Starting phenix.real_space_refine on Sat Mar 16 15:19:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rqj_4983/03_2024/6rqj_4983.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rqj_4983/03_2024/6rqj_4983.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rqj_4983/03_2024/6rqj_4983.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rqj_4983/03_2024/6rqj_4983.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rqj_4983/03_2024/6rqj_4983.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rqj_4983/03_2024/6rqj_4983.pdb" } resolution = 3.5 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= -0.000 sd= 0.002 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: 4 Type Number sf(0) Gaussians S 79 5.16 5 C 9532 2.51 5 N 2475 2.21 5 O 2885 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 690": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 700": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 701": "OD1" <-> "OD2" Residue "A GLU 712": "OE1" <-> "OE2" Residue "A GLU 771": "OE1" <-> "OE2" Residue "A PHE 788": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 846": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 869": "OE1" <-> "OE2" Residue "A PHE 918": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 939": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 945": "OD1" <-> "OD2" Residue "A TYR 961": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1022": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1034": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1051": "OE1" <-> "OE2" Residue "A TYR 1059": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1064": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1066": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1094": "OE1" <-> "OE2" Residue "A GLU 1109": "OE1" <-> "OE2" Residue "A PHE 1118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1289": "OD1" <-> "OD2" Residue "A ASP 1312": "OD1" <-> "OD2" Residue "A TYR 1317": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1339": "OE1" <-> "OE2" Residue "A ASP 1344": "OD1" <-> "OD2" Residue "A ASP 1345": "OD1" <-> "OD2" Residue "A PHE 1352": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1372": "OE1" <-> "OE2" Residue "A PHE 1377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1450": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1483": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1497": "OE1" <-> "OE2" Residue "A PHE 1508": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1521": "OE1" <-> "OE2" Residue "A GLU 1529": "OE1" <-> "OE2" Residue "A ASP 1540": "OD1" <-> "OD2" Residue "A GLU 1546": "OE1" <-> "OE2" Residue "A TYR 1561": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1593": "OE1" <-> "OE2" Residue "A ASP 1595": "OD1" <-> "OD2" Residue "A GLU 1610": "OE1" <-> "OE2" Residue "A ASP 1651": "OD1" <-> "OD2" Residue "A PHE 1660": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1665": "OD1" <-> "OD2" Residue "A GLU 1666": "OE1" <-> "OE2" Residue "A GLU 1669": "OE1" <-> "OE2" Residue "A ASP 1670": "OD1" <-> "OD2" Residue "A PHE 1672": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 64": "OE1" <-> "OE2" Residue "C GLU 141": "OE1" <-> "OE2" Residue "C GLU 145": "OE1" <-> "OE2" Residue "C GLU 152": "OE1" <-> "OE2" Residue "D GLU 20": "OE1" <-> "OE2" Residue "D ARG 21": "NH1" <-> "NH2" Residue "B GLU 20": "OE1" <-> "OE2" Residue "B TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 105": "OE1" <-> "OE2" Residue "B TYR 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 158": "OE1" <-> "OE2" Residue "B GLU 170": "OE1" <-> "OE2" Residue "B ASP 172": "OD1" <-> "OD2" Residue "B ASP 178": "OD1" <-> "OD2" Residue "B PHE 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 208": "OD1" <-> "OD2" Residue "B PHE 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 221": "OE1" <-> "OE2" Residue "B GLU 247": "OE1" <-> "OE2" Residue "B TYR 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 278": "OD1" <-> "OD2" Residue "B ASP 302": "OD1" <-> "OD2" Residue "B TYR 322": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 380": "OD1" <-> "OD2" Residue "B GLU 445": "OE1" <-> "OE2" Residue "B GLU 450": "OE1" <-> "OE2" Residue "B ASP 471": "OD1" <-> "OD2" Residue "B ASP 494": "OD1" <-> "OD2" Residue "B GLU 516": "OE1" <-> "OE2" Residue "B TYR 523": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 544": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 565": "OE1" <-> "OE2" Residue "B ASP 606": "OD1" <-> "OD2" Residue "B PHE 624": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 626": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 628": "OE1" <-> "OE2" Residue "B ASP 660": "OD1" <-> "OD2" Residue "B ASP 661": "OD1" <-> "OD2" Residue "B ASP 666": "OD1" <-> "OD2" Residue "E GLU 32": "OE1" <-> "OE2" Residue "E ASP 49": "OD1" <-> "OD2" Residue "E ASP 63": "OD1" <-> "OD2" Residue "E GLU 69": "OE1" <-> "OE2" Residue "E TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 14971 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 7768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 981, 7768 Classifications: {'peptide': 981} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 33, 'TRANS': 945} Chain breaks: 2 Chain: "C" Number of atoms: 1151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1151 Classifications: {'peptide': 147} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 140} Chain: "D" Number of atoms: 324 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 324 Classifications: {'peptide': 46} Link IDs: {'PCIS': 1, 'PTRANS': 1, 'TRANS': 43} Chain: "B" Number of atoms: 5080 Number of conformers: 1 Conformer: "" Number of residues, atoms: 643, 5080 Classifications: {'peptide': 643} Link IDs: {'PCIS': 3, 'PTRANS': 30, 'TRANS': 609} Chain breaks: 1 Chain: "E" Number of atoms: 620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 620 Classifications: {'peptide': 82} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 74} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 8.28, per 1000 atoms: 0.55 Number of scatterers: 14971 At special positions: 0 Unit cell: (87.954, 179.196, 115.08, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 79 16.00 O 2885 8.00 N 2475 7.00 C 9532 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=24, symmetry=0 Simple disulfide: pdb=" SG CYS A 698 " - pdb=" SG CYS A 724 " distance=2.03 Simple disulfide: pdb=" SG CYS A 699 " - pdb=" SG CYS A 731 " distance=2.04 Simple disulfide: pdb=" SG CYS A 711 " - pdb=" SG CYS A 732 " distance=2.03 Simple disulfide: pdb=" SG CYS A 810 " - pdb=" SG CYS B 567 " distance=2.03 Simple disulfide: pdb=" SG CYS A 856 " - pdb=" SG CYS A 883 " distance=2.04 Simple disulfide: pdb=" SG CYS A 866 " - pdb=" SG CYS A1527 " distance=2.03 Simple disulfide: pdb=" SG CYS A1101 " - pdb=" SG CYS A1159 " distance=2.02 Simple disulfide: pdb=" SG CYS A1375 " - pdb=" SG CYS A1505 " distance=2.05 Simple disulfide: pdb=" SG CYS A1405 " - pdb=" SG CYS A1474 " distance=2.03 Simple disulfide: pdb=" SG CYS A1520 " - pdb=" SG CYS A1525 " distance=2.03 Simple disulfide: pdb=" SG CYS A1532 " - pdb=" SG CYS A1606 " distance=2.03 Simple disulfide: pdb=" SG CYS A1553 " - pdb=" SG CYS A1676 " distance=2.03 Simple disulfide: pdb=" SG CYS A1654 " - pdb=" SG CYS A1657 " distance=2.03 Simple disulfide: pdb=" SG CYS C 24 " - pdb=" SG CYS C 146 " distance=2.03 Simple disulfide: pdb=" SG CYS C 56 " - pdb=" SG CYS C 168 " distance=2.03 Simple disulfide: pdb=" SG CYS C 118 " - pdb=" SG CYS C 147 " distance=2.03 Simple disulfide: pdb=" SG CYS D 14 " - pdb=" SG CYS D 38 " distance=2.03 Simple disulfide: pdb=" SG CYS D 19 " - pdb=" SG CYS D 40 " distance=2.03 Simple disulfide: pdb=" SG CYS D 34 " - pdb=" SG CYS D 55 " distance=2.03 Simple disulfide: pdb=" SG CYS B 634 " - pdb=" SG CYS B 669 " distance=2.03 Simple disulfide: pdb=" SG CYS E 21 " - pdb=" SG CYS E 45 " distance=2.03 Simple disulfide: pdb=" SG CYS E 40 " - pdb=" SG CYS E 79 " distance=2.03 Simple disulfide: pdb=" SG CYS E 57 " - pdb=" SG CYS E 80 " distance=2.03 Simple disulfide: pdb=" SG CYS E 66 " - pdb=" SG CYS E 85 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG F 1 " - " NAG F 2 " NAG-ASN " NAG F 1 " - " ASN A 911 " Time building additional restraints: 5.36 Conformation dependent library (CDL) restraints added in 2.8 seconds 3766 Ramachandran restraints generated. 1883 Oldfield, 0 Emsley, 1883 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3582 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 34 sheets defined 19.2% alpha, 30.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.52 Creating SS restraints... Processing helix chain 'A' and resid 680 through 690 removed outlier: 4.510A pdb=" N ILE A 686 " --> pdb=" O LYS A 682 " (cutoff:3.500A) Processing helix chain 'A' and resid 695 through 704 removed outlier: 4.665A pdb=" N CYS A 699 " --> pdb=" O VAL A 695 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N TYR A 700 " --> pdb=" O LYS A 696 " (cutoff:3.500A) Processing helix chain 'A' and resid 710 through 715 Processing helix chain 'A' and resid 716 through 718 No H-bonds generated for 'chain 'A' and resid 716 through 718' Processing helix chain 'A' and resid 720 through 737 removed outlier: 3.937A pdb=" N CYS A 724 " --> pdb=" O LEU A 720 " (cutoff:3.500A) Processing helix chain 'A' and resid 743 through 758 Processing helix chain 'A' and resid 984 through 992 Processing helix chain 'A' and resid 1009 through 1014 Processing helix chain 'A' and resid 1015 through 1029 Processing helix chain 'A' and resid 1030 through 1034 Processing helix chain 'A' and resid 1039 through 1056 removed outlier: 3.777A pdb=" N SER A1055 " --> pdb=" O GLU A1051 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ILE A1056 " --> pdb=" O GLY A1052 " (cutoff:3.500A) Processing helix chain 'A' and resid 1057 through 1060 removed outlier: 3.523A pdb=" N ARG A1060 " --> pdb=" O MET A1057 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1057 through 1060' Processing helix chain 'A' and resid 1075 through 1090 Processing helix chain 'A' and resid 1096 through 1111 Processing helix chain 'A' and resid 1132 through 1156 Processing helix chain 'A' and resid 1162 through 1179 Processing helix chain 'A' and resid 1184 through 1197 Processing helix chain 'A' and resid 1202 through 1214 Processing helix chain 'A' and resid 1244 through 1261 Processing helix chain 'A' and resid 1267 through 1278 Processing helix chain 'A' and resid 1286 through 1302 removed outlier: 3.501A pdb=" N THR A1290 " --> pdb=" O SER A1286 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ILE A1291 " --> pdb=" O THR A1287 " (cutoff:3.500A) Processing helix chain 'A' and resid 1435 through 1445 removed outlier: 3.800A pdb=" N LEU A1439 " --> pdb=" O ASN A1435 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N GLY A1445 " --> pdb=" O ALA A1441 " (cutoff:3.500A) Processing helix chain 'A' and resid 1527 through 1532 removed outlier: 4.440A pdb=" N ASP A1531 " --> pdb=" O VAL A1528 " (cutoff:3.500A) Processing helix chain 'A' and resid 1546 through 1553 removed outlier: 3.617A pdb=" N CYS A1553 " --> pdb=" O LYS A1549 " (cutoff:3.500A) Processing helix chain 'A' and resid 1657 through 1675 removed outlier: 4.574A pdb=" N PHE A1672 " --> pdb=" O ALA A1668 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N LEU A1673 " --> pdb=" O GLU A1669 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N ASN A1674 " --> pdb=" O ASP A1670 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLY A1675 " --> pdb=" O ILE A1671 " (cutoff:3.500A) Processing helix chain 'C' and resid 33 through 40 removed outlier: 6.480A pdb=" N GLU C 38 " --> pdb=" O ALA C 35 " (cutoff:3.500A) Processing helix chain 'C' and resid 141 through 156 Processing helix chain 'B' and resid 88 through 92 removed outlier: 3.712A pdb=" N LEU B 92 " --> pdb=" O PRO B 89 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 307 Processing helix chain 'B' and resid 492 through 496 Processing helix chain 'B' and resid 641 through 650 Processing sheet with id=AA1, first strand: chain 'A' and resid 764 through 765 Processing sheet with id=AA2, first strand: chain 'A' and resid 777 through 780 removed outlier: 3.807A pdb=" N TRP B 599 " --> pdb=" O ILE A 804 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 783 through 789 Processing sheet with id=AA4, first strand: chain 'A' and resid 815 through 818 Processing sheet with id=AA5, first strand: chain 'A' and resid 823 through 827 Processing sheet with id=AA6, first strand: chain 'A' and resid 832 through 834 removed outlier: 5.760A pdb=" N VAL A 833 " --> pdb=" O VAL A 930 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLY A 919 " --> pdb=" O THR A 916 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N MET A 853 " --> pdb=" O VAL A 888 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N VAL A 888 " --> pdb=" O MET A 853 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 839 through 840 Processing sheet with id=AA8, first strand: chain 'A' and resid 936 through 944 removed outlier: 3.632A pdb=" N LYS A 974 " --> pdb=" O VAL A1364 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 956 through 959 removed outlier: 3.930A pdb=" N VAL A1315 " --> pdb=" O HIS A1324 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N TYR A1317 " --> pdb=" O ALA A1322 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N ALA A1322 " --> pdb=" O TYR A1317 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 1225 through 1227 removed outlier: 3.682A pdb=" N TYR A1225 " --> pdb=" O LYS A1219 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 1377 through 1384 removed outlier: 4.046A pdb=" N LYS A1380 " --> pdb=" O CYS A1405 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 1461 through 1463 Processing sheet with id=AB4, first strand: chain 'A' and resid 1461 through 1463 Processing sheet with id=AB5, first strand: chain 'A' and resid 1625 through 1628 removed outlier: 8.850A pdb=" N GLU A1597 " --> pdb=" O PHE A1633 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N TYR A1635 " --> pdb=" O GLU A1597 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N THR A1599 " --> pdb=" O TYR A1635 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N THR A1580 " --> pdb=" O ILE A1565 " (cutoff:3.500A) removed outlier: 5.872A pdb=" N ILE A1565 " --> pdb=" O THR A1580 " (cutoff:3.500A) removed outlier: 5.976A pdb=" N LEU A1582 " --> pdb=" O VAL A1563 " (cutoff:3.500A) removed outlier: 7.397A pdb=" N VAL A1563 " --> pdb=" O LEU A1582 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N ILE A1584 " --> pdb=" O TYR A1561 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N TYR A1561 " --> pdb=" O ILE A1584 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N LYS A1586 " --> pdb=" O TYR A1559 " (cutoff:3.500A) removed outlier: 4.939A pdb=" N TYR A1559 " --> pdb=" O LYS A1586 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N TYR A1559 " --> pdb=" O GLY A1621 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLY A1621 " --> pdb=" O TYR A1559 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ILE A1619 " --> pdb=" O TYR A1561 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 43 through 48 removed outlier: 5.359A pdb=" N LEU C 57 " --> pdb=" O LEU C 45 " (cutoff:3.500A) removed outlier: 11.371A pdb=" N ARG C 47 " --> pdb=" O ASP C 55 " (cutoff:3.500A) removed outlier: 10.965A pdb=" N ASP C 55 " --> pdb=" O ARG C 47 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ASP C 55 " --> pdb=" O LYS C 77 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N LEU C 57 " --> pdb=" O THR C 75 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N THR C 75 " --> pdb=" O LEU C 57 " (cutoff:3.500A) removed outlier: 5.080A pdb=" N GLY C 59 " --> pdb=" O MET C 73 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N MET C 73 " --> pdb=" O GLY C 59 " (cutoff:3.500A) removed outlier: 5.785A pdb=" N VAL C 109 " --> pdb=" O LYS C 122 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N LYS C 122 " --> pdb=" O VAL C 109 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N TYR C 111 " --> pdb=" O VAL C 120 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N TYR C 130 " --> pdb=" O SER C 48 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N SER C 48 " --> pdb=" O TYR C 130 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N MET C 132 " --> pdb=" O VAL C 46 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 29 through 31 removed outlier: 3.555A pdb=" N ALA D 51 " --> pdb=" O ARG D 21 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 38 through 41 Processing sheet with id=AB9, first strand: chain 'B' and resid 80 through 86 removed outlier: 8.159A pdb=" N ASN B 38 " --> pdb=" O PRO B 28 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ALA B 27 " --> pdb=" O THR B 652 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 31 through 32 removed outlier: 6.450A pdb=" N PHE B 31 " --> pdb=" O THR B 120 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LYS B 113 " --> pdb=" O VAL B 106 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N SER B 67 " --> pdb=" O ILE B 56 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 31 through 32 removed outlier: 6.450A pdb=" N PHE B 31 " --> pdb=" O THR B 120 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LYS B 113 " --> pdb=" O VAL B 106 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ALA B 52 " --> pdb=" O VAL B 71 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 125 through 130 Processing sheet with id=AC4, first strand: chain 'B' and resid 134 through 135 removed outlier: 3.520A pdb=" N PHE B 217 " --> pdb=" O TRP B 199 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N THR B 159 " --> pdb=" O GLU B 176 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N VAL B 174 " --> pdb=" O LEU B 161 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 140 through 141 Processing sheet with id=AC6, first strand: chain 'B' and resid 228 through 233 Processing sheet with id=AC7, first strand: chain 'B' and resid 280 through 282 Processing sheet with id=AC8, first strand: chain 'B' and resid 280 through 282 Processing sheet with id=AC9, first strand: chain 'B' and resid 353 through 356 Processing sheet with id=AD1, first strand: chain 'B' and resid 362 through 363 removed outlier: 7.426A pdb=" N THR B 429 " --> pdb=" O ALA B 456 " (cutoff:3.500A) removed outlier: 5.278A pdb=" N ALA B 392 " --> pdb=" O ASP B 405 " (cutoff:3.500A) removed outlier: 5.843A pdb=" N ASP B 405 " --> pdb=" O ALA B 392 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N THR B 394 " --> pdb=" O ASP B 403 " (cutoff:3.500A) removed outlier: 5.816A pdb=" N ASP B 403 " --> pdb=" O THR B 394 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 362 through 363 removed outlier: 7.426A pdb=" N THR B 429 " --> pdb=" O ALA B 456 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 464 through 468 Processing sheet with id=AD4, first strand: chain 'B' and resid 508 through 509 removed outlier: 3.549A pdb=" N ARG B 539 " --> pdb=" O LEU B 504 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N TYR B 544 " --> pdb=" O VAL B 555 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 8 through 12 removed outlier: 3.535A pdb=" N SER E 54 " --> pdb=" O TYR E 9 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N THR E 11 " --> pdb=" O VAL E 52 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N VAL E 52 " --> pdb=" O THR E 11 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 16 through 17 Processing sheet with id=AD7, first strand: chain 'E' and resid 67 through 69 removed outlier: 3.541A pdb=" N GLU E 69 " --> pdb=" O LYS E 82 " (cutoff:3.500A) 588 hydrogen bonds defined for protein. 1578 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: 6.72 Time building geometry restraints manager: 5.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 2521 1.32 - 1.45: 4071 1.45 - 1.58: 8585 1.58 - 1.71: 0 1.71 - 1.85: 109 Bond restraints: 15286 Sorted by residual: bond pdb=" C7 NAG F 2 " pdb=" N2 NAG F 2 " ideal model delta sigma weight residual 1.346 1.462 -0.116 2.00e-02 2.50e+03 3.36e+01 bond pdb=" C7 NAG F 1 " pdb=" N2 NAG F 1 " ideal model delta sigma weight residual 1.346 1.458 -0.112 2.00e-02 2.50e+03 3.16e+01 bond pdb=" C1 NAG F 2 " pdb=" O5 NAG F 2 " ideal model delta sigma weight residual 1.406 1.504 -0.098 2.00e-02 2.50e+03 2.38e+01 bond pdb=" C1 NAG F 1 " pdb=" O5 NAG F 1 " ideal model delta sigma weight residual 1.406 1.503 -0.097 2.00e-02 2.50e+03 2.33e+01 bond pdb=" C5 NAG F 2 " pdb=" O5 NAG F 2 " ideal model delta sigma weight residual 1.413 1.472 -0.059 2.00e-02 2.50e+03 8.69e+00 ... (remaining 15281 not shown) Histogram of bond angle deviations from ideal: 99.07 - 106.06: 329 106.06 - 113.05: 8458 113.05 - 120.04: 5066 120.04 - 127.03: 6731 127.03 - 134.02: 158 Bond angle restraints: 20742 Sorted by residual: angle pdb=" N VAL A 984 " pdb=" CA VAL A 984 " pdb=" C VAL A 984 " ideal model delta sigma weight residual 111.91 106.69 5.22 8.90e-01 1.26e+00 3.44e+01 angle pdb=" N GLY A1522 " pdb=" CA GLY A1522 " pdb=" C GLY A1522 " ideal model delta sigma weight residual 111.35 117.61 -6.26 1.20e+00 6.94e-01 2.72e+01 angle pdb=" N ILE A 683 " pdb=" CA ILE A 683 " pdb=" C ILE A 683 " ideal model delta sigma weight residual 111.81 108.64 3.17 8.60e-01 1.35e+00 1.36e+01 angle pdb=" N ILE A 997 " pdb=" CA ILE A 997 " pdb=" C ILE A 997 " ideal model delta sigma weight residual 113.20 109.77 3.43 9.60e-01 1.09e+00 1.27e+01 angle pdb=" CA TYR B 256 " pdb=" CB TYR B 256 " pdb=" CG TYR B 256 " ideal model delta sigma weight residual 113.90 120.21 -6.31 1.80e+00 3.09e-01 1.23e+01 ... (remaining 20737 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.59: 8246 17.59 - 35.17: 868 35.17 - 52.76: 154 52.76 - 70.35: 26 70.35 - 87.93: 14 Dihedral angle restraints: 9308 sinusoidal: 3747 harmonic: 5561 Sorted by residual: dihedral pdb=" CB CYS D 14 " pdb=" SG CYS D 14 " pdb=" SG CYS D 38 " pdb=" CB CYS D 38 " ideal model delta sinusoidal sigma weight residual -86.00 -162.42 76.42 1 1.00e+01 1.00e-02 7.35e+01 dihedral pdb=" CB CYS B 634 " pdb=" SG CYS B 634 " pdb=" SG CYS B 669 " pdb=" CB CYS B 669 " ideal model delta sinusoidal sigma weight residual -86.00 -16.02 -69.98 1 1.00e+01 1.00e-02 6.31e+01 dihedral pdb=" CB CYS A 699 " pdb=" SG CYS A 699 " pdb=" SG CYS A 731 " pdb=" CB CYS A 731 " ideal model delta sinusoidal sigma weight residual 93.00 26.57 66.43 1 1.00e+01 1.00e-02 5.76e+01 ... (remaining 9305 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.990: 2366 0.990 - 1.980: 0 1.980 - 2.970: 0 2.970 - 3.960: 0 3.960 - 4.949: 1 Chirality restraints: 2367 Sorted by residual: chirality pdb=" C1 NAG F 2 " pdb=" O4 NAG F 1 " pdb=" C2 NAG F 2 " pdb=" O5 NAG F 2 " both_signs ideal model delta sigma weight residual False -2.40 2.55 -4.95 2.00e-02 2.50e+03 6.12e+04 chirality pdb=" CA TYR B 256 " pdb=" N TYR B 256 " pdb=" C TYR B 256 " pdb=" CB TYR B 256 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.74e+00 chirality pdb=" CB VAL A1015 " pdb=" CA VAL A1015 " pdb=" CG1 VAL A1015 " pdb=" CG2 VAL A1015 " both_signs ideal model delta sigma weight residual False -2.63 -2.47 -0.16 2.00e-01 2.50e+01 6.49e-01 ... (remaining 2364 not shown) Planarity restraints: 2649 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C CYS D 34 " -0.056 5.00e-02 4.00e+02 8.51e-02 1.16e+01 pdb=" N PRO D 35 " 0.147 5.00e-02 4.00e+02 pdb=" CA PRO D 35 " -0.044 5.00e-02 4.00e+02 pdb=" CD PRO D 35 " -0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A1268 " 0.038 5.00e-02 4.00e+02 5.78e-02 5.35e+00 pdb=" N PRO A1269 " -0.100 5.00e-02 4.00e+02 pdb=" CA PRO A1269 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO A1269 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A1037 " 0.029 5.00e-02 4.00e+02 4.36e-02 3.04e+00 pdb=" N PRO A1038 " -0.075 5.00e-02 4.00e+02 pdb=" CA PRO A1038 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO A1038 " 0.024 5.00e-02 4.00e+02 ... (remaining 2646 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 186 2.61 - 3.18: 13333 3.18 - 3.76: 21573 3.76 - 4.33: 30818 4.33 - 4.90: 51882 Nonbonded interactions: 117792 Sorted by model distance: nonbonded pdb=" OH TYR B 44 " pdb=" OD1 ASN B 500 " model vdw 2.041 2.440 nonbonded pdb=" NZ LYS B 566 " pdb=" O CYS B 567 " model vdw 2.153 2.520 nonbonded pdb=" O ARG A1060 " pdb=" NH2 ARG B 195 " model vdw 2.164 2.520 nonbonded pdb=" OG1 THR C 49 " pdb=" OD1 ASP C 129 " model vdw 2.167 2.440 nonbonded pdb=" O GLU B 232 " pdb=" OG1 THR B 249 " model vdw 2.203 2.440 ... (remaining 117787 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: 0.960 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: 0.010 Extract box with map and model: 5.800 Check model and map are aligned: 0.230 Set scattering table: 0.140 Process input model: 41.630 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.050 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:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7419 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 : 0.006 0.116 15286 Z= 0.415 Angle : 0.740 8.642 20742 Z= 0.432 Chirality : 0.112 4.949 2367 Planarity : 0.004 0.085 2648 Dihedral : 14.346 87.932 5654 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.85 % Favored : 92.94 % Rotamer: Outliers : 0.06 % Allowed : 6.32 % Favored : 93.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.84 % 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: -4.28 (0.16), residues: 1883 helix: -2.84 (0.20), residues: 335 sheet: -2.42 (0.18), residues: 626 loop : -3.12 (0.16), residues: 922 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1077 HIS 0.005 0.001 HIS A 692 PHE 0.023 0.002 PHE B 255 TYR 0.026 0.002 TYR B 256 ARG 0.003 0.000 ARG A1214 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3766 Ramachandran restraints generated. 1883 Oldfield, 0 Emsley, 1883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3766 Ramachandran restraints generated. 1883 Oldfield, 0 Emsley, 1883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 113 time to evaluate : 1.863 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 53 ASN cc_start: 0.7679 (m-40) cc_final: 0.7015 (p0) outliers start: 1 outliers final: 1 residues processed: 114 average time/residue: 0.2892 time to fit residues: 49.2192 Evaluate side-chains 81 residues out of total 1676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 80 time to evaluate : 1.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 699 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 158 optimal weight: 20.0000 chunk 142 optimal weight: 0.9990 chunk 79 optimal weight: 6.9990 chunk 48 optimal weight: 3.9990 chunk 96 optimal weight: 0.8980 chunk 76 optimal weight: 1.9990 chunk 147 optimal weight: 9.9990 chunk 57 optimal weight: 0.9990 chunk 89 optimal weight: 10.0000 chunk 109 optimal weight: 8.9990 chunk 170 optimal weight: 0.9980 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 680 GLN A 692 HIS A 787 GLN A1035 HIS A1088 GLN A1125 GLN A1178 ASN A1319 HIS A1343 ASN A1360 HIS A1608 ASN ** A1616 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 446 ASN B 532 GLN E 37 ASN E 59 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7393 moved from start: 0.1393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15286 Z= 0.176 Angle : 0.576 7.612 20742 Z= 0.303 Chirality : 0.044 0.254 2367 Planarity : 0.004 0.076 2648 Dihedral : 5.351 51.443 2085 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.15 % Favored : 94.80 % Rotamer: Outliers : 1.01 % Allowed : 11.63 % Favored : 87.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.91 (0.17), residues: 1883 helix: -0.90 (0.27), residues: 345 sheet: -1.76 (0.19), residues: 635 loop : -2.43 (0.17), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1273 HIS 0.004 0.001 HIS A1030 PHE 0.015 0.001 PHE A 728 TYR 0.017 0.001 TYR A1111 ARG 0.002 0.000 ARG A1279 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3766 Ramachandran restraints generated. 1883 Oldfield, 0 Emsley, 1883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3766 Ramachandran restraints generated. 1883 Oldfield, 0 Emsley, 1883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 96 time to evaluate : 1.718 Fit side-chains revert: symmetry clash REVERT: A 1635 TYR cc_start: 0.8176 (m-80) cc_final: 0.7884 (m-10) outliers start: 17 outliers final: 10 residues processed: 109 average time/residue: 0.2530 time to fit residues: 43.1878 Evaluate side-chains 94 residues out of total 1676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 84 time to evaluate : 1.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 699 CYS Chi-restraints excluded: chain A residue 792 ASP Chi-restraints excluded: chain A residue 952 THR Chi-restraints excluded: chain A residue 1009 GLU Chi-restraints excluded: chain A residue 1114 ASP Chi-restraints excluded: chain A residue 1132 THR Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 134 MET Chi-restraints excluded: chain E residue 33 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 94 optimal weight: 50.0000 chunk 52 optimal weight: 6.9990 chunk 142 optimal weight: 5.9990 chunk 116 optimal weight: 9.9990 chunk 47 optimal weight: 4.9990 chunk 171 optimal weight: 4.9990 chunk 184 optimal weight: 50.0000 chunk 152 optimal weight: 6.9990 chunk 169 optimal weight: 8.9990 chunk 58 optimal weight: 2.9990 chunk 137 optimal weight: 5.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 753 HIS A 828 ASN A1110 ASN ** A1616 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 78 GLN ** B 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 562 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7514 moved from start: 0.1773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 15286 Z= 0.416 Angle : 0.640 8.272 20742 Z= 0.329 Chirality : 0.044 0.256 2367 Planarity : 0.004 0.071 2648 Dihedral : 5.285 47.250 2085 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 12.09 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.27 % Favored : 93.68 % Rotamer: Outliers : 2.27 % Allowed : 13.90 % Favored : 83.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.36 (0.18), residues: 1883 helix: -0.27 (0.28), residues: 344 sheet: -1.53 (0.19), residues: 634 loop : -2.06 (0.18), residues: 905 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1644 HIS 0.006 0.001 HIS A1499 PHE 0.016 0.002 PHE A1019 TYR 0.016 0.002 TYR B 312 ARG 0.010 0.001 ARG E 50 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3766 Ramachandran restraints generated. 1883 Oldfield, 0 Emsley, 1883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3766 Ramachandran restraints generated. 1883 Oldfield, 0 Emsley, 1883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 86 time to evaluate : 1.823 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1635 TYR cc_start: 0.8096 (m-80) cc_final: 0.7882 (m-10) outliers start: 38 outliers final: 16 residues processed: 116 average time/residue: 0.2463 time to fit residues: 44.9774 Evaluate side-chains 93 residues out of total 1676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 77 time to evaluate : 1.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 686 ILE Chi-restraints excluded: chain A residue 792 ASP Chi-restraints excluded: chain A residue 952 THR Chi-restraints excluded: chain A residue 1114 ASP Chi-restraints excluded: chain A residue 1132 THR Chi-restraints excluded: chain A residue 1247 MET Chi-restraints excluded: chain A residue 1383 THR Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 134 MET Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 417 VAL Chi-restraints excluded: chain B residue 484 ILE Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 67 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 168 optimal weight: 2.9990 chunk 128 optimal weight: 2.9990 chunk 88 optimal weight: 20.0000 chunk 18 optimal weight: 4.9990 chunk 81 optimal weight: 3.9990 chunk 114 optimal weight: 20.0000 chunk 171 optimal weight: 5.9990 chunk 181 optimal weight: 20.0000 chunk 89 optimal weight: 1.9990 chunk 162 optimal weight: 5.9990 chunk 48 optimal weight: 0.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1088 GLN ** A1616 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7466 moved from start: 0.2108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 15286 Z= 0.240 Angle : 0.559 7.274 20742 Z= 0.289 Chirality : 0.043 0.234 2367 Planarity : 0.004 0.069 2648 Dihedral : 4.978 44.730 2084 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.42 % Favored : 94.53 % Rotamer: Outliers : 2.15 % Allowed : 15.69 % Favored : 82.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.84 % 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: -1.87 (0.18), residues: 1883 helix: 0.34 (0.28), residues: 343 sheet: -1.28 (0.20), residues: 628 loop : -1.80 (0.19), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A1644 HIS 0.004 0.001 HIS A1030 PHE 0.012 0.001 PHE A1019 TYR 0.014 0.001 TYR B 312 ARG 0.006 0.000 ARG E 50 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3766 Ramachandran restraints generated. 1883 Oldfield, 0 Emsley, 1883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3766 Ramachandran restraints generated. 1883 Oldfield, 0 Emsley, 1883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 86 time to evaluate : 1.726 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1635 TYR cc_start: 0.8075 (m-80) cc_final: 0.7859 (m-10) REVERT: E 42 LEU cc_start: 0.8005 (tp) cc_final: 0.7801 (mt) outliers start: 36 outliers final: 18 residues processed: 115 average time/residue: 0.2446 time to fit residues: 44.4169 Evaluate side-chains 92 residues out of total 1676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 74 time to evaluate : 1.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 686 ILE Chi-restraints excluded: chain A residue 792 ASP Chi-restraints excluded: chain A residue 822 ASP Chi-restraints excluded: chain A residue 1114 ASP Chi-restraints excluded: chain A residue 1132 THR Chi-restraints excluded: chain A residue 1383 THR Chi-restraints excluded: chain A residue 1645 ILE Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 134 MET Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 417 VAL Chi-restraints excluded: chain B residue 484 ILE Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 67 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 151 optimal weight: 7.9990 chunk 103 optimal weight: 6.9990 chunk 2 optimal weight: 0.6980 chunk 135 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 155 optimal weight: 8.9990 chunk 125 optimal weight: 7.9990 chunk 0 optimal weight: 20.0000 chunk 92 optimal weight: 3.9990 chunk 163 optimal weight: 9.9990 chunk 45 optimal weight: 1.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1616 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 159 ASN ** B 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7461 moved from start: 0.2356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 15286 Z= 0.224 Angle : 0.561 9.557 20742 Z= 0.286 Chirality : 0.043 0.223 2367 Planarity : 0.004 0.063 2648 Dihedral : 4.814 40.112 2084 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.36 % Favored : 94.58 % Rotamer: Outliers : 2.09 % Allowed : 16.83 % Favored : 81.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.84 % 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: -1.50 (0.19), residues: 1883 helix: 0.53 (0.29), residues: 344 sheet: -0.96 (0.20), residues: 628 loop : -1.59 (0.19), residues: 911 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 133 HIS 0.004 0.001 HIS A1030 PHE 0.012 0.001 PHE A1019 TYR 0.019 0.001 TYR A1561 ARG 0.004 0.000 ARG E 50 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3766 Ramachandran restraints generated. 1883 Oldfield, 0 Emsley, 1883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3766 Ramachandran restraints generated. 1883 Oldfield, 0 Emsley, 1883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 79 time to evaluate : 1.826 Fit side-chains revert: symmetry clash REVERT: A 747 MET cc_start: 0.6712 (OUTLIER) cc_final: 0.6111 (ptm) REVERT: A 1635 TYR cc_start: 0.8054 (m-80) cc_final: 0.7831 (m-10) outliers start: 35 outliers final: 21 residues processed: 108 average time/residue: 0.2326 time to fit residues: 40.4664 Evaluate side-chains 97 residues out of total 1676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 75 time to evaluate : 1.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 686 ILE Chi-restraints excluded: chain A residue 699 CYS Chi-restraints excluded: chain A residue 747 MET Chi-restraints excluded: chain A residue 792 ASP Chi-restraints excluded: chain A residue 859 MET Chi-restraints excluded: chain A residue 952 THR Chi-restraints excluded: chain A residue 1114 ASP Chi-restraints excluded: chain A residue 1132 THR Chi-restraints excluded: chain A residue 1247 MET Chi-restraints excluded: chain A residue 1290 THR Chi-restraints excluded: chain A residue 1645 ILE Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 134 MET Chi-restraints excluded: chain B residue 25 ILE Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 417 VAL Chi-restraints excluded: chain B residue 533 ASN Chi-restraints excluded: chain E residue 67 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 61 optimal weight: 0.8980 chunk 163 optimal weight: 5.9990 chunk 35 optimal weight: 8.9990 chunk 106 optimal weight: 2.9990 chunk 44 optimal weight: 0.9990 chunk 181 optimal weight: 0.8980 chunk 150 optimal weight: 9.9990 chunk 84 optimal weight: 6.9990 chunk 15 optimal weight: 0.8980 chunk 60 optimal weight: 0.7980 chunk 95 optimal weight: 6.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1616 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 80 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7412 moved from start: 0.2584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 15286 Z= 0.144 Angle : 0.532 8.314 20742 Z= 0.272 Chirality : 0.043 0.209 2367 Planarity : 0.003 0.061 2648 Dihedral : 4.586 36.419 2084 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 1.61 % Allowed : 17.12 % Favored : 81.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.84 % 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: -1.20 (0.19), residues: 1883 helix: 0.84 (0.29), residues: 346 sheet: -0.72 (0.20), residues: 638 loop : -1.47 (0.19), residues: 899 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A1273 HIS 0.005 0.001 HIS A1030 PHE 0.013 0.001 PHE A 728 TYR 0.029 0.001 TYR E 23 ARG 0.008 0.000 ARG E 50 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3766 Ramachandran restraints generated. 1883 Oldfield, 0 Emsley, 1883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3766 Ramachandran restraints generated. 1883 Oldfield, 0 Emsley, 1883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 83 time to evaluate : 1.726 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 747 MET cc_start: 0.6769 (OUTLIER) cc_final: 0.6174 (ptm) REVERT: A 1635 TYR cc_start: 0.8058 (m-80) cc_final: 0.7834 (m-10) REVERT: E 42 LEU cc_start: 0.7839 (mt) cc_final: 0.7566 (mt) outliers start: 27 outliers final: 18 residues processed: 106 average time/residue: 0.2353 time to fit residues: 41.1311 Evaluate side-chains 97 residues out of total 1676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 78 time to evaluate : 1.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 686 ILE Chi-restraints excluded: chain A residue 699 CYS Chi-restraints excluded: chain A residue 747 MET Chi-restraints excluded: chain A residue 792 ASP Chi-restraints excluded: chain A residue 822 ASP Chi-restraints excluded: chain A residue 859 MET Chi-restraints excluded: chain A residue 884 VAL Chi-restraints excluded: chain A residue 952 THR Chi-restraints excluded: chain A residue 1114 ASP Chi-restraints excluded: chain A residue 1132 THR Chi-restraints excluded: chain A residue 1247 MET Chi-restraints excluded: chain A residue 1645 ILE Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain B residue 417 VAL Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain B residue 493 ILE Chi-restraints excluded: chain E residue 67 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 175 optimal weight: 8.9990 chunk 20 optimal weight: 6.9990 chunk 103 optimal weight: 9.9990 chunk 132 optimal weight: 5.9990 chunk 102 optimal weight: 3.9990 chunk 153 optimal weight: 4.9990 chunk 101 optimal weight: 5.9990 chunk 181 optimal weight: 8.9990 chunk 113 optimal weight: 1.9990 chunk 110 optimal weight: 5.9990 chunk 83 optimal weight: 8.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1366 HIS A1534 GLN ** A1616 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 481 HIS B 527 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7526 moved from start: 0.2635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 15286 Z= 0.383 Angle : 0.622 9.155 20742 Z= 0.314 Chirality : 0.044 0.231 2367 Planarity : 0.004 0.058 2648 Dihedral : 4.799 30.010 2084 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 12.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer: Outliers : 2.51 % Allowed : 17.36 % Favored : 80.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.84 % 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: -1.12 (0.19), residues: 1883 helix: 0.80 (0.29), residues: 344 sheet: -0.68 (0.20), residues: 638 loop : -1.35 (0.20), residues: 901 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1106 HIS 0.004 0.001 HIS A1023 PHE 0.014 0.001 PHE A1019 TYR 0.031 0.002 TYR E 23 ARG 0.005 0.001 ARG E 50 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3766 Ramachandran restraints generated. 1883 Oldfield, 0 Emsley, 1883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3766 Ramachandran restraints generated. 1883 Oldfield, 0 Emsley, 1883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 78 time to evaluate : 1.821 Fit side-chains REVERT: A 747 MET cc_start: 0.6825 (OUTLIER) cc_final: 0.6306 (ptm) REVERT: A 1635 TYR cc_start: 0.8067 (m-80) cc_final: 0.7824 (m-10) REVERT: C 73 MET cc_start: 0.6514 (OUTLIER) cc_final: 0.6066 (tpt) outliers start: 42 outliers final: 29 residues processed: 113 average time/residue: 0.2389 time to fit residues: 43.9581 Evaluate side-chains 106 residues out of total 1676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 75 time to evaluate : 1.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 686 ILE Chi-restraints excluded: chain A residue 699 CYS Chi-restraints excluded: chain A residue 747 MET Chi-restraints excluded: chain A residue 792 ASP Chi-restraints excluded: chain A residue 822 ASP Chi-restraints excluded: chain A residue 884 VAL Chi-restraints excluded: chain A residue 952 THR Chi-restraints excluded: chain A residue 979 VAL Chi-restraints excluded: chain A residue 1114 ASP Chi-restraints excluded: chain A residue 1132 THR Chi-restraints excluded: chain A residue 1247 MET Chi-restraints excluded: chain A residue 1475 VAL Chi-restraints excluded: chain A residue 1645 ILE Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 73 MET Chi-restraints excluded: chain C residue 118 CYS Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 134 MET Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain B residue 417 VAL Chi-restraints excluded: chain B residue 484 ILE Chi-restraints excluded: chain B residue 493 ILE Chi-restraints excluded: chain B residue 533 ASN Chi-restraints excluded: chain E residue 15 THR Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 66 CYS Chi-restraints excluded: chain E residue 67 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 112 optimal weight: 4.9990 chunk 72 optimal weight: 10.0000 chunk 108 optimal weight: 0.9990 chunk 54 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 115 optimal weight: 0.5980 chunk 123 optimal weight: 0.2980 chunk 89 optimal weight: 7.9990 chunk 16 optimal weight: 1.9990 chunk 142 optimal weight: 10.0000 chunk 164 optimal weight: 4.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 753 HIS A1088 GLN ** A1616 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7435 moved from start: 0.2824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 15286 Z= 0.163 Angle : 0.553 8.716 20742 Z= 0.281 Chirality : 0.043 0.215 2367 Planarity : 0.003 0.059 2648 Dihedral : 4.554 26.200 2084 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 1.97 % Allowed : 17.84 % Favored : 80.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.84 % 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: -0.86 (0.19), residues: 1883 helix: 0.98 (0.29), residues: 346 sheet: -0.51 (0.20), residues: 646 loop : -1.19 (0.20), residues: 891 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 469 HIS 0.007 0.001 HIS A1030 PHE 0.013 0.001 PHE A 728 TYR 0.040 0.001 TYR E 23 ARG 0.008 0.000 ARG E 50 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3766 Ramachandran restraints generated. 1883 Oldfield, 0 Emsley, 1883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3766 Ramachandran restraints generated. 1883 Oldfield, 0 Emsley, 1883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 79 time to evaluate : 1.928 Fit side-chains REVERT: A 747 MET cc_start: 0.6837 (OUTLIER) cc_final: 0.6357 (ptm) REVERT: A 1635 TYR cc_start: 0.8063 (m-80) cc_final: 0.7815 (m-10) REVERT: C 73 MET cc_start: 0.6649 (OUTLIER) cc_final: 0.6210 (tpt) outliers start: 33 outliers final: 24 residues processed: 106 average time/residue: 0.2319 time to fit residues: 40.6193 Evaluate side-chains 102 residues out of total 1676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 76 time to evaluate : 1.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 686 ILE Chi-restraints excluded: chain A residue 699 CYS Chi-restraints excluded: chain A residue 747 MET Chi-restraints excluded: chain A residue 792 ASP Chi-restraints excluded: chain A residue 822 ASP Chi-restraints excluded: chain A residue 884 VAL Chi-restraints excluded: chain A residue 952 THR Chi-restraints excluded: chain A residue 1114 ASP Chi-restraints excluded: chain A residue 1132 THR Chi-restraints excluded: chain A residue 1247 MET Chi-restraints excluded: chain A residue 1475 VAL Chi-restraints excluded: chain A residue 1645 ILE Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 73 MET Chi-restraints excluded: chain C residue 118 CYS Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain B residue 417 VAL Chi-restraints excluded: chain B residue 484 ILE Chi-restraints excluded: chain B residue 493 ILE Chi-restraints excluded: chain E residue 66 CYS Chi-restraints excluded: chain E residue 67 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 173 optimal weight: 9.9990 chunk 158 optimal weight: 5.9990 chunk 168 optimal weight: 4.9990 chunk 101 optimal weight: 3.9990 chunk 73 optimal weight: 3.9990 chunk 132 optimal weight: 4.9990 chunk 51 optimal weight: 0.9980 chunk 152 optimal weight: 9.9990 chunk 159 optimal weight: 5.9990 chunk 110 optimal weight: 7.9990 chunk 178 optimal weight: 2.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 753 HIS A1088 GLN ** A1616 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7491 moved from start: 0.2851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 15286 Z= 0.293 Angle : 0.582 8.191 20742 Z= 0.295 Chirality : 0.043 0.222 2367 Planarity : 0.004 0.056 2648 Dihedral : 4.607 27.072 2084 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 1.85 % Allowed : 18.38 % Favored : 79.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.84 % 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: -0.88 (0.19), residues: 1883 helix: 0.97 (0.29), residues: 346 sheet: -0.56 (0.20), residues: 659 loop : -1.17 (0.21), residues: 878 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 917 HIS 0.004 0.001 HIS A1030 PHE 0.012 0.001 PHE A1019 TYR 0.042 0.001 TYR E 23 ARG 0.003 0.000 ARG E 50 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3766 Ramachandran restraints generated. 1883 Oldfield, 0 Emsley, 1883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3766 Ramachandran restraints generated. 1883 Oldfield, 0 Emsley, 1883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 77 time to evaluate : 1.887 Fit side-chains REVERT: A 747 MET cc_start: 0.6876 (OUTLIER) cc_final: 0.6384 (ptm) REVERT: A 1635 TYR cc_start: 0.8065 (m-80) cc_final: 0.7802 (m-10) REVERT: C 73 MET cc_start: 0.6645 (OUTLIER) cc_final: 0.6224 (tpt) outliers start: 31 outliers final: 26 residues processed: 102 average time/residue: 0.2277 time to fit residues: 38.0991 Evaluate side-chains 103 residues out of total 1676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 75 time to evaluate : 1.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 686 ILE Chi-restraints excluded: chain A residue 699 CYS Chi-restraints excluded: chain A residue 747 MET Chi-restraints excluded: chain A residue 792 ASP Chi-restraints excluded: chain A residue 822 ASP Chi-restraints excluded: chain A residue 884 VAL Chi-restraints excluded: chain A residue 952 THR Chi-restraints excluded: chain A residue 1114 ASP Chi-restraints excluded: chain A residue 1132 THR Chi-restraints excluded: chain A residue 1247 MET Chi-restraints excluded: chain A residue 1475 VAL Chi-restraints excluded: chain A residue 1645 ILE Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 73 MET Chi-restraints excluded: chain C residue 118 CYS Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 134 MET Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain B residue 417 VAL Chi-restraints excluded: chain B residue 484 ILE Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain B residue 493 ILE Chi-restraints excluded: chain E residue 66 CYS Chi-restraints excluded: chain E residue 67 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 108 optimal weight: 3.9990 chunk 84 optimal weight: 6.9990 chunk 124 optimal weight: 9.9990 chunk 187 optimal weight: 50.0000 chunk 172 optimal weight: 0.0370 chunk 149 optimal weight: 0.0970 chunk 15 optimal weight: 0.6980 chunk 115 optimal weight: 8.9990 chunk 91 optimal weight: 0.9990 chunk 118 optimal weight: 2.9990 chunk 158 optimal weight: 0.9980 overall best weight: 0.5658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1088 GLN A1278 GLN ** A1616 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7394 moved from start: 0.3104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 15286 Z= 0.133 Angle : 0.556 14.554 20742 Z= 0.278 Chirality : 0.043 0.217 2367 Planarity : 0.004 0.060 2648 Dihedral : 4.371 25.797 2084 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 1.31 % Allowed : 18.68 % Favored : 80.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.19), residues: 1883 helix: 1.22 (0.29), residues: 346 sheet: -0.38 (0.21), residues: 636 loop : -1.07 (0.20), residues: 901 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 917 HIS 0.004 0.001 HIS A1030 PHE 0.014 0.001 PHE A 728 TYR 0.038 0.001 TYR E 23 ARG 0.005 0.000 ARG E 50 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3766 Ramachandran restraints generated. 1883 Oldfield, 0 Emsley, 1883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3766 Ramachandran restraints generated. 1883 Oldfield, 0 Emsley, 1883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 86 time to evaluate : 1.908 Fit side-chains revert: symmetry clash REVERT: A 747 MET cc_start: 0.6857 (ptt) cc_final: 0.6365 (ptm) REVERT: A 1635 TYR cc_start: 0.8072 (m-80) cc_final: 0.7793 (m-10) REVERT: C 73 MET cc_start: 0.6684 (tpp) cc_final: 0.6265 (tpt) REVERT: E 78 ASN cc_start: 0.7893 (m110) cc_final: 0.7110 (m-40) outliers start: 22 outliers final: 21 residues processed: 107 average time/residue: 0.2457 time to fit residues: 42.2155 Evaluate side-chains 100 residues out of total 1676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 79 time to evaluate : 1.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 686 ILE Chi-restraints excluded: chain A residue 699 CYS Chi-restraints excluded: chain A residue 792 ASP Chi-restraints excluded: chain A residue 822 ASP Chi-restraints excluded: chain A residue 884 VAL Chi-restraints excluded: chain A residue 952 THR Chi-restraints excluded: chain A residue 1132 THR Chi-restraints excluded: chain A residue 1383 THR Chi-restraints excluded: chain A residue 1475 VAL Chi-restraints excluded: chain A residue 1645 ILE Chi-restraints excluded: chain C residue 118 CYS Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain B residue 484 ILE Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain E residue 66 CYS Chi-restraints excluded: chain E residue 67 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 45 optimal weight: 0.9990 chunk 137 optimal weight: 0.8980 chunk 22 optimal weight: 8.9990 chunk 41 optimal weight: 0.0970 chunk 149 optimal weight: 0.9990 chunk 62 optimal weight: 3.9990 chunk 153 optimal weight: 8.9990 chunk 18 optimal weight: 0.0570 chunk 27 optimal weight: 6.9990 chunk 131 optimal weight: 2.9990 chunk 8 optimal weight: 5.9990 overall best weight: 0.6100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1088 GLN A1095 GLN ** A1616 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 = 0.3615 r_free = 0.3615 target = 0.073796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.053998 restraints weight = 59724.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.055823 restraints weight = 29278.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.056265 restraints weight = 18584.694| |-----------------------------------------------------------------------------| r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.3213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 15286 Z= 0.140 Angle : 0.558 14.151 20742 Z= 0.278 Chirality : 0.043 0.212 2367 Planarity : 0.003 0.057 2648 Dihedral : 4.258 26.130 2084 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 1.31 % Allowed : 18.91 % Favored : 79.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.84 % 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: -0.45 (0.20), residues: 1883 helix: 1.35 (0.29), residues: 346 sheet: -0.20 (0.21), residues: 639 loop : -0.99 (0.20), residues: 898 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 917 HIS 0.004 0.001 HIS A1030 PHE 0.015 0.001 PHE A 728 TYR 0.037 0.001 TYR E 23 ARG 0.006 0.000 ARG E 50 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2496.84 seconds wall clock time: 46 minutes 41.11 seconds (2801.11 seconds total)