 (mt-10) cc_final: 0.7855 (mp0) REVERT: A 1273 ASP cc_start: 0.8959 (p0) cc_final: 0.8575 (p0) REVERT: A 1333 ASP cc_start: 0.9124 (OUTLIER) cc_final: 0.8633 (m-30) REVERT: A 1377 MET cc_start: 0.9171 (tpp) cc_final: 0.8710 (tpp) REVERT: A 1498 GLU cc_start: 0.8948 (tt0) cc_final: 0.8467 (pt0) REVERT: A 1649 LYS cc_start: 0.3494 (mmtt) cc_final: 0.2830 (mmtt) REVERT: B 185 GLU cc_start: 0.8874 (mt-10) cc_final: 0.8526 (mt-10) REVERT: B 290 MET cc_start: 0.9386 (mmt) cc_final: 0.9132 (mmt) REVERT: B 301 ASP cc_start: 0.8449 (t0) cc_final: 0.8180 (t0) REVERT: G 167 ASP cc_start: 0.8426 (p0) cc_final: 0.8144 (p0) REVERT: G 245 GLN cc_start: 0.8897 (OUTLIER) cc_final: 0.8422 (mm-40) REVERT: G 447 ASN cc_start: 0.9023 (m-40) cc_final: 0.8397 (p0) REVERT: G 794 MET cc_start: 0.9133 (tpp) cc_final: 0.8495 (mmt) REVERT: G 870 GLU cc_start: 0.9245 (mt-10) cc_final: 0.8985 (pt0) REVERT: G 1221 MET cc_start: 0.8595 (tmm) cc_final: 0.8338 (tmm) REVERT: G 1265 MET cc_start: 0.9445 (tmm) cc_final: 0.9196 (tmm) REVERT: G 1359 MET cc_start: 0.5864 (tpp) cc_final: 0.5042 (tpt) REVERT: G 1736 MET cc_start: 0.8799 (OUTLIER) cc_final: 0.8585 (mpp) REVERT: G 1784 MET cc_start: 0.8518 (tmm) cc_final: 0.7925 (tmm) REVERT: G 1822 MET cc_start: 0.8498 (ptp) cc_final: 0.8141 (ptp) REVERT: G 1838 MET cc_start: 0.9096 (tmm) cc_final: 0.8799 (tmm) REVERT: G 1876 GLU cc_start: 0.7391 (tp30) cc_final: 0.7071 (tp30) REVERT: G 2005 ARG cc_start: 0.8300 (mtp85) cc_final: 0.7904 (tpp-160) outliers start: 52 outliers final: 32 residues processed: 257 average time/residue: 0.3945 time to fit residues: 166.1709 Evaluate side-chains 240 residues out of total 3246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 204 time to evaluate : 3.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 366 ASP Chi-restraints excluded: chain A residue 707 THR Chi-restraints excluded: chain A residue 774 ILE Chi-restraints excluded: chain A residue 817 THR Chi-restraints excluded: chain A residue 946 GLU Chi-restraints excluded: chain A residue 1112 ASN Chi-restraints excluded: chain A residue 1150 ASP Chi-restraints excluded: chain A residue 1168 LEU Chi-restraints excluded: chain A residue 1189 ILE Chi-restraints excluded: chain A residue 1260 MET Chi-restraints excluded: chain A residue 1270 VAL Chi-restraints excluded: chain A residue 1294 SER Chi-restraints excluded: chain A residue 1333 ASP Chi-restraints excluded: chain A residue 1730 SER Chi-restraints excluded: chain A residue 1732 THR Chi-restraints excluded: chain A residue 1746 ASN Chi-restraints excluded: chain A residue 1873 HIS Chi-restraints excluded: chain B residue 174 ASP Chi-restraints excluded: chain G residue 119 THR Chi-restraints excluded: chain G residue 245 GLN Chi-restraints excluded: chain G residue 250 VAL Chi-restraints excluded: chain G residue 329 GLU Chi-restraints excluded: chain G residue 351 ASP Chi-restraints excluded: chain G residue 389 LEU Chi-restraints excluded: chain G residue 417 SER Chi-restraints excluded: chain G residue 1223 MET Chi-restraints excluded: chain G residue 1245 ASP Chi-restraints excluded: chain G residue 1417 THR Chi-restraints excluded: chain G residue 1427 VAL Chi-restraints excluded: chain G residue 1511 SER Chi-restraints excluded: chain G residue 1646 ASP Chi-restraints excluded: chain G residue 1736 MET Chi-restraints excluded: chain G residue 1760 THR Chi-restraints excluded: chain G residue 1774 THR Chi-restraints excluded: chain G residue 1939 HIS Chi-restraints excluded: chain G residue 1983 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 122 optimal weight: 7.9990 chunk 327 optimal weight: 8.9990 chunk 71 optimal weight: 7.9990 chunk 213 optimal weight: 0.9990 chunk 89 optimal weight: 7.9990 chunk 363 optimal weight: 5.9990 chunk 301 optimal weight: 0.1980 chunk 168 optimal weight: 7.9990 chunk 30 optimal weight: 20.0000 chunk 120 optimal weight: 5.9990 chunk 190 optimal weight: 30.0000 overall best weight: 4.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 713 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1549 ASN ** B 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1055 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G1161 GLN G1619 ASN ** G1896 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1897 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.2204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 30228 Z= 0.243 Angle : 0.520 10.407 40944 Z= 0.263 Chirality : 0.041 0.161 4603 Planarity : 0.003 0.036 5285 Dihedral : 4.453 58.817 4028 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.80 % Favored : 96.17 % Rotamer: Outliers : 1.82 % Allowed : 11.96 % Favored : 86.22 % 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: 0.20 (0.14), residues: 3761 helix: 1.00 (0.13), residues: 1654 sheet: -1.12 (0.22), residues: 511 loop : -0.22 (0.16), residues: 1596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1030 HIS 0.008 0.001 HIS G 102 PHE 0.013 0.001 PHE A 450 TYR 0.017 0.001 TYR G 67 ARG 0.006 0.000 ARG A 709 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 3246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 220 time to evaluate : 3.368 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 384 GLU cc_start: 0.9163 (mt-10) cc_final: 0.8920 (pt0) REVERT: A 419 GLU cc_start: 0.9302 (mt-10) cc_final: 0.9083 (mt-10) REVERT: A 826 MET cc_start: 0.9025 (mmm) cc_final: 0.8685 (mtp) REVERT: A 847 GLU cc_start: 0.9284 (mp0) cc_final: 0.9032 (mp0) REVERT: A 946 GLU cc_start: 0.9156 (OUTLIER) cc_final: 0.8847 (pp20) REVERT: A 1124 GLU cc_start: 0.9235 (tt0) cc_final: 0.8910 (tt0) REVERT: A 1128 GLU cc_start: 0.8621 (mt-10) cc_final: 0.7872 (mp0) REVERT: A 1273 ASP cc_start: 0.8977 (p0) cc_final: 0.8621 (p0) REVERT: A 1333 ASP cc_start: 0.9118 (OUTLIER) cc_final: 0.8629 (m-30) REVERT: A 1338 GLU cc_start: 0.8671 (mp0) cc_final: 0.7982 (mt-10) REVERT: A 1498 GLU cc_start: 0.8947 (tt0) cc_final: 0.8476 (pt0) REVERT: A 1649 LYS cc_start: 0.3503 (mmtt) cc_final: 0.2844 (mmtt) REVERT: A 1759 MET cc_start: 0.7666 (tmm) cc_final: 0.7443 (tmm) REVERT: B 290 MET cc_start: 0.9364 (mmt) cc_final: 0.9049 (mmt) REVERT: B 301 ASP cc_start: 0.8496 (t0) cc_final: 0.8225 (t0) REVERT: G 167 ASP cc_start: 0.8378 (p0) cc_final: 0.8093 (p0) REVERT: G 245 GLN cc_start: 0.8897 (OUTLIER) cc_final: 0.8422 (mm-40) REVERT: G 447 ASN cc_start: 0.9042 (m-40) cc_final: 0.8479 (p0) REVERT: G 794 MET cc_start: 0.9113 (tpp) cc_final: 0.8481 (mmt) REVERT: G 870 GLU cc_start: 0.9242 (mt-10) cc_final: 0.8987 (pt0) REVERT: G 1164 MET cc_start: 0.8424 (mmm) cc_final: 0.7630 (tpp) REVERT: G 1221 MET cc_start: 0.8560 (tmm) cc_final: 0.8257 (tmm) REVERT: G 1265 MET cc_start: 0.9443 (tmm) cc_final: 0.9182 (tmm) REVERT: G 1359 MET cc_start: 0.5822 (tpp) cc_final: 0.4990 (tpt) REVERT: G 1379 GLU cc_start: 0.7687 (tp30) cc_final: 0.7438 (tp30) REVERT: G 1639 LYS cc_start: 0.9246 (pttp) cc_final: 0.9017 (ptpp) REVERT: G 1736 MET cc_start: 0.8809 (mpp) cc_final: 0.8568 (mpp) REVERT: G 1784 MET cc_start: 0.8562 (tmm) cc_final: 0.7965 (tmm) REVERT: G 1838 MET cc_start: 0.9095 (tmm) cc_final: 0.8783 (tmm) REVERT: G 1876 GLU cc_start: 0.7362 (tp30) cc_final: 0.7056 (tp30) REVERT: G 1877 ARG cc_start: 0.6831 (mmp80) cc_final: 0.6558 (mmp80) REVERT: G 2005 ARG cc_start: 0.8306 (mtp85) cc_final: 0.7858 (tpp-160) outliers start: 59 outliers final: 40 residues processed: 259 average time/residue: 0.4021 time to fit residues: 170.5015 Evaluate side-chains 251 residues out of total 3246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 208 time to evaluate : 3.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 366 ASP Chi-restraints excluded: chain A residue 485 ASP Chi-restraints excluded: chain A residue 707 THR Chi-restraints excluded: chain A residue 774 ILE Chi-restraints excluded: chain A residue 817 THR Chi-restraints excluded: chain A residue 946 GLU Chi-restraints excluded: chain A residue 1112 ASN Chi-restraints excluded: chain A residue 1150 ASP Chi-restraints excluded: chain A residue 1168 LEU Chi-restraints excluded: chain A residue 1189 ILE Chi-restraints excluded: chain A residue 1234 MET Chi-restraints excluded: chain A residue 1260 MET Chi-restraints excluded: chain A residue 1270 VAL Chi-restraints excluded: chain A residue 1282 THR Chi-restraints excluded: chain A residue 1294 SER Chi-restraints excluded: chain A residue 1333 ASP Chi-restraints excluded: chain A residue 1730 SER Chi-restraints excluded: chain A residue 1732 THR Chi-restraints excluded: chain A residue 1746 ASN Chi-restraints excluded: chain B residue 174 ASP Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain G residue 119 THR Chi-restraints excluded: chain G residue 245 GLN Chi-restraints excluded: chain G residue 250 VAL Chi-restraints excluded: chain G residue 329 GLU Chi-restraints excluded: chain G residue 351 ASP Chi-restraints excluded: chain G residue 389 LEU Chi-restraints excluded: chain G residue 417 SER Chi-restraints excluded: chain G residue 502 LEU Chi-restraints excluded: chain G residue 1223 MET Chi-restraints excluded: chain G residue 1245 ASP Chi-restraints excluded: chain G residue 1381 VAL Chi-restraints excluded: chain G residue 1417 THR Chi-restraints excluded: chain G residue 1427 VAL Chi-restraints excluded: chain G residue 1511 SER Chi-restraints excluded: chain G residue 1516 VAL Chi-restraints excluded: chain G residue 1646 ASP Chi-restraints excluded: chain G residue 1690 VAL Chi-restraints excluded: chain G residue 1698 PHE Chi-restraints excluded: chain G residue 1760 THR Chi-restraints excluded: chain G residue 1774 THR Chi-restraints excluded: chain G residue 1939 HIS Chi-restraints excluded: chain G residue 1983 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 350 optimal weight: 6.9990 chunk 41 optimal weight: 3.9990 chunk 207 optimal weight: 9.9990 chunk 265 optimal weight: 6.9990 chunk 205 optimal weight: 20.0000 chunk 306 optimal weight: 20.0000 chunk 203 optimal weight: 6.9990 chunk 362 optimal weight: 7.9990 chunk 226 optimal weight: 5.9990 chunk 220 optimal weight: 6.9990 chunk 167 optimal weight: 7.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 694 GLN ** A 713 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 758 ASN A1483 ASN ** B 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1055 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G1619 ASN ** G1896 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1897 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G2027 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.2357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 30228 Z= 0.330 Angle : 0.568 10.956 40944 Z= 0.288 Chirality : 0.042 0.163 4603 Planarity : 0.004 0.036 5285 Dihedral : 4.616 59.536 4028 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 12.34 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.36 % Favored : 95.61 % Rotamer: Outliers : 2.00 % Allowed : 12.54 % Favored : 85.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.14), residues: 3761 helix: 0.89 (0.13), residues: 1651 sheet: -1.12 (0.23), residues: 510 loop : -0.24 (0.16), residues: 1600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1030 HIS 0.009 0.001 HIS G 102 PHE 0.017 0.001 PHE A1376 TYR 0.017 0.002 TYR G 67 ARG 0.007 0.000 ARG A 709 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 3246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 222 time to evaluate : 3.522 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 384 GLU cc_start: 0.9166 (mt-10) cc_final: 0.8907 (pt0) REVERT: A 435 GLU cc_start: 0.9209 (tt0) cc_final: 0.8894 (tt0) REVERT: A 826 MET cc_start: 0.9122 (mmm) cc_final: 0.8817 (mtp) REVERT: A 847 GLU cc_start: 0.9297 (mp0) cc_final: 0.9041 (mp0) REVERT: A 946 GLU cc_start: 0.9142 (mp0) cc_final: 0.8847 (pp20) REVERT: A 1124 GLU cc_start: 0.9242 (tt0) cc_final: 0.9038 (tt0) REVERT: A 1128 GLU cc_start: 0.8641 (mt-10) cc_final: 0.7878 (mp0) REVERT: A 1273 ASP cc_start: 0.8951 (p0) cc_final: 0.8574 (p0) REVERT: A 1333 ASP cc_start: 0.9112 (OUTLIER) cc_final: 0.8612 (m-30) REVERT: A 1338 GLU cc_start: 0.8664 (mp0) cc_final: 0.7925 (mt-10) REVERT: A 1498 GLU cc_start: 0.8952 (tt0) cc_final: 0.8487 (pt0) REVERT: A 1649 LYS cc_start: 0.3393 (mmtt) cc_final: 0.2713 (mmtt) REVERT: A 1759 MET cc_start: 0.7656 (tmm) cc_final: 0.7410 (tmm) REVERT: B 290 MET cc_start: 0.9355 (mmt) cc_final: 0.9085 (mmt) REVERT: B 301 ASP cc_start: 0.8487 (t0) cc_final: 0.8248 (t0) REVERT: G 245 GLN cc_start: 0.8906 (OUTLIER) cc_final: 0.8442 (mm-40) REVERT: G 447 ASN cc_start: 0.9093 (m-40) cc_final: 0.8572 (p0) REVERT: G 553 ASN cc_start: 0.8989 (m-40) cc_final: 0.8775 (t0) REVERT: G 764 MET cc_start: 0.8778 (ttm) cc_final: 0.8470 (ttm) REVERT: G 794 MET cc_start: 0.9156 (tpp) cc_final: 0.8588 (mmt) REVERT: G 870 GLU cc_start: 0.9243 (mt-10) cc_final: 0.8983 (pt0) REVERT: G 1221 MET cc_start: 0.8590 (tmm) cc_final: 0.8289 (tmm) REVERT: G 1265 MET cc_start: 0.9435 (tmm) cc_final: 0.9159 (tmm) REVERT: G 1359 MET cc_start: 0.5893 (tpp) cc_final: 0.5066 (tpt) REVERT: G 1379 GLU cc_start: 0.7700 (tp30) cc_final: 0.7477 (tp30) REVERT: G 1496 LYS cc_start: 0.7739 (tptt) cc_final: 0.7324 (mmtt) REVERT: G 1736 MET cc_start: 0.8779 (OUTLIER) cc_final: 0.8540 (mpp) REVERT: G 1784 MET cc_start: 0.8548 (tmm) cc_final: 0.7971 (tmm) REVERT: G 1838 MET cc_start: 0.9115 (tmm) cc_final: 0.8783 (tmm) REVERT: G 1876 GLU cc_start: 0.7382 (tp30) cc_final: 0.7078 (tp30) REVERT: G 2005 ARG cc_start: 0.8349 (mtp85) cc_final: 0.7898 (tpp-160) outliers start: 65 outliers final: 49 residues processed: 268 average time/residue: 0.4046 time to fit residues: 177.2463 Evaluate side-chains 265 residues out of total 3246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 213 time to evaluate : 3.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 366 ASP Chi-restraints excluded: chain A residue 485 ASP Chi-restraints excluded: chain A residue 707 THR Chi-restraints excluded: chain A residue 758 ASN Chi-restraints excluded: chain A residue 774 ILE Chi-restraints excluded: chain A residue 817 THR Chi-restraints excluded: chain A residue 838 MET Chi-restraints excluded: chain A residue 1112 ASN Chi-restraints excluded: chain A residue 1150 ASP Chi-restraints excluded: chain A residue 1168 LEU Chi-restraints excluded: chain A residue 1189 ILE Chi-restraints excluded: chain A residue 1234 MET Chi-restraints excluded: chain A residue 1260 MET Chi-restraints excluded: chain A residue 1270 VAL Chi-restraints excluded: chain A residue 1282 THR Chi-restraints excluded: chain A residue 1294 SER Chi-restraints excluded: chain A residue 1298 ILE Chi-restraints excluded: chain A residue 1333 ASP Chi-restraints excluded: chain A residue 1730 SER Chi-restraints excluded: chain A residue 1732 THR Chi-restraints excluded: chain A residue 1746 ASN Chi-restraints excluded: chain B residue 148 SER Chi-restraints excluded: chain B residue 174 ASP Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain G residue 86 LEU Chi-restraints excluded: chain G residue 115 THR Chi-restraints excluded: chain G residue 119 THR Chi-restraints excluded: chain G residue 245 GLN Chi-restraints excluded: chain G residue 250 VAL Chi-restraints excluded: chain G residue 329 GLU Chi-restraints excluded: chain G residue 351 ASP Chi-restraints excluded: chain G residue 389 LEU Chi-restraints excluded: chain G residue 417 SER Chi-restraints excluded: chain G residue 433 VAL Chi-restraints excluded: chain G residue 502 LEU Chi-restraints excluded: chain G residue 1223 MET Chi-restraints excluded: chain G residue 1245 ASP Chi-restraints excluded: chain G residue 1374 THR Chi-restraints excluded: chain G residue 1381 VAL Chi-restraints excluded: chain G residue 1417 THR Chi-restraints excluded: chain G residue 1427 VAL Chi-restraints excluded: chain G residue 1511 SER Chi-restraints excluded: chain G residue 1516 VAL Chi-restraints excluded: chain G residue 1646 ASP Chi-restraints excluded: chain G residue 1690 VAL Chi-restraints excluded: chain G residue 1698 PHE Chi-restraints excluded: chain G residue 1736 MET Chi-restraints excluded: chain G residue 1760 THR Chi-restraints excluded: chain G residue 1774 THR Chi-restraints excluded: chain G residue 1939 HIS Chi-restraints excluded: chain G residue 1983 ASN Chi-restraints excluded: chain G residue 2003 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 224 optimal weight: 20.0000 chunk 144 optimal weight: 10.0000 chunk 216 optimal weight: 20.0000 chunk 109 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 70 optimal weight: 0.5980 chunk 230 optimal weight: 7.9990 chunk 246 optimal weight: 10.0000 chunk 179 optimal weight: 20.0000 chunk 33 optimal weight: 5.9990 chunk 284 optimal weight: 0.0060 overall best weight: 2.3202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 508 ASN A 713 GLN A 758 ASN ** A1380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1549 ASN A1854 ASN ** B 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1055 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G1619 ASN ** G1896 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.2424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 30228 Z= 0.164 Angle : 0.509 11.537 40944 Z= 0.254 Chirality : 0.041 0.333 4603 Planarity : 0.003 0.036 5285 Dihedral : 4.314 59.294 4028 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.27 % Favored : 96.70 % Rotamer: Outliers : 1.79 % Allowed : 13.28 % Favored : 84.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.14), residues: 3761 helix: 1.11 (0.13), residues: 1652 sheet: -0.87 (0.23), residues: 502 loop : -0.11 (0.16), residues: 1607 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1030 HIS 0.007 0.001 HIS G 102 PHE 0.013 0.001 PHE G 946 TYR 0.031 0.001 TYR G 180 ARG 0.007 0.000 ARG A 709 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 3246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 226 time to evaluate : 3.547 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 342 GLN cc_start: 0.9260 (mt0) cc_final: 0.8936 (mt0) REVERT: A 384 GLU cc_start: 0.9155 (mt-10) cc_final: 0.8903 (pt0) REVERT: A 826 MET cc_start: 0.8996 (mmm) cc_final: 0.8663 (mtp) REVERT: A 847 GLU cc_start: 0.9296 (mp0) cc_final: 0.9007 (mp0) REVERT: A 1124 GLU cc_start: 0.9214 (tt0) cc_final: 0.8843 (tt0) REVERT: A 1128 GLU cc_start: 0.8629 (mt-10) cc_final: 0.7831 (mp0) REVERT: A 1273 ASP cc_start: 0.9014 (p0) cc_final: 0.8635 (p0) REVERT: A 1289 MET cc_start: 0.8788 (mtp) cc_final: 0.7775 (tpt) REVERT: A 1333 ASP cc_start: 0.9025 (OUTLIER) cc_final: 0.8539 (m-30) REVERT: A 1378 GLU cc_start: 0.8945 (tt0) cc_final: 0.8386 (pm20) REVERT: A 1498 GLU cc_start: 0.8935 (tt0) cc_final: 0.8415 (pt0) REVERT: A 1649 LYS cc_start: 0.3643 (mmtt) cc_final: 0.3041 (mmtt) REVERT: A 1759 MET cc_start: 0.7705 (tmm) cc_final: 0.7447 (tmm) REVERT: B 290 MET cc_start: 0.9388 (mmt) cc_final: 0.9079 (mmt) REVERT: B 301 ASP cc_start: 0.8431 (t0) cc_final: 0.8187 (t0) REVERT: G 245 GLN cc_start: 0.8890 (OUTLIER) cc_final: 0.8409 (mm-40) REVERT: G 447 ASN cc_start: 0.9079 (m-40) cc_final: 0.8550 (p0) REVERT: G 553 ASN cc_start: 0.8941 (m-40) cc_final: 0.8735 (t0) REVERT: G 794 MET cc_start: 0.9095 (tpp) cc_final: 0.8567 (mmt) REVERT: G 870 GLU cc_start: 0.9223 (mt-10) cc_final: 0.8965 (pt0) REVERT: G 956 GLU cc_start: 0.9251 (mt-10) cc_final: 0.8855 (tt0) REVERT: G 1164 MET cc_start: 0.8134 (mmm) cc_final: 0.7469 (tpp) REVERT: G 1221 MET cc_start: 0.8572 (tmm) cc_final: 0.8277 (tmm) REVERT: G 1265 MET cc_start: 0.9450 (tmm) cc_final: 0.9218 (tmm) REVERT: G 1359 MET cc_start: 0.5888 (tpp) cc_final: 0.5189 (tpt) REVERT: G 1631 MET cc_start: 0.8365 (mmm) cc_final: 0.7460 (mmm) REVERT: G 1736 MET cc_start: 0.8783 (OUTLIER) cc_final: 0.8544 (mpp) REVERT: G 1784 MET cc_start: 0.8582 (tmm) cc_final: 0.8021 (tmm) REVERT: G 1838 MET cc_start: 0.9160 (tmm) cc_final: 0.8871 (tmm) REVERT: G 1876 GLU cc_start: 0.7422 (tp30) cc_final: 0.7124 (tp30) REVERT: G 2005 ARG cc_start: 0.8302 (mtp85) cc_final: 0.7851 (tpp-160) outliers start: 58 outliers final: 41 residues processed: 267 average time/residue: 0.3973 time to fit residues: 174.3595 Evaluate side-chains 255 residues out of total 3246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 211 time to evaluate : 3.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 366 ASP Chi-restraints excluded: chain A residue 485 ASP Chi-restraints excluded: chain A residue 707 THR Chi-restraints excluded: chain A residue 758 ASN Chi-restraints excluded: chain A residue 817 THR Chi-restraints excluded: chain A residue 1168 LEU Chi-restraints excluded: chain A residue 1189 ILE Chi-restraints excluded: chain A residue 1234 MET Chi-restraints excluded: chain A residue 1260 MET Chi-restraints excluded: chain A residue 1270 VAL Chi-restraints excluded: chain A residue 1282 THR Chi-restraints excluded: chain A residue 1294 SER Chi-restraints excluded: chain A residue 1333 ASP Chi-restraints excluded: chain A residue 1409 THR Chi-restraints excluded: chain A residue 1730 SER Chi-restraints excluded: chain A residue 1732 THR Chi-restraints excluded: chain A residue 1746 ASN Chi-restraints excluded: chain A residue 1812 THR Chi-restraints excluded: chain B residue 174 ASP Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain G residue 115 THR Chi-restraints excluded: chain G residue 119 THR Chi-restraints excluded: chain G residue 145 LEU Chi-restraints excluded: chain G residue 245 GLN Chi-restraints excluded: chain G residue 250 VAL Chi-restraints excluded: chain G residue 325 GLU Chi-restraints excluded: chain G residue 329 GLU Chi-restraints excluded: chain G residue 351 ASP Chi-restraints excluded: chain G residue 379 VAL Chi-restraints excluded: chain G residue 433 VAL Chi-restraints excluded: chain G residue 1245 ASP Chi-restraints excluded: chain G residue 1374 THR Chi-restraints excluded: chain G residue 1381 VAL Chi-restraints excluded: chain G residue 1417 THR Chi-restraints excluded: chain G residue 1440 ASP Chi-restraints excluded: chain G residue 1472 VAL Chi-restraints excluded: chain G residue 1511 SER Chi-restraints excluded: chain G residue 1646 ASP Chi-restraints excluded: chain G residue 1698 PHE Chi-restraints excluded: chain G residue 1736 MET Chi-restraints excluded: chain G residue 1821 VAL Chi-restraints excluded: chain G residue 1939 HIS Chi-restraints excluded: chain G residue 1983 ASN Chi-restraints excluded: chain G residue 2003 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: 0.9980 chunk 316 optimal weight: 3.9990 chunk 337 optimal weight: 6.9990 chunk 203 optimal weight: 8.9990 chunk 147 optimal weight: 10.0000 chunk 265 optimal weight: 4.9990 chunk 103 optimal weight: 7.9990 chunk 305 optimal weight: 5.9990 chunk 319 optimal weight: 6.9990 chunk 336 optimal weight: 6.9990 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1055 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G1619 ASN ** G1896 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1897 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G2027 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.2496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 30228 Z= 0.253 Angle : 0.545 12.004 40944 Z= 0.273 Chirality : 0.042 0.320 4603 Planarity : 0.004 0.036 5285 Dihedral : 4.350 57.235 4028 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.94 % Favored : 96.04 % Rotamer: Outliers : 1.76 % Allowed : 13.47 % Favored : 84.78 % 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: 0.36 (0.14), residues: 3761 helix: 1.07 (0.13), residues: 1651 sheet: -0.87 (0.23), residues: 505 loop : -0.11 (0.16), residues: 1605 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1030 HIS 0.008 0.001 HIS G 102 PHE 0.017 0.001 PHE B 241 TYR 0.020 0.001 TYR G 67 ARG 0.017 0.000 ARG A 348 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 3246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 214 time to evaluate : 3.370 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 384 GLU cc_start: 0.9155 (mt-10) cc_final: 0.8899 (pt0) REVERT: A 435 GLU cc_start: 0.9078 (tt0) cc_final: 0.8859 (tt0) REVERT: A 826 MET cc_start: 0.8892 (mmm) cc_final: 0.8596 (mtp) REVERT: A 847 GLU cc_start: 0.9310 (OUTLIER) cc_final: 0.9028 (mp0) REVERT: A 1008 GLU cc_start: 0.9236 (mp0) cc_final: 0.8902 (pm20) REVERT: A 1128 GLU cc_start: 0.8619 (mt-10) cc_final: 0.7842 (mp0) REVERT: A 1273 ASP cc_start: 0.8972 (p0) cc_final: 0.8595 (p0) REVERT: A 1333 ASP cc_start: 0.9054 (OUTLIER) cc_final: 0.8563 (m-30) REVERT: A 1338 GLU cc_start: 0.8688 (mp0) cc_final: 0.7987 (mt-10) REVERT: A 1498 GLU cc_start: 0.8929 (tt0) cc_final: 0.8469 (pt0) REVERT: A 1649 LYS cc_start: 0.3707 (mmtt) cc_final: 0.3050 (mmtt) REVERT: B 301 ASP cc_start: 0.8483 (t0) cc_final: 0.8263 (t0) REVERT: G 245 GLN cc_start: 0.8874 (OUTLIER) cc_final: 0.8386 (mm-40) REVERT: G 447 ASN cc_start: 0.9073 (m-40) cc_final: 0.8596 (p0) REVERT: G 553 ASN cc_start: 0.8952 (m-40) cc_final: 0.8737 (t0) REVERT: G 764 MET cc_start: 0.8714 (ttm) cc_final: 0.8450 (ttm) REVERT: G 794 MET cc_start: 0.9138 (tpp) cc_final: 0.8514 (mmt) REVERT: G 930 MET cc_start: 0.9436 (mtt) cc_final: 0.9224 (mtt) REVERT: G 1221 MET cc_start: 0.8571 (tmm) cc_final: 0.8273 (tmm) REVERT: G 1241 ASN cc_start: 0.8642 (OUTLIER) cc_final: 0.7675 (t0) REVERT: G 1265 MET cc_start: 0.9435 (tmm) cc_final: 0.9183 (tmm) REVERT: G 1323 MET cc_start: 0.7485 (ptp) cc_final: 0.7089 (ptp) REVERT: G 1359 MET cc_start: 0.5840 (tpp) cc_final: 0.5104 (tpt) REVERT: G 1736 MET cc_start: 0.8781 (OUTLIER) cc_final: 0.8534 (mpp) REVERT: G 1784 MET cc_start: 0.8548 (tmm) cc_final: 0.7977 (tmm) REVERT: G 1838 MET cc_start: 0.9164 (tmm) cc_final: 0.8857 (tmm) REVERT: G 1876 GLU cc_start: 0.7417 (tp30) cc_final: 0.7124 (tp30) REVERT: G 1880 LYS cc_start: 0.8660 (tttt) cc_final: 0.8381 (ttmt) REVERT: G 2005 ARG cc_start: 0.8237 (mtp85) cc_final: 0.7867 (tpp-160) outliers start: 57 outliers final: 45 residues processed: 256 average time/residue: 0.4190 time to fit residues: 175.9367 Evaluate side-chains 256 residues out of total 3246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 206 time to evaluate : 3.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 366 ASP Chi-restraints excluded: chain A residue 485 ASP Chi-restraints excluded: chain A residue 668 PHE Chi-restraints excluded: chain A residue 707 THR Chi-restraints excluded: chain A residue 817 THR Chi-restraints excluded: chain A residue 847 GLU Chi-restraints excluded: chain A residue 1130 ASP Chi-restraints excluded: chain A residue 1168 LEU Chi-restraints excluded: chain A residue 1189 ILE Chi-restraints excluded: chain A residue 1234 MET Chi-restraints excluded: chain A residue 1260 MET Chi-restraints excluded: chain A residue 1270 VAL Chi-restraints excluded: chain A residue 1282 THR Chi-restraints excluded: chain A residue 1294 SER Chi-restraints excluded: chain A residue 1333 ASP Chi-restraints excluded: chain A residue 1409 THR Chi-restraints excluded: chain A residue 1730 SER Chi-restraints excluded: chain A residue 1732 THR Chi-restraints excluded: chain A residue 1746 ASN Chi-restraints excluded: chain A residue 1812 THR Chi-restraints excluded: chain B residue 148 SER Chi-restraints excluded: chain B residue 174 ASP Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain G residue 115 THR Chi-restraints excluded: chain G residue 119 THR Chi-restraints excluded: chain G residue 245 GLN Chi-restraints excluded: chain G residue 250 VAL Chi-restraints excluded: chain G residue 325 GLU Chi-restraints excluded: chain G residue 329 GLU Chi-restraints excluded: chain G residue 351 ASP Chi-restraints excluded: chain G residue 379 VAL Chi-restraints excluded: chain G residue 433 VAL Chi-restraints excluded: chain G residue 995 LEU Chi-restraints excluded: chain G residue 1241 ASN Chi-restraints excluded: chain G residue 1245 ASP Chi-restraints excluded: chain G residue 1374 THR Chi-restraints excluded: chain G residue 1381 VAL Chi-restraints excluded: chain G residue 1417 THR Chi-restraints excluded: chain G residue 1427 VAL Chi-restraints excluded: chain G residue 1440 ASP Chi-restraints excluded: chain G residue 1472 VAL Chi-restraints excluded: chain G residue 1511 SER Chi-restraints excluded: chain G residue 1615 MET Chi-restraints excluded: chain G residue 1646 ASP Chi-restraints excluded: chain G residue 1698 PHE Chi-restraints excluded: chain G residue 1736 MET Chi-restraints excluded: chain G residue 1760 THR Chi-restraints excluded: chain G residue 1939 HIS Chi-restraints excluded: chain G residue 1983 ASN Chi-restraints excluded: chain G residue 2003 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 221 optimal weight: 0.0050 chunk 357 optimal weight: 20.0000 chunk 217 optimal weight: 0.4980 chunk 169 optimal weight: 7.9990 chunk 248 optimal weight: 7.9990 chunk 374 optimal weight: 9.9990 chunk 344 optimal weight: 9.9990 chunk 298 optimal weight: 6.9990 chunk 30 optimal weight: 3.9990 chunk 230 optimal weight: 8.9990 chunk 182 optimal weight: 30.0000 overall best weight: 3.9000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 758 ASN A1549 ASN ** B 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1055 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G1619 ASN ** G1896 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1897 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.2556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 30228 Z= 0.229 Angle : 0.538 11.918 40944 Z= 0.269 Chirality : 0.041 0.288 4603 Planarity : 0.003 0.036 5285 Dihedral : 4.313 54.966 4028 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.70 % Favored : 96.28 % Rotamer: Outliers : 1.82 % Allowed : 13.78 % Favored : 84.41 % 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: 0.39 (0.14), residues: 3761 helix: 1.07 (0.13), residues: 1650 sheet: -0.76 (0.23), residues: 499 loop : -0.11 (0.16), residues: 1612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1030 HIS 0.007 0.001 HIS G 102 PHE 0.019 0.001 PHE B 241 TYR 0.022 0.001 TYR G 67 ARG 0.012 0.000 ARG A 348 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 3246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 213 time to evaluate : 4.235 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 342 GLN cc_start: 0.9249 (mt0) cc_final: 0.8906 (mt0) REVERT: A 384 GLU cc_start: 0.9150 (mt-10) cc_final: 0.8890 (pt0) REVERT: A 826 MET cc_start: 0.8892 (mmm) cc_final: 0.8603 (mtp) REVERT: A 847 GLU cc_start: 0.9276 (OUTLIER) cc_final: 0.8972 (mp0) REVERT: A 1128 GLU cc_start: 0.8616 (mt-10) cc_final: 0.7829 (mp0) REVERT: A 1273 ASP cc_start: 0.9012 (p0) cc_final: 0.8656 (p0) REVERT: A 1289 MET cc_start: 0.8822 (mtp) cc_final: 0.7808 (tpt) REVERT: A 1333 ASP cc_start: 0.9032 (OUTLIER) cc_final: 0.8541 (m-30) REVERT: A 1498 GLU cc_start: 0.8926 (tt0) cc_final: 0.8468 (pt0) REVERT: A 1649 LYS cc_start: 0.3692 (mmtt) cc_final: 0.3029 (mmtt) REVERT: B 290 MET cc_start: 0.9379 (mmt) cc_final: 0.9082 (mmt) REVERT: B 301 ASP cc_start: 0.8500 (t0) cc_final: 0.8289 (t0) REVERT: G 245 GLN cc_start: 0.8881 (OUTLIER) cc_final: 0.8395 (mm-40) REVERT: G 447 ASN cc_start: 0.9063 (m-40) cc_final: 0.8610 (p0) REVERT: G 764 MET cc_start: 0.8663 (ttm) cc_final: 0.8379 (ttm) REVERT: G 794 MET cc_start: 0.9136 (tpp) cc_final: 0.8522 (mmt) REVERT: G 930 MET cc_start: 0.9416 (mtt) cc_final: 0.9179 (mtt) REVERT: G 1221 MET cc_start: 0.8582 (tmm) cc_final: 0.8292 (tmm) REVERT: G 1241 ASN cc_start: 0.8643 (OUTLIER) cc_final: 0.7668 (t0) REVERT: G 1265 MET cc_start: 0.9432 (tmm) cc_final: 0.9195 (tmm) REVERT: G 1323 MET cc_start: 0.7469 (ptp) cc_final: 0.7082 (ptp) REVERT: G 1359 MET cc_start: 0.5820 (tpp) cc_final: 0.5070 (tpt) REVERT: G 1736 MET cc_start: 0.8791 (OUTLIER) cc_final: 0.8548 (mpp) REVERT: G 1784 MET cc_start: 0.8598 (tmm) cc_final: 0.8030 (tmm) REVERT: G 1838 MET cc_start: 0.9178 (tmm) cc_final: 0.8888 (tmm) REVERT: G 1876 GLU cc_start: 0.7417 (tp30) cc_final: 0.7112 (tp30) REVERT: G 1880 LYS cc_start: 0.8659 (tttt) cc_final: 0.8367 (ttmt) REVERT: G 2005 ARG cc_start: 0.8271 (mtp85) cc_final: 0.7867 (tpp-160) outliers start: 59 outliers final: 48 residues processed: 255 average time/residue: 0.4124 time to fit residues: 172.5411 Evaluate side-chains 256 residues out of total 3246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 203 time to evaluate : 3.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 366 ASP Chi-restraints excluded: chain A residue 485 ASP Chi-restraints excluded: chain A residue 668 PHE Chi-restraints excluded: chain A residue 707 THR Chi-restraints excluded: chain A residue 817 THR Chi-restraints excluded: chain A residue 847 GLU Chi-restraints excluded: chain A residue 1130 ASP Chi-restraints excluded: chain A residue 1168 LEU Chi-restraints excluded: chain A residue 1189 ILE Chi-restraints excluded: chain A residue 1234 MET Chi-restraints excluded: chain A residue 1260 MET Chi-restraints excluded: chain A residue 1270 VAL Chi-restraints excluded: chain A residue 1282 THR Chi-restraints excluded: chain A residue 1294 SER Chi-restraints excluded: chain A residue 1298 ILE Chi-restraints excluded: chain A residue 1333 ASP Chi-restraints excluded: chain A residue 1409 THR Chi-restraints excluded: chain A residue 1713 ASP Chi-restraints excluded: chain A residue 1730 SER Chi-restraints excluded: chain A residue 1732 THR Chi-restraints excluded: chain A residue 1746 ASN Chi-restraints excluded: chain A residue 1812 THR Chi-restraints excluded: chain B residue 148 SER Chi-restraints excluded: chain B residue 174 ASP Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain G residue 115 THR Chi-restraints excluded: chain G residue 119 THR Chi-restraints excluded: chain G residue 245 GLN Chi-restraints excluded: chain G residue 250 VAL Chi-restraints excluded: chain G residue 325 GLU Chi-restraints excluded: chain G residue 329 GLU Chi-restraints excluded: chain G residue 351 ASP Chi-restraints excluded: chain G residue 379 VAL Chi-restraints excluded: chain G residue 391 LEU Chi-restraints excluded: chain G residue 433 VAL Chi-restraints excluded: chain G residue 995 LEU Chi-restraints excluded: chain G residue 1241 ASN Chi-restraints excluded: chain G residue 1245 ASP Chi-restraints excluded: chain G residue 1280 ASP Chi-restraints excluded: chain G residue 1374 THR Chi-restraints excluded: chain G residue 1417 THR Chi-restraints excluded: chain G residue 1427 VAL Chi-restraints excluded: chain G residue 1440 ASP Chi-restraints excluded: chain G residue 1472 VAL Chi-restraints excluded: chain G residue 1511 SER Chi-restraints excluded: chain G residue 1615 MET Chi-restraints excluded: chain G residue 1646 ASP Chi-restraints excluded: chain G residue 1698 PHE Chi-restraints excluded: chain G residue 1736 MET Chi-restraints excluded: chain G residue 1760 THR Chi-restraints excluded: chain G residue 1939 HIS Chi-restraints excluded: chain G residue 1983 ASN Chi-restraints excluded: chain G residue 2003 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 236 optimal weight: 5.9990 chunk 317 optimal weight: 30.0000 chunk 91 optimal weight: 0.8980 chunk 275 optimal weight: 3.9990 chunk 44 optimal weight: 5.9990 chunk 82 optimal weight: 0.7980 chunk 298 optimal weight: 6.9990 chunk 125 optimal weight: 4.9990 chunk 306 optimal weight: 7.9990 chunk 37 optimal weight: 8.9990 chunk 55 optimal weight: 9.9990 overall best weight: 3.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1549 ASN ** B 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1055 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G1619 ASN ** G1896 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1897 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.075936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.058344 restraints weight = 126084.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.059360 restraints weight = 63205.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.059682 restraints weight = 35852.555| |-----------------------------------------------------------------------------| r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.2606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 30228 Z= 0.207 Angle : 0.533 12.976 40944 Z= 0.265 Chirality : 0.041 0.270 4603 Planarity : 0.003 0.036 5285 Dihedral : 4.255 53.489 4028 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.96 % Favored : 96.01 % Rotamer: Outliers : 1.85 % Allowed : 13.74 % Favored : 84.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.14), residues: 3761 helix: 1.13 (0.13), residues: 1646 sheet: -0.70 (0.23), residues: 505 loop : -0.08 (0.16), residues: 1610 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1030 HIS 0.007 0.001 HIS G 102 PHE 0.022 0.001 PHE B 241 TYR 0.021 0.001 TYR G 67 ARG 0.012 0.000 ARG A 348 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4963.87 seconds wall clock time: 92 minutes 5.20 seconds (5525.20 seconds total)