Starting phenix.real_space_refine on Sun Apr 7 15:09:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kyb_23074/04_2024/7kyb_23074_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kyb_23074/04_2024/7kyb_23074.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kyb_23074/04_2024/7kyb_23074.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kyb_23074/04_2024/7kyb_23074.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kyb_23074/04_2024/7kyb_23074_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kyb_23074/04_2024/7kyb_23074_updated.pdb" } resolution = 3.2 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= 0.004 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: 8 Type Number sf(0) Gaussians Al 1 5.89 5 P 3 5.49 5 Mg 2 5.21 5 S 50 5.16 5 C 6985 2.51 5 N 1763 2.21 5 O 2006 1.98 5 F 4 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 206": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 264": "NH1" <-> "NH2" Residue "A ARG 265": "NH1" <-> "NH2" Residue "A GLU 548": "OE1" <-> "OE2" Residue "A ASP 576": "OD1" <-> "OD2" Residue "A ARG 580": "NH1" <-> "NH2" Residue "A PHE 587": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 599": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 602": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 622": "OE1" <-> "OE2" Residue "A TYR 645": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 667": "OD1" <-> "OD2" Residue "A TYR 693": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 695": "OE1" <-> "OE2" Residue "A ARG 701": "NH1" <-> "NH2" Residue "A ARG 703": "NH1" <-> "NH2" Residue "A GLU 709": "OE1" <-> "OE2" Residue "A GLU 718": "OE1" <-> "OE2" Residue "A ARG 723": "NH1" <-> "NH2" Residue "A ASP 724": "OD1" <-> "OD2" Residue "A ASP 728": "OD1" <-> "OD2" Residue "A PHE 739": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 742": "OE1" <-> "OE2" Residue "A PHE 746": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 750": "OE1" <-> "OE2" Residue "A GLU 761": "OE1" <-> "OE2" Residue "A ASP 787": "OD1" <-> "OD2" Residue "A ASP 793": "OD1" <-> "OD2" Residue "A ARG 809": "NH1" <-> "NH2" Residue "A ASP 810": "OD1" <-> "OD2" Residue "A PHE 813": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 815": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 826": "OE1" <-> "OE2" Residue "A PHE 834": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 842": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 846": "NH1" <-> "NH2" Residue "A ARG 848": "NH1" <-> "NH2" Residue "A ASP 874": "OD1" <-> "OD2" Residue "A GLU 890": "OE1" <-> "OE2" Residue "A GLU 894": "OE1" <-> "OE2" Residue "A ARG 916": "NH1" <-> "NH2" Residue "A GLU 917": "OE1" <-> "OE2" Residue "A ARG 940": "NH1" <-> "NH2" Residue "A GLU 941": "OE1" <-> "OE2" Residue "A ASP 949": "OD1" <-> "OD2" Residue "A ARG 953": "NH1" <-> "NH2" Residue "A GLU 954": "OE1" <-> "OE2" Residue "A GLU 964": "OE1" <-> "OE2" Residue "A ARG 966": "NH1" <-> "NH2" Residue "A ASP 991": "OD1" <-> "OD2" Residue "A GLU 1011": "OE1" <-> "OE2" Residue "A ASP 1021": "OD1" <-> "OD2" Residue "A GLU 1024": "OE1" <-> "OE2" Residue "A PHE 1025": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1028": "OE1" <-> "OE2" Residue "A GLU 1031": "OE1" <-> "OE2" Residue "A ASP 1034": "OD1" <-> "OD2" Residue "A GLU 1043": "OE1" <-> "OE2" Residue "A TYR 1044": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1051": "OE1" <-> "OE2" Residue "A GLU 1052": "OE1" <-> "OE2" Residue "A GLU 1056": "OE1" <-> "OE2" Residue "A PHE 1063": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1084": "OE1" <-> "OE2" Residue "A ASP 1085": "OD1" <-> "OD2" Residue "A PHE 1090": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1104": "NH1" <-> "NH2" Residue "A ASP 1122": "OD1" <-> "OD2" Residue "A ASP 1134": "OD1" <-> "OD2" Residue "A GLU 1150": "OE1" <-> "OE2" Residue "A ASP 1160": "OD1" <-> "OD2" Residue "A TYR 1161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1167": "NH1" <-> "NH2" Residue "A PHE 1191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1210": "OD1" <-> "OD2" Residue "A ASP 1212": "OD1" <-> "OD2" Residue "A TYR 1215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1243": "OD1" <-> "OD2" Residue "A ARG 1262": "NH1" <-> "NH2" Residue "A PHE 1270": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1273": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1276": "OD1" <-> "OD2" Residue "A TYR 1279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1306": "OD1" <-> "OD2" Residue "A ARG 1308": "NH1" <-> "NH2" Residue "A PHE 1310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1314": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1326": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1335": "OD1" <-> "OD2" Residue "A PHE 1337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1341": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1350": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1388": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1394": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1421": "OD1" <-> "OD2" Residue "A TYR 1427": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 51": "NH1" <-> "NH2" Residue "B ARG 52": "NH1" <-> "NH2" Residue "B ASP 56": "OD1" <-> "OD2" Residue "B ARG 62": "NH1" <-> "NH2" Residue "B ARG 73": "NH1" <-> "NH2" Residue "B ASP 101": "OD1" <-> "OD2" Residue "B GLU 102": "OE1" <-> "OE2" Residue "B TYR 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 109": "OD1" <-> "OD2" Residue "B ARG 143": "NH1" <-> "NH2" Residue "B PHE 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 146": "OD1" <-> "OD2" Residue "B ASP 147": "OD1" <-> "OD2" Residue "B GLU 148": "OE1" <-> "OE2" Residue "B ASP 150": "OD1" <-> "OD2" Residue "B ARG 156": "NH1" <-> "NH2" Residue "B TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 187": "NH1" <-> "NH2" Residue "B TYR 189": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 201": "OE1" <-> "OE2" Residue "B ASP 202": "OD1" <-> "OD2" Residue "B ASP 210": "OD1" <-> "OD2" Residue "B ASP 252": "OD1" <-> "OD2" Residue "B GLU 267": "OE1" <-> "OE2" Residue "B TYR 273": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 280": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 290": "OE1" <-> "OE2" Residue "B ASP 295": "OD1" <-> "OD2" Residue "B TYR 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 299": "OE1" <-> "OE2" Residue "B ARG 328": "NH1" <-> "NH2" Residue "B ASP 333": "OD1" <-> "OD2" Residue "B ASP 343": "OD1" <-> "OD2" Residue "B PHE 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 373": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 401": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 10814 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 7646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 957, 7646 Classifications: {'peptide': 957} Link IDs: {'PTRANS': 29, 'TRANS': 927} Chain breaks: 2 Chain: "B" Number of atoms: 2959 Number of conformers: 1 Conformer: "" Number of residues, atoms: 365, 2959 Classifications: {'peptide': 365} Link IDs: {'PTRANS': 19, 'TRANS': 345} Chain: "C" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "D" 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 Chain: "E" 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 Chain: "A" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 86 Unusual residues: {' MG': 2, 'ADP': 1, 'ALF': 1, 'POV': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "B" 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: 6.35, per 1000 atoms: 0.59 Number of scatterers: 10814 At special positions: 0 Unit cell: (127.204, 113.988, 132.16, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) S 50 16.00 P 3 15.00 Al 1 13.00 Mg 2 11.99 F 4 9.00 O 2006 8.00 N 1763 7.00 C 6985 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS B 110 " - pdb=" SG CYS B 159 " distance=2.03 Simple disulfide: pdb=" SG CYS B 216 " - pdb=" SG CYS B 231 " distance=2.02 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 ALPHA1-4 " NAG C 2 " - " MAN C 3 " BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " NAG-ASN " NAG B1001 " - " ASN B 298 " " NAG B1002 " - " ASN B 113 " " NAG C 1 " - " ASN B 240 " " NAG D 1 " - " ASN B 256 " " NAG E 1 " - " ASN B 332 " Time building additional restraints: 4.94 Conformation dependent library (CDL) restraints added in 2.3 seconds 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2478 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 47 helices and 5 sheets defined 46.5% alpha, 9.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.46 Creating SS restraints... Processing helix chain 'A' and resid 207 through 215 Processing helix chain 'A' and resid 218 through 231 Processing helix chain 'A' and resid 242 through 266 Proline residue: A 246 - end of helix Processing helix chain 'A' and resid 544 through 575 Processing helix chain 'A' and resid 581 through 585 removed outlier: 4.240A pdb=" N TYR A 585 " --> pdb=" O ARG A 582 " (cutoff:3.500A) Processing helix chain 'A' and resid 594 through 608 removed outlier: 3.927A pdb=" N VAL A 606 " --> pdb=" O TRP A 603 " (cutoff:3.500A) Processing helix chain 'A' and resid 617 through 634 Processing helix chain 'A' and resid 695 through 704 Processing helix chain 'A' and resid 708 through 733 removed outlier: 3.995A pdb=" N ARG A 714 " --> pdb=" O THR A 710 " (cutoff:3.500A) Processing helix chain 'A' and resid 741 through 743 No H-bonds generated for 'chain 'A' and resid 741 through 743' Processing helix chain 'A' and resid 749 through 756 Processing helix chain 'A' and resid 761 through 776 Processing helix chain 'A' and resid 799 through 811 Processing helix chain 'A' and resid 874 through 879 Processing helix chain 'A' and resid 892 through 906 Processing helix chain 'A' and resid 920 through 934 Processing helix chain 'A' and resid 940 through 953 removed outlier: 3.878A pdb=" N ARG A 953 " --> pdb=" O ASP A 949 " (cutoff:3.500A) Processing helix chain 'A' and resid 971 through 980 Processing helix chain 'A' and resid 993 through 1003 Processing helix chain 'A' and resid 1019 through 1025 removed outlier: 4.818A pdb=" N GLU A1024 " --> pdb=" O ASP A1020 " (cutoff:3.500A) Processing helix chain 'A' and resid 1032 through 1044 Processing helix chain 'A' and resid 1051 through 1057 Processing helix chain 'A' and resid 1074 through 1082 removed outlier: 3.576A pdb=" N LEU A1079 " --> pdb=" O ASP A1075 " (cutoff:3.500A) Processing helix chain 'A' and resid 1084 through 1095 Processing helix chain 'A' and resid 1107 through 1119 Processing helix chain 'A' and resid 1132 through 1139 removed outlier: 4.002A pdb=" N ALA A1136 " --> pdb=" O SER A1132 " (cutoff:3.500A) Processing helix chain 'A' and resid 1166 through 1208 removed outlier: 3.715A pdb=" N ALA A1170 " --> pdb=" O ARG A1167 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU A1172 " --> pdb=" O LEU A1169 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL A1173 " --> pdb=" O ALA A1170 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU A1174 " --> pdb=" O ARG A1171 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N VAL A1175 " --> pdb=" O LEU A1172 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N HIS A1176 " --> pdb=" O VAL A1173 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N GLY A1177 " --> pdb=" O LEU A1174 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ARG A1178 " --> pdb=" O VAL A1175 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N ILE A1188 " --> pdb=" O ALA A1185 " (cutoff:3.500A) Proline residue: A1189 - end of helix removed outlier: 3.986A pdb=" N ILE A1197 " --> pdb=" O LYS A1194 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N PHE A1198 " --> pdb=" O ASN A1195 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N LEU A1202 " --> pdb=" O ALA A1199 " (cutoff:3.500A) Processing helix chain 'A' and resid 1219 through 1228 removed outlier: 4.808A pdb=" N ASN A1226 " --> pdb=" O MET A1222 " (cutoff:3.500A) Processing helix chain 'A' and resid 1231 through 1240 Processing helix chain 'A' and resid 1246 through 1251 Processing helix chain 'A' and resid 1253 through 1261 removed outlier: 3.719A pdb=" N VAL A1258 " --> pdb=" O LEU A1255 " (cutoff:3.500A) Processing helix chain 'A' and resid 1267 through 1292 Proline residue: A1288 - end of helix Processing helix chain 'A' and resid 1308 through 1330 Processing helix chain 'A' and resid 1336 through 1357 Processing helix chain 'A' and resid 1368 through 1372 Processing helix chain 'A' and resid 1376 through 1403 Proline residue: A1392 - end of helix Processing helix chain 'A' and resid 1407 through 1417 removed outlier: 3.654A pdb=" N HIS A1417 " --> pdb=" O GLU A1413 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 98 Proline residue: B 77 - end of helix Processing helix chain 'B' and resid 108 through 110 No H-bonds generated for 'chain 'B' and resid 108 through 110' Processing helix chain 'B' and resid 189 through 191 No H-bonds generated for 'chain 'B' and resid 189 through 191' Processing helix chain 'B' and resid 195 through 198 No H-bonds generated for 'chain 'B' and resid 195 through 198' Processing helix chain 'B' and resid 205 through 209 Processing helix chain 'B' and resid 232 through 236 Processing helix chain 'B' and resid 267 through 271 removed outlier: 3.520A pdb=" N LYS B 270 " --> pdb=" O GLU B 267 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LYS B 271 " --> pdb=" O SER B 268 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 267 through 271' Processing helix chain 'B' and resid 309 through 314 Processing helix chain 'B' and resid 373 through 398 Processing helix chain 'B' and resid 410 through 413 No H-bonds generated for 'chain 'B' and resid 410 through 413' Processing sheet with id= A, first strand: chain 'A' and resid 1161 through 1163 removed outlier: 3.509A pdb=" N TYR A1161 " --> pdb=" O GLY A1144 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N TYR A 663 " --> pdb=" O LEU A1126 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N ILE A1128 " --> pdb=" O TYR A 663 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N PHE A 665 " --> pdb=" O ILE A1128 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N LYS A 984 " --> pdb=" O ILE A 664 " (cutoff:3.500A) removed outlier: 7.691A pdb=" N SER A 666 " --> pdb=" O LYS A 984 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N TRP A 986 " --> pdb=" O SER A 666 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N VAL A1100 " --> pdb=" O LEU A 985 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ALA A1099 " --> pdb=" O TYR A1068 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N GLU A1011 " --> pdb=" O ALA A1069 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N VAL A1071 " --> pdb=" O GLU A1011 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N LEU A1013 " --> pdb=" O VAL A1071 " (cutoff:3.500A) removed outlier: 8.175A pdb=" N ASP A1073 " --> pdb=" O LEU A1013 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 687 through 689 removed outlier: 6.938A pdb=" N ALA A 962 " --> pdb=" O LYS A 680 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N CYS A 682 " --> pdb=" O GLY A 960 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N GLY A 960 " --> pdb=" O CYS A 682 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N ILE A 684 " --> pdb=" O LEU A 958 " (cutoff:3.500A) removed outlier: 8.536A pdb=" N LEU A 958 " --> pdb=" O ILE A 684 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N ILE A 913 " --> pdb=" O LEU A 958 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N GLY A 960 " --> pdb=" O LEU A 911 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N LEU A 911 " --> pdb=" O GLY A 960 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N ALA A 962 " --> pdb=" O ARG A 909 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N ARG A 909 " --> pdb=" O ALA A 962 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ASN A 838 " --> pdb=" O ILE A 852 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N LYS A 854 " --> pdb=" O ILE A 836 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N ILE A 836 " --> pdb=" O LYS A 854 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 823 through 827 Processing sheet with id= D, first strand: chain 'B' and resid 127 through 129 removed outlier: 5.856A pdb=" N TYR B 177 " --> pdb=" O LEU B 326 " (cutoff:3.500A) removed outlier: 5.641A pdb=" N LEU B 326 " --> pdb=" O TYR B 177 " (cutoff:3.500A) removed outlier: 7.633A pdb=" N LEU B 179 " --> pdb=" O THR B 324 " (cutoff:3.500A) removed outlier: 5.608A pdb=" N THR B 324 " --> pdb=" O LEU B 179 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 141 through 144 477 hydrogen bonds defined for protein. 1209 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: 3.55 Time building geometry restraints manager: 5.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 1742 1.30 - 1.43: 3076 1.43 - 1.56: 6168 1.56 - 1.69: 6 1.69 - 1.81: 77 Bond restraints: 11069 Sorted by residual: bond pdb=" F2 ALF A1603 " pdb="AL ALF A1603 " ideal model delta sigma weight residual 1.685 1.784 -0.099 2.00e-02 2.50e+03 2.44e+01 bond pdb=" F4 ALF A1603 " pdb="AL ALF A1603 " ideal model delta sigma weight residual 1.686 1.783 -0.097 2.00e-02 2.50e+03 2.36e+01 bond pdb=" C31 POV A1601 " pdb=" O31 POV A1601 " ideal model delta sigma weight residual 1.327 1.421 -0.094 2.00e-02 2.50e+03 2.23e+01 bond pdb=" F1 ALF A1603 " pdb="AL ALF A1603 " ideal model delta sigma weight residual 1.684 1.778 -0.094 2.00e-02 2.50e+03 2.20e+01 bond pdb=" F3 ALF A1603 " pdb="AL ALF A1603 " ideal model delta sigma weight residual 1.685 1.776 -0.091 2.00e-02 2.50e+03 2.05e+01 ... (remaining 11064 not shown) Histogram of bond angle deviations from ideal: 88.61 - 106.56: 259 106.56 - 124.52: 14559 124.52 - 142.47: 185 142.47 - 160.43: 0 160.43 - 178.39: 2 Bond angle restraints: 15005 Sorted by residual: angle pdb=" F1 ALF A1603 " pdb="AL ALF A1603 " pdb=" F2 ALF A1603 " ideal model delta sigma weight residual 108.68 178.37 -69.69 3.00e+00 1.11e-01 5.40e+02 angle pdb=" F3 ALF A1603 " pdb="AL ALF A1603 " pdb=" F4 ALF A1603 " ideal model delta sigma weight residual 109.63 178.39 -68.76 3.00e+00 1.11e-01 5.25e+02 angle pdb=" F1 ALF A1603 " pdb="AL ALF A1603 " pdb=" F3 ALF A1603 " ideal model delta sigma weight residual 109.69 88.61 21.08 3.00e+00 1.11e-01 4.94e+01 angle pdb=" F2 ALF A1603 " pdb="AL ALF A1603 " pdb=" F4 ALF A1603 " ideal model delta sigma weight residual 110.21 90.24 19.97 3.00e+00 1.11e-01 4.43e+01 angle pdb=" F1 ALF A1603 " pdb="AL ALF A1603 " pdb=" F4 ALF A1603 " ideal model delta sigma weight residual 109.02 90.13 18.89 3.00e+00 1.11e-01 3.96e+01 ... (remaining 15000 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.11: 6406 35.11 - 70.22: 235 70.22 - 105.33: 14 105.33 - 140.45: 5 140.45 - 175.56: 1 Dihedral angle restraints: 6661 sinusoidal: 2798 harmonic: 3863 Sorted by residual: dihedral pdb=" C5' ADP A1602 " pdb=" O5' ADP A1602 " pdb=" PA ADP A1602 " pdb=" O2A ADP A1602 " ideal model delta sinusoidal sigma weight residual -60.00 115.56 -175.56 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb=" CA LYS B 170 " pdb=" C LYS B 170 " pdb=" N ASN B 171 " pdb=" CA ASN B 171 " ideal model delta harmonic sigma weight residual 180.00 148.60 31.40 0 5.00e+00 4.00e-02 3.94e+01 dihedral pdb=" CA PHE A1365 " pdb=" C PHE A1365 " pdb=" N PHE A1366 " pdb=" CA PHE A1366 " ideal model delta harmonic sigma weight residual -180.00 -154.95 -25.05 0 5.00e+00 4.00e-02 2.51e+01 ... (remaining 6658 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 1066 0.046 - 0.093: 469 0.093 - 0.139: 119 0.139 - 0.185: 13 0.185 - 0.232: 5 Chirality restraints: 1672 Sorted by residual: chirality pdb=" C1 NAG C 1 " pdb=" ND2 ASN B 240 " pdb=" C2 NAG C 1 " pdb=" O5 NAG C 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.63 0.23 2.00e-01 2.50e+01 1.34e+00 chirality pdb=" CB VAL B 190 " pdb=" CA VAL B 190 " pdb=" CG1 VAL B 190 " pdb=" CG2 VAL B 190 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.23 2.00e-01 2.50e+01 1.29e+00 chirality pdb=" C1 NAG E 1 " pdb=" ND2 ASN B 332 " pdb=" C2 NAG E 1 " pdb=" O5 NAG E 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.21 -0.19 2.00e-01 2.50e+01 9.29e-01 ... (remaining 1669 not shown) Planarity restraints: 1887 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL A1173 " 0.013 2.00e-02 2.50e+03 2.54e-02 6.44e+00 pdb=" C VAL A1173 " -0.044 2.00e-02 2.50e+03 pdb=" O VAL A1173 " 0.016 2.00e-02 2.50e+03 pdb=" N LEU A1174 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR A1225 " 0.011 2.00e-02 2.50e+03 2.30e-02 5.31e+00 pdb=" C TYR A1225 " -0.040 2.00e-02 2.50e+03 pdb=" O TYR A1225 " 0.015 2.00e-02 2.50e+03 pdb=" N ASN A1226 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A1174 " 0.011 2.00e-02 2.50e+03 2.27e-02 5.17e+00 pdb=" C LEU A1174 " -0.039 2.00e-02 2.50e+03 pdb=" O LEU A1174 " 0.014 2.00e-02 2.50e+03 pdb=" N VAL A1175 " 0.013 2.00e-02 2.50e+03 ... (remaining 1884 not shown) Histogram of nonbonded interaction distances: 1.92 - 2.51: 84 2.51 - 3.11: 8411 3.11 - 3.71: 16296 3.71 - 4.30: 24687 4.30 - 4.90: 41953 Nonbonded interactions: 91431 Sorted by model distance: nonbonded pdb=" OD2 ASP A 667 " pdb=" F2 ALF A1603 " model vdw 1.917 2.390 nonbonded pdb=" OD2 ASP A 667 " pdb=" F3 ALF A1603 " model vdw 1.942 2.390 nonbonded pdb=" O1B ADP A1602 " pdb=" F2 ALF A1603 " model vdw 2.159 2.390 nonbonded pdb=" O VAL A 237 " pdb=" OG1 THR A 238 " model vdw 2.160 2.440 nonbonded pdb=" O SER B 237 " pdb=" OG SER B 237 " model vdw 2.164 2.440 ... (remaining 91426 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'D' selection = chain 'E' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.910 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: 4.900 Check model and map are aligned: 0.170 Set scattering table: 0.110 Process input model: 33.850 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 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 : 0.012 0.099 11069 Z= 0.779 Angle : 1.233 69.693 15005 Z= 0.549 Chirality : 0.053 0.232 1672 Planarity : 0.005 0.047 1882 Dihedral : 17.754 175.557 4177 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 12.45 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.91 % Favored : 91.93 % Rotamer: Outliers : 8.04 % Allowed : 13.99 % Favored : 77.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -2.75 (0.20), residues: 1314 helix: -0.96 (0.19), residues: 616 sheet: -1.61 (0.36), residues: 158 loop : -2.89 (0.22), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 603 HIS 0.008 0.002 HIS B 347 PHE 0.022 0.002 PHE A1365 TYR 0.024 0.003 TYR A1326 ARG 0.008 0.001 ARG A1167 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 114 time to evaluate : 1.150 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 795 LYS cc_start: 0.8453 (mtpt) cc_final: 0.8010 (mmtp) REVERT: A 849 MET cc_start: 0.8053 (ttm) cc_final: 0.7773 (ttt) REVERT: A 1006 LEU cc_start: 0.8423 (OUTLIER) cc_final: 0.7985 (mt) REVERT: A 1150 GLU cc_start: 0.7254 (mm-30) cc_final: 0.7028 (tp30) REVERT: A 1190 GLU cc_start: 0.8304 (OUTLIER) cc_final: 0.6855 (mt-10) REVERT: A 1196 MET cc_start: 0.8255 (ttt) cc_final: 0.7862 (ttt) REVERT: A 1264 GLU cc_start: 0.7652 (mm-30) cc_final: 0.7283 (mm-30) REVERT: B 188 ARG cc_start: 0.8112 (tpm170) cc_final: 0.7739 (ttp-170) REVERT: B 236 ASN cc_start: 0.9004 (OUTLIER) cc_final: 0.8684 (t0) outliers start: 92 outliers final: 71 residues processed: 197 average time/residue: 0.2155 time to fit residues: 62.3290 Evaluate side-chains 171 residues out of total 1144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 97 time to evaluate : 1.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 540 THR Chi-restraints excluded: chain A residue 574 TYR Chi-restraints excluded: chain A residue 581 SER Chi-restraints excluded: chain A residue 615 ILE Chi-restraints excluded: chain A residue 651 SER Chi-restraints excluded: chain A residue 747 VAL Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 824 ILE Chi-restraints excluded: chain A residue 830 ILE Chi-restraints excluded: chain A residue 920 TRP Chi-restraints excluded: chain A residue 985 LEU Chi-restraints excluded: chain A residue 989 THR Chi-restraints excluded: chain A residue 1006 LEU Chi-restraints excluded: chain A residue 1024 GLU Chi-restraints excluded: chain A residue 1047 LEU Chi-restraints excluded: chain A residue 1054 ILE Chi-restraints excluded: chain A residue 1060 ASP Chi-restraints excluded: chain A residue 1072 ILE Chi-restraints excluded: chain A residue 1143 VAL Chi-restraints excluded: chain A residue 1151 GLU Chi-restraints excluded: chain A residue 1153 ARG Chi-restraints excluded: chain A residue 1169 LEU Chi-restraints excluded: chain A residue 1190 GLU Chi-restraints excluded: chain A residue 1197 ILE Chi-restraints excluded: chain A residue 1218 GLU Chi-restraints excluded: chain A residue 1243 ASP Chi-restraints excluded: chain A residue 1246 ASP Chi-restraints excluded: chain A residue 1258 VAL Chi-restraints excluded: chain A residue 1291 VAL Chi-restraints excluded: chain A residue 1295 ASN Chi-restraints excluded: chain A residue 1299 THR Chi-restraints excluded: chain A residue 1300 SER Chi-restraints excluded: chain A residue 1323 CYS Chi-restraints excluded: chain A residue 1348 VAL Chi-restraints excluded: chain A residue 1377 SER Chi-restraints excluded: chain A residue 1387 LEU Chi-restraints excluded: chain A residue 1391 LEU Chi-restraints excluded: chain A residue 1400 GLN Chi-restraints excluded: chain A residue 1406 THR Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 112 THR Chi-restraints excluded: chain B residue 113 ASN Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 155 GLN Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 176 ASN Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 195 GLU Chi-restraints excluded: chain B residue 198 ILE Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 216 CYS Chi-restraints excluded: chain B residue 220 SER Chi-restraints excluded: chain B residue 224 ASP Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain B residue 236 ASN Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 280 TYR Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain B residue 282 GLN Chi-restraints excluded: chain B residue 300 THR Chi-restraints excluded: chain B residue 351 LEU Chi-restraints excluded: chain B residue 352 GLU Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 390 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 110 optimal weight: 0.9980 chunk 99 optimal weight: 1.9990 chunk 55 optimal weight: 0.9990 chunk 33 optimal weight: 10.0000 chunk 66 optimal weight: 0.9980 chunk 53 optimal weight: 8.9990 chunk 102 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 76 optimal weight: 0.8980 chunk 118 optimal weight: 0.0570 overall best weight: 0.7900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 210 ASN A 220 ASN A 550 ASN A 640 ASN A 685 ASN ** A 738 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 763 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 797 GLN A 902 GLN A 939 ASN ** A 998 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1139 GLN A1195 ASN A1293 HIS A1295 ASN A1331 GLN A1417 HIS B 60 GLN B 97 ASN B 131 HIS B 155 GLN B 186 HIS B 246 GLN B 341 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.1067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11069 Z= 0.195 Angle : 0.603 14.231 15005 Z= 0.309 Chirality : 0.042 0.171 1672 Planarity : 0.004 0.038 1882 Dihedral : 13.759 167.991 1811 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 5.68 % Allowed : 17.83 % Favored : 76.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.62 (0.22), residues: 1314 helix: -0.10 (0.20), residues: 624 sheet: -0.97 (0.37), residues: 157 loop : -2.27 (0.25), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 926 HIS 0.003 0.001 HIS A1293 PHE 0.018 0.001 PHE A1198 TYR 0.020 0.001 TYR B 280 ARG 0.002 0.000 ARG A 723 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 111 time to evaluate : 1.244 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 264 ARG cc_start: 0.2628 (OUTLIER) cc_final: 0.1738 (ttm-80) REVERT: A 726 MET cc_start: 0.8018 (ttt) cc_final: 0.7392 (ttt) REVERT: A 729 GLU cc_start: 0.7452 (mt-10) cc_final: 0.6569 (mp0) REVERT: A 795 LYS cc_start: 0.8409 (mtpt) cc_final: 0.8062 (mmtp) REVERT: A 849 MET cc_start: 0.8009 (ttm) cc_final: 0.7772 (ttt) REVERT: A 868 LEU cc_start: 0.8985 (OUTLIER) cc_final: 0.8636 (tt) REVERT: A 954 GLU cc_start: 0.6428 (OUTLIER) cc_final: 0.5710 (tp30) REVERT: A 1087 ARG cc_start: 0.7742 (mtm180) cc_final: 0.7309 (mtm-85) REVERT: A 1153 ARG cc_start: 0.8484 (OUTLIER) cc_final: 0.7570 (mtt90) REVERT: A 1190 GLU cc_start: 0.8049 (OUTLIER) cc_final: 0.6843 (mt-10) REVERT: A 1196 MET cc_start: 0.7981 (ttt) cc_final: 0.7451 (ttt) REVERT: A 1258 VAL cc_start: 0.8924 (OUTLIER) cc_final: 0.8560 (m) REVERT: A 1409 GLU cc_start: 0.7332 (OUTLIER) cc_final: 0.6417 (mt-10) REVERT: B 181 LYS cc_start: 0.8550 (mttt) cc_final: 0.8230 (mttm) REVERT: B 188 ARG cc_start: 0.8067 (tpm170) cc_final: 0.7673 (ttp-170) REVERT: B 190 VAL cc_start: 0.8951 (OUTLIER) cc_final: 0.8450 (m) REVERT: B 236 ASN cc_start: 0.8913 (OUTLIER) cc_final: 0.8647 (t0) outliers start: 65 outliers final: 41 residues processed: 167 average time/residue: 0.2226 time to fit residues: 54.2756 Evaluate side-chains 153 residues out of total 1144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 103 time to evaluate : 1.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 264 ARG Chi-restraints excluded: chain A residue 540 THR Chi-restraints excluded: chain A residue 574 TYR Chi-restraints excluded: chain A residue 747 VAL Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 823 LEU Chi-restraints excluded: chain A residue 868 LEU Chi-restraints excluded: chain A residue 893 LEU Chi-restraints excluded: chain A residue 920 TRP Chi-restraints excluded: chain A residue 954 GLU Chi-restraints excluded: chain A residue 958 LEU Chi-restraints excluded: chain A residue 985 LEU Chi-restraints excluded: chain A residue 989 THR Chi-restraints excluded: chain A residue 1024 GLU Chi-restraints excluded: chain A residue 1047 LEU Chi-restraints excluded: chain A residue 1054 ILE Chi-restraints excluded: chain A residue 1060 ASP Chi-restraints excluded: chain A residue 1133 ASN Chi-restraints excluded: chain A residue 1135 VAL Chi-restraints excluded: chain A residue 1143 VAL Chi-restraints excluded: chain A residue 1151 GLU Chi-restraints excluded: chain A residue 1153 ARG Chi-restraints excluded: chain A residue 1169 LEU Chi-restraints excluded: chain A residue 1190 GLU Chi-restraints excluded: chain A residue 1218 GLU Chi-restraints excluded: chain A residue 1243 ASP Chi-restraints excluded: chain A residue 1246 ASP Chi-restraints excluded: chain A residue 1258 VAL Chi-restraints excluded: chain A residue 1266 ASN Chi-restraints excluded: chain A residue 1274 MET Chi-restraints excluded: chain A residue 1291 VAL Chi-restraints excluded: chain A residue 1299 THR Chi-restraints excluded: chain A residue 1323 CYS Chi-restraints excluded: chain A residue 1348 VAL Chi-restraints excluded: chain A residue 1409 GLU Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 113 ASN Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 176 ASN Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 236 ASN Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 300 THR Chi-restraints excluded: chain B residue 348 TRP Chi-restraints excluded: chain B residue 352 GLU Chi-restraints excluded: chain B residue 390 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 66 optimal weight: 5.9990 chunk 36 optimal weight: 9.9990 chunk 99 optimal weight: 0.1980 chunk 81 optimal weight: 1.9990 chunk 32 optimal weight: 5.9990 chunk 119 optimal weight: 2.9990 chunk 128 optimal weight: 2.9990 chunk 106 optimal weight: 0.8980 chunk 118 optimal weight: 0.7980 chunk 40 optimal weight: 0.0970 chunk 95 optimal weight: 3.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 738 GLN ** A 998 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1417 HIS B 97 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.1448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11069 Z= 0.181 Angle : 0.558 14.354 15005 Z= 0.282 Chirality : 0.041 0.167 1672 Planarity : 0.004 0.039 1882 Dihedral : 12.448 162.646 1750 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 5.33 % Allowed : 19.93 % Favored : 74.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.09 (0.22), residues: 1314 helix: 0.29 (0.20), residues: 626 sheet: -0.63 (0.38), residues: 157 loop : -1.98 (0.26), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 926 HIS 0.002 0.001 HIS B 209 PHE 0.014 0.001 PHE A1285 TYR 0.019 0.001 TYR B 280 ARG 0.002 0.000 ARG A 723 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 115 time to evaluate : 1.199 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 695 GLU cc_start: 0.6696 (OUTLIER) cc_final: 0.6207 (tm-30) REVERT: A 726 MET cc_start: 0.8058 (ttt) cc_final: 0.7362 (ttt) REVERT: A 729 GLU cc_start: 0.7402 (mt-10) cc_final: 0.6570 (mp0) REVERT: A 795 LYS cc_start: 0.8394 (mtpt) cc_final: 0.8054 (mmtp) REVERT: A 849 MET cc_start: 0.7980 (ttm) cc_final: 0.7742 (ttt) REVERT: A 954 GLU cc_start: 0.6385 (OUTLIER) cc_final: 0.5666 (tp30) REVERT: A 1024 GLU cc_start: 0.5575 (OUTLIER) cc_final: 0.4846 (pm20) REVERT: A 1087 ARG cc_start: 0.7747 (mtm180) cc_final: 0.7304 (mtm-85) REVERT: A 1153 ARG cc_start: 0.8501 (OUTLIER) cc_final: 0.7550 (mtt90) REVERT: A 1190 GLU cc_start: 0.8076 (OUTLIER) cc_final: 0.6820 (mt-10) REVERT: A 1227 LEU cc_start: 0.8095 (OUTLIER) cc_final: 0.7705 (mt) REVERT: A 1409 GLU cc_start: 0.7295 (OUTLIER) cc_final: 0.6372 (mt-10) REVERT: B 181 LYS cc_start: 0.8480 (mttt) cc_final: 0.8186 (mttm) REVERT: B 188 ARG cc_start: 0.8077 (tpm170) cc_final: 0.7677 (ttp-170) REVERT: B 190 VAL cc_start: 0.8973 (OUTLIER) cc_final: 0.8542 (m) REVERT: B 236 ASN cc_start: 0.8884 (OUTLIER) cc_final: 0.8604 (t0) outliers start: 61 outliers final: 34 residues processed: 169 average time/residue: 0.2342 time to fit residues: 57.3380 Evaluate side-chains 151 residues out of total 1144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 108 time to evaluate : 1.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 540 THR Chi-restraints excluded: chain A residue 574 TYR Chi-restraints excluded: chain A residue 695 GLU Chi-restraints excluded: chain A residue 747 VAL Chi-restraints excluded: chain A residue 893 LEU Chi-restraints excluded: chain A residue 920 TRP Chi-restraints excluded: chain A residue 954 GLU Chi-restraints excluded: chain A residue 985 LEU Chi-restraints excluded: chain A residue 989 THR Chi-restraints excluded: chain A residue 1024 GLU Chi-restraints excluded: chain A residue 1047 LEU Chi-restraints excluded: chain A residue 1054 ILE Chi-restraints excluded: chain A residue 1060 ASP Chi-restraints excluded: chain A residue 1133 ASN Chi-restraints excluded: chain A residue 1135 VAL Chi-restraints excluded: chain A residue 1151 GLU Chi-restraints excluded: chain A residue 1153 ARG Chi-restraints excluded: chain A residue 1169 LEU Chi-restraints excluded: chain A residue 1190 GLU Chi-restraints excluded: chain A residue 1218 GLU Chi-restraints excluded: chain A residue 1227 LEU Chi-restraints excluded: chain A residue 1246 ASP Chi-restraints excluded: chain A residue 1258 VAL Chi-restraints excluded: chain A residue 1291 VAL Chi-restraints excluded: chain A residue 1299 THR Chi-restraints excluded: chain A residue 1323 CYS Chi-restraints excluded: chain A residue 1348 VAL Chi-restraints excluded: chain A residue 1409 GLU Chi-restraints excluded: chain B residue 113 ASN Chi-restraints excluded: chain B residue 172 ASN Chi-restraints excluded: chain B residue 176 ASN Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 195 GLU Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 224 ASP Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain B residue 236 ASN Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain B residue 298 ASN Chi-restraints excluded: chain B residue 348 TRP Chi-restraints excluded: chain B residue 352 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 117 optimal weight: 3.9990 chunk 89 optimal weight: 0.8980 chunk 61 optimal weight: 5.9990 chunk 13 optimal weight: 3.9990 chunk 56 optimal weight: 4.9990 chunk 80 optimal weight: 0.5980 chunk 119 optimal weight: 3.9990 chunk 126 optimal weight: 3.9990 chunk 62 optimal weight: 0.5980 chunk 113 optimal weight: 1.9990 chunk 34 optimal weight: 9.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 998 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1417 HIS B 97 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.1451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 11069 Z= 0.288 Angle : 0.587 13.456 15005 Z= 0.296 Chirality : 0.043 0.165 1672 Planarity : 0.004 0.041 1882 Dihedral : 12.092 162.396 1738 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 5.86 % Allowed : 19.67 % Favored : 74.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.96 (0.23), residues: 1314 helix: 0.29 (0.20), residues: 630 sheet: -0.45 (0.38), residues: 157 loop : -1.81 (0.26), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 926 HIS 0.003 0.001 HIS B 209 PHE 0.015 0.001 PHE A1198 TYR 0.019 0.002 TYR B 280 ARG 0.007 0.000 ARG A 264 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 108 time to evaluate : 1.182 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 597 ASN cc_start: 0.7162 (OUTLIER) cc_final: 0.6616 (m-40) REVERT: A 695 GLU cc_start: 0.6705 (OUTLIER) cc_final: 0.6207 (tm-30) REVERT: A 726 MET cc_start: 0.8047 (ttt) cc_final: 0.7352 (ttt) REVERT: A 729 GLU cc_start: 0.7433 (mt-10) cc_final: 0.6623 (mp0) REVERT: A 795 LYS cc_start: 0.8415 (mtpt) cc_final: 0.8064 (mmtp) REVERT: A 849 MET cc_start: 0.8006 (ttm) cc_final: 0.7754 (ttt) REVERT: A 954 GLU cc_start: 0.6481 (OUTLIER) cc_final: 0.5752 (tp30) REVERT: A 1087 ARG cc_start: 0.7775 (mtm180) cc_final: 0.7289 (mtm-85) REVERT: A 1098 ARG cc_start: 0.7493 (OUTLIER) cc_final: 0.7028 (mtt180) REVERT: A 1153 ARG cc_start: 0.8481 (OUTLIER) cc_final: 0.7526 (mtp85) REVERT: A 1227 LEU cc_start: 0.8176 (OUTLIER) cc_final: 0.7748 (mp) REVERT: A 1409 GLU cc_start: 0.7291 (OUTLIER) cc_final: 0.6349 (mt-10) REVERT: B 181 LYS cc_start: 0.8507 (mttt) cc_final: 0.8220 (mttm) REVERT: B 188 ARG cc_start: 0.8097 (tpm170) cc_final: 0.7699 (ttp-170) REVERT: B 236 ASN cc_start: 0.8936 (OUTLIER) cc_final: 0.8646 (t0) outliers start: 67 outliers final: 48 residues processed: 165 average time/residue: 0.2272 time to fit residues: 54.5984 Evaluate side-chains 160 residues out of total 1144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 104 time to evaluate : 1.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 540 THR Chi-restraints excluded: chain A residue 574 TYR Chi-restraints excluded: chain A residue 597 ASN Chi-restraints excluded: chain A residue 612 LEU Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 695 GLU Chi-restraints excluded: chain A residue 747 VAL Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 823 LEU Chi-restraints excluded: chain A residue 893 LEU Chi-restraints excluded: chain A residue 920 TRP Chi-restraints excluded: chain A residue 954 GLU Chi-restraints excluded: chain A residue 985 LEU Chi-restraints excluded: chain A residue 989 THR Chi-restraints excluded: chain A residue 1054 ILE Chi-restraints excluded: chain A residue 1060 ASP Chi-restraints excluded: chain A residue 1098 ARG Chi-restraints excluded: chain A residue 1133 ASN Chi-restraints excluded: chain A residue 1135 VAL Chi-restraints excluded: chain A residue 1143 VAL Chi-restraints excluded: chain A residue 1151 GLU Chi-restraints excluded: chain A residue 1153 ARG Chi-restraints excluded: chain A residue 1169 LEU Chi-restraints excluded: chain A residue 1190 GLU Chi-restraints excluded: chain A residue 1218 GLU Chi-restraints excluded: chain A residue 1227 LEU Chi-restraints excluded: chain A residue 1243 ASP Chi-restraints excluded: chain A residue 1246 ASP Chi-restraints excluded: chain A residue 1258 VAL Chi-restraints excluded: chain A residue 1266 ASN Chi-restraints excluded: chain A residue 1274 MET Chi-restraints excluded: chain A residue 1291 VAL Chi-restraints excluded: chain A residue 1299 THR Chi-restraints excluded: chain A residue 1323 CYS Chi-restraints excluded: chain A residue 1335 ASP Chi-restraints excluded: chain A residue 1348 VAL Chi-restraints excluded: chain A residue 1387 LEU Chi-restraints excluded: chain A residue 1409 GLU Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 97 ASN Chi-restraints excluded: chain B residue 113 ASN Chi-restraints excluded: chain B residue 176 ASN Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 195 GLU Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 224 ASP Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain B residue 236 ASN Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 280 TYR Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain B residue 300 THR Chi-restraints excluded: chain B residue 348 TRP Chi-restraints excluded: chain B residue 352 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 105 optimal weight: 3.9990 chunk 71 optimal weight: 0.5980 chunk 1 optimal weight: 0.0170 chunk 94 optimal weight: 1.9990 chunk 52 optimal weight: 5.9990 chunk 108 optimal weight: 3.9990 chunk 87 optimal weight: 0.4980 chunk 0 optimal weight: 5.9990 chunk 64 optimal weight: 3.9990 chunk 113 optimal weight: 0.8980 chunk 31 optimal weight: 20.0000 overall best weight: 0.8020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 998 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.1668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11069 Z= 0.174 Angle : 0.541 12.189 15005 Z= 0.273 Chirality : 0.041 0.169 1672 Planarity : 0.004 0.039 1882 Dihedral : 11.465 159.908 1733 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 5.51 % Allowed : 20.45 % Favored : 74.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.23), residues: 1314 helix: 0.52 (0.21), residues: 625 sheet: -0.23 (0.39), residues: 157 loop : -1.66 (0.26), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 926 HIS 0.002 0.001 HIS B 209 PHE 0.013 0.001 PHE A1285 TYR 0.019 0.001 TYR B 280 ARG 0.005 0.000 ARG A 264 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 106 time to evaluate : 1.208 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 597 ASN cc_start: 0.7042 (OUTLIER) cc_final: 0.6509 (m-40) REVERT: A 695 GLU cc_start: 0.6697 (OUTLIER) cc_final: 0.6201 (tm-30) REVERT: A 795 LYS cc_start: 0.8386 (mtpt) cc_final: 0.8091 (mmtp) REVERT: A 849 MET cc_start: 0.7888 (ttm) cc_final: 0.7649 (ttt) REVERT: A 1087 ARG cc_start: 0.7808 (mtm180) cc_final: 0.7270 (mtm-85) REVERT: A 1098 ARG cc_start: 0.7409 (OUTLIER) cc_final: 0.6964 (mtt180) REVERT: A 1153 ARG cc_start: 0.8465 (OUTLIER) cc_final: 0.7640 (mtp85) REVERT: A 1190 GLU cc_start: 0.8168 (OUTLIER) cc_final: 0.6946 (mt-10) REVERT: A 1227 LEU cc_start: 0.8027 (OUTLIER) cc_final: 0.7670 (mt) REVERT: A 1409 GLU cc_start: 0.7284 (OUTLIER) cc_final: 0.6324 (mt-10) REVERT: B 181 LYS cc_start: 0.8444 (mttt) cc_final: 0.8151 (mttm) REVERT: B 188 ARG cc_start: 0.8097 (tpm170) cc_final: 0.7728 (ttp-170) REVERT: B 190 VAL cc_start: 0.8991 (OUTLIER) cc_final: 0.8486 (m) REVERT: B 236 ASN cc_start: 0.8887 (OUTLIER) cc_final: 0.8615 (t0) outliers start: 63 outliers final: 40 residues processed: 159 average time/residue: 0.2340 time to fit residues: 54.2116 Evaluate side-chains 155 residues out of total 1144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 106 time to evaluate : 1.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 540 THR Chi-restraints excluded: chain A residue 574 TYR Chi-restraints excluded: chain A residue 597 ASN Chi-restraints excluded: chain A residue 612 LEU Chi-restraints excluded: chain A residue 695 GLU Chi-restraints excluded: chain A residue 747 VAL Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 823 LEU Chi-restraints excluded: chain A residue 893 LEU Chi-restraints excluded: chain A residue 920 TRP Chi-restraints excluded: chain A residue 985 LEU Chi-restraints excluded: chain A residue 989 THR Chi-restraints excluded: chain A residue 1054 ILE Chi-restraints excluded: chain A residue 1060 ASP Chi-restraints excluded: chain A residue 1098 ARG Chi-restraints excluded: chain A residue 1133 ASN Chi-restraints excluded: chain A residue 1135 VAL Chi-restraints excluded: chain A residue 1143 VAL Chi-restraints excluded: chain A residue 1151 GLU Chi-restraints excluded: chain A residue 1153 ARG Chi-restraints excluded: chain A residue 1169 LEU Chi-restraints excluded: chain A residue 1190 GLU Chi-restraints excluded: chain A residue 1218 GLU Chi-restraints excluded: chain A residue 1227 LEU Chi-restraints excluded: chain A residue 1246 ASP Chi-restraints excluded: chain A residue 1266 ASN Chi-restraints excluded: chain A residue 1274 MET Chi-restraints excluded: chain A residue 1291 VAL Chi-restraints excluded: chain A residue 1299 THR Chi-restraints excluded: chain A residue 1348 VAL Chi-restraints excluded: chain A residue 1387 LEU Chi-restraints excluded: chain A residue 1409 GLU Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 113 ASN Chi-restraints excluded: chain B residue 176 ASN Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 195 GLU Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 224 ASP Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain B residue 236 ASN Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 280 TYR Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain B residue 300 THR Chi-restraints excluded: chain B residue 348 TRP Chi-restraints excluded: chain B residue 352 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 42 optimal weight: 8.9990 chunk 114 optimal weight: 0.7980 chunk 25 optimal weight: 4.9990 chunk 74 optimal weight: 3.9990 chunk 31 optimal weight: 20.0000 chunk 126 optimal weight: 3.9990 chunk 105 optimal weight: 0.2980 chunk 58 optimal weight: 5.9990 chunk 10 optimal weight: 3.9990 chunk 41 optimal weight: 0.9980 chunk 66 optimal weight: 0.0030 overall best weight: 1.2192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 998 ASN A1417 HIS B 97 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.1723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 11069 Z= 0.226 Angle : 0.564 11.880 15005 Z= 0.283 Chirality : 0.042 0.167 1672 Planarity : 0.004 0.039 1882 Dihedral : 11.257 159.262 1731 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 5.77 % Allowed : 20.72 % Favored : 73.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.57 (0.23), residues: 1314 helix: 0.52 (0.21), residues: 634 sheet: -0.09 (0.39), residues: 157 loop : -1.55 (0.27), residues: 523 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 926 HIS 0.002 0.001 HIS B 209 PHE 0.014 0.001 PHE A1285 TYR 0.018 0.001 TYR B 280 ARG 0.004 0.000 ARG A 264 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 111 time to evaluate : 1.263 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 597 ASN cc_start: 0.7131 (OUTLIER) cc_final: 0.6581 (m-40) REVERT: A 695 GLU cc_start: 0.6700 (OUTLIER) cc_final: 0.6177 (tm-30) REVERT: A 795 LYS cc_start: 0.8466 (mtpt) cc_final: 0.8173 (mmtp) REVERT: A 824 ILE cc_start: 0.8059 (OUTLIER) cc_final: 0.7650 (tp) REVERT: A 849 MET cc_start: 0.7886 (ttm) cc_final: 0.7646 (ttt) REVERT: A 954 GLU cc_start: 0.6480 (OUTLIER) cc_final: 0.5714 (tp30) REVERT: A 1087 ARG cc_start: 0.7871 (mtm180) cc_final: 0.7280 (mtm-85) REVERT: A 1098 ARG cc_start: 0.7398 (OUTLIER) cc_final: 0.6950 (mtt180) REVERT: A 1153 ARG cc_start: 0.8451 (OUTLIER) cc_final: 0.7686 (mtp85) REVERT: A 1190 GLU cc_start: 0.8188 (OUTLIER) cc_final: 0.6924 (mt-10) REVERT: A 1227 LEU cc_start: 0.8052 (OUTLIER) cc_final: 0.7710 (mt) REVERT: A 1409 GLU cc_start: 0.7284 (OUTLIER) cc_final: 0.6362 (mt-10) REVERT: B 181 LYS cc_start: 0.8468 (mttt) cc_final: 0.8172 (mttm) REVERT: B 188 ARG cc_start: 0.8117 (tpm170) cc_final: 0.7734 (ttp-170) REVERT: B 190 VAL cc_start: 0.9003 (OUTLIER) cc_final: 0.8444 (m) REVERT: B 236 ASN cc_start: 0.8894 (OUTLIER) cc_final: 0.8640 (t0) outliers start: 66 outliers final: 45 residues processed: 165 average time/residue: 0.2475 time to fit residues: 59.1397 Evaluate side-chains 158 residues out of total 1144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 102 time to evaluate : 1.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 540 THR Chi-restraints excluded: chain A residue 597 ASN Chi-restraints excluded: chain A residue 612 LEU Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 695 GLU Chi-restraints excluded: chain A residue 747 VAL Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 823 LEU Chi-restraints excluded: chain A residue 824 ILE Chi-restraints excluded: chain A residue 893 LEU Chi-restraints excluded: chain A residue 920 TRP Chi-restraints excluded: chain A residue 954 GLU Chi-restraints excluded: chain A residue 957 LEU Chi-restraints excluded: chain A residue 985 LEU Chi-restraints excluded: chain A residue 989 THR Chi-restraints excluded: chain A residue 1054 ILE Chi-restraints excluded: chain A residue 1060 ASP Chi-restraints excluded: chain A residue 1098 ARG Chi-restraints excluded: chain A residue 1133 ASN Chi-restraints excluded: chain A residue 1135 VAL Chi-restraints excluded: chain A residue 1143 VAL Chi-restraints excluded: chain A residue 1151 GLU Chi-restraints excluded: chain A residue 1153 ARG Chi-restraints excluded: chain A residue 1169 LEU Chi-restraints excluded: chain A residue 1190 GLU Chi-restraints excluded: chain A residue 1218 GLU Chi-restraints excluded: chain A residue 1227 LEU Chi-restraints excluded: chain A residue 1243 ASP Chi-restraints excluded: chain A residue 1246 ASP Chi-restraints excluded: chain A residue 1266 ASN Chi-restraints excluded: chain A residue 1274 MET Chi-restraints excluded: chain A residue 1291 VAL Chi-restraints excluded: chain A residue 1299 THR Chi-restraints excluded: chain A residue 1348 VAL Chi-restraints excluded: chain A residue 1387 LEU Chi-restraints excluded: chain A residue 1406 THR Chi-restraints excluded: chain A residue 1409 GLU Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 113 ASN Chi-restraints excluded: chain B residue 172 ASN Chi-restraints excluded: chain B residue 176 ASN Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 195 GLU Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 216 CYS Chi-restraints excluded: chain B residue 224 ASP Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain B residue 236 ASN Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 280 TYR Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain B residue 300 THR Chi-restraints excluded: chain B residue 348 TRP Chi-restraints excluded: chain B residue 352 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 122 optimal weight: 2.9990 chunk 14 optimal weight: 3.9990 chunk 72 optimal weight: 0.9980 chunk 92 optimal weight: 2.9990 chunk 71 optimal weight: 0.5980 chunk 106 optimal weight: 1.9990 chunk 70 optimal weight: 0.8980 chunk 126 optimal weight: 2.9990 chunk 79 optimal weight: 0.5980 chunk 76 optimal weight: 0.9980 chunk 58 optimal weight: 6.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 97 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.1907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11069 Z= 0.176 Angle : 0.544 13.386 15005 Z= 0.272 Chirality : 0.041 0.170 1672 Planarity : 0.004 0.038 1882 Dihedral : 10.860 156.384 1729 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 5.42 % Allowed : 21.24 % Favored : 73.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.41 (0.23), residues: 1314 helix: 0.67 (0.21), residues: 630 sheet: 0.02 (0.39), residues: 162 loop : -1.51 (0.27), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 926 HIS 0.002 0.000 HIS B 347 PHE 0.013 0.001 PHE A1285 TYR 0.019 0.001 TYR B 280 ARG 0.004 0.000 ARG A 264 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 108 time to evaluate : 1.171 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 597 ASN cc_start: 0.6958 (OUTLIER) cc_final: 0.6427 (m-40) REVERT: A 695 GLU cc_start: 0.6725 (OUTLIER) cc_final: 0.6242 (tm-30) REVERT: A 702 LYS cc_start: 0.8844 (tppt) cc_final: 0.8629 (ttmt) REVERT: A 747 VAL cc_start: 0.7321 (OUTLIER) cc_final: 0.7011 (t) REVERT: A 795 LYS cc_start: 0.8385 (mtpt) cc_final: 0.8088 (mmtp) REVERT: A 824 ILE cc_start: 0.8038 (OUTLIER) cc_final: 0.7622 (tp) REVERT: A 849 MET cc_start: 0.7763 (ttm) cc_final: 0.7522 (ttt) REVERT: A 954 GLU cc_start: 0.6528 (OUTLIER) cc_final: 0.5743 (tp30) REVERT: A 1087 ARG cc_start: 0.7877 (mtm180) cc_final: 0.7295 (mtm-85) REVERT: A 1098 ARG cc_start: 0.7288 (OUTLIER) cc_final: 0.6879 (mtt180) REVERT: A 1153 ARG cc_start: 0.8429 (OUTLIER) cc_final: 0.7766 (mtp85) REVERT: A 1190 GLU cc_start: 0.8141 (OUTLIER) cc_final: 0.7150 (mt-10) REVERT: A 1227 LEU cc_start: 0.7935 (OUTLIER) cc_final: 0.7509 (mp) REVERT: B 181 LYS cc_start: 0.8405 (mttt) cc_final: 0.8118 (mttm) REVERT: B 188 ARG cc_start: 0.8107 (tpm170) cc_final: 0.7732 (ttp-170) REVERT: B 190 VAL cc_start: 0.8991 (OUTLIER) cc_final: 0.8488 (m) outliers start: 62 outliers final: 45 residues processed: 160 average time/residue: 0.2302 time to fit residues: 54.8529 Evaluate side-chains 156 residues out of total 1144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 101 time to evaluate : 1.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 540 THR Chi-restraints excluded: chain A residue 597 ASN Chi-restraints excluded: chain A residue 612 LEU Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 695 GLU Chi-restraints excluded: chain A residue 747 VAL Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 823 LEU Chi-restraints excluded: chain A residue 824 ILE Chi-restraints excluded: chain A residue 893 LEU Chi-restraints excluded: chain A residue 920 TRP Chi-restraints excluded: chain A residue 954 GLU Chi-restraints excluded: chain A residue 957 LEU Chi-restraints excluded: chain A residue 989 THR Chi-restraints excluded: chain A residue 1054 ILE Chi-restraints excluded: chain A residue 1098 ARG Chi-restraints excluded: chain A residue 1133 ASN Chi-restraints excluded: chain A residue 1143 VAL Chi-restraints excluded: chain A residue 1151 GLU Chi-restraints excluded: chain A residue 1153 ARG Chi-restraints excluded: chain A residue 1169 LEU Chi-restraints excluded: chain A residue 1190 GLU Chi-restraints excluded: chain A residue 1218 GLU Chi-restraints excluded: chain A residue 1227 LEU Chi-restraints excluded: chain A residue 1246 ASP Chi-restraints excluded: chain A residue 1266 ASN Chi-restraints excluded: chain A residue 1274 MET Chi-restraints excluded: chain A residue 1291 VAL Chi-restraints excluded: chain A residue 1299 THR Chi-restraints excluded: chain A residue 1348 VAL Chi-restraints excluded: chain A residue 1387 LEU Chi-restraints excluded: chain A residue 1406 THR Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 97 ASN Chi-restraints excluded: chain B residue 113 ASN Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 172 ASN Chi-restraints excluded: chain B residue 176 ASN Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 195 GLU Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 216 CYS Chi-restraints excluded: chain B residue 224 ASP Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 280 TYR Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain B residue 300 THR Chi-restraints excluded: chain B residue 348 TRP Chi-restraints excluded: chain B residue 352 GLU Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 390 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 78 optimal weight: 0.3980 chunk 50 optimal weight: 0.9980 chunk 75 optimal weight: 0.9990 chunk 38 optimal weight: 0.9990 chunk 24 optimal weight: 5.9990 chunk 80 optimal weight: 0.7980 chunk 86 optimal weight: 0.6980 chunk 62 optimal weight: 1.9990 chunk 11 optimal weight: 5.9990 chunk 99 optimal weight: 0.0870 chunk 114 optimal weight: 1.9990 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 96 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.2003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 11069 Z= 0.153 Angle : 0.540 14.928 15005 Z= 0.270 Chirality : 0.041 0.169 1672 Planarity : 0.004 0.038 1882 Dihedral : 10.562 154.859 1723 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 4.72 % Allowed : 21.94 % Favored : 73.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.23), residues: 1314 helix: 0.75 (0.21), residues: 630 sheet: 0.11 (0.39), residues: 162 loop : -1.45 (0.27), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 926 HIS 0.001 0.000 HIS B 209 PHE 0.013 0.001 PHE A1285 TYR 0.018 0.001 TYR B 280 ARG 0.003 0.000 ARG A 264 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 105 time to evaluate : 1.218 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 597 ASN cc_start: 0.6899 (OUTLIER) cc_final: 0.6403 (m-40) REVERT: A 695 GLU cc_start: 0.6724 (OUTLIER) cc_final: 0.6234 (tm-30) REVERT: A 795 LYS cc_start: 0.8388 (mtpt) cc_final: 0.8106 (mmtp) REVERT: A 824 ILE cc_start: 0.8038 (OUTLIER) cc_final: 0.7634 (tp) REVERT: A 849 MET cc_start: 0.7742 (ttm) cc_final: 0.7502 (ttt) REVERT: A 954 GLU cc_start: 0.6534 (OUTLIER) cc_final: 0.5752 (tp30) REVERT: A 1087 ARG cc_start: 0.7867 (mtm180) cc_final: 0.7286 (mtm-85) REVERT: A 1098 ARG cc_start: 0.7322 (OUTLIER) cc_final: 0.6911 (mtt180) REVERT: A 1153 ARG cc_start: 0.8412 (OUTLIER) cc_final: 0.7734 (mtp85) REVERT: A 1190 GLU cc_start: 0.8120 (OUTLIER) cc_final: 0.6927 (mt-10) REVERT: A 1208 TYR cc_start: 0.8922 (m-80) cc_final: 0.8248 (m-80) REVERT: B 181 LYS cc_start: 0.8392 (mttt) cc_final: 0.8092 (mttm) REVERT: B 188 ARG cc_start: 0.8104 (tpm170) cc_final: 0.7736 (ttp-170) REVERT: B 190 VAL cc_start: 0.8976 (OUTLIER) cc_final: 0.8482 (m) outliers start: 54 outliers final: 41 residues processed: 152 average time/residue: 0.2374 time to fit residues: 52.5509 Evaluate side-chains 153 residues out of total 1144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 104 time to evaluate : 1.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 540 THR Chi-restraints excluded: chain A residue 597 ASN Chi-restraints excluded: chain A residue 612 LEU Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 695 GLU Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 823 LEU Chi-restraints excluded: chain A residue 824 ILE Chi-restraints excluded: chain A residue 893 LEU Chi-restraints excluded: chain A residue 954 GLU Chi-restraints excluded: chain A residue 957 LEU Chi-restraints excluded: chain A residue 985 LEU Chi-restraints excluded: chain A residue 1054 ILE Chi-restraints excluded: chain A residue 1098 ARG Chi-restraints excluded: chain A residue 1133 ASN Chi-restraints excluded: chain A residue 1143 VAL Chi-restraints excluded: chain A residue 1151 GLU Chi-restraints excluded: chain A residue 1153 ARG Chi-restraints excluded: chain A residue 1169 LEU Chi-restraints excluded: chain A residue 1190 GLU Chi-restraints excluded: chain A residue 1218 GLU Chi-restraints excluded: chain A residue 1246 ASP Chi-restraints excluded: chain A residue 1266 ASN Chi-restraints excluded: chain A residue 1274 MET Chi-restraints excluded: chain A residue 1291 VAL Chi-restraints excluded: chain A residue 1299 THR Chi-restraints excluded: chain A residue 1348 VAL Chi-restraints excluded: chain A residue 1387 LEU Chi-restraints excluded: chain A residue 1406 THR Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 113 ASN Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 176 ASN Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 195 GLU Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 216 CYS Chi-restraints excluded: chain B residue 224 ASP Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 280 TYR Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain B residue 298 ASN Chi-restraints excluded: chain B residue 300 THR Chi-restraints excluded: chain B residue 348 TRP Chi-restraints excluded: chain B residue 352 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 120 optimal weight: 2.9990 chunk 110 optimal weight: 4.9990 chunk 117 optimal weight: 0.9990 chunk 70 optimal weight: 0.9980 chunk 51 optimal weight: 0.9990 chunk 92 optimal weight: 2.9990 chunk 36 optimal weight: 0.6980 chunk 106 optimal weight: 0.9980 chunk 111 optimal weight: 4.9990 chunk 77 optimal weight: 0.8980 chunk 124 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1417 HIS B 96 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.2042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11069 Z= 0.188 Angle : 0.552 14.960 15005 Z= 0.275 Chirality : 0.041 0.169 1672 Planarity : 0.004 0.038 1882 Dihedral : 10.270 154.100 1719 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 4.72 % Allowed : 21.85 % Favored : 73.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.31 (0.23), residues: 1314 helix: 0.78 (0.21), residues: 627 sheet: 0.13 (0.40), residues: 162 loop : -1.50 (0.27), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 926 HIS 0.002 0.001 HIS B 209 PHE 0.014 0.001 PHE A1285 TYR 0.018 0.001 TYR B 280 ARG 0.003 0.000 ARG A 264 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 110 time to evaluate : 1.324 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 597 ASN cc_start: 0.6883 (OUTLIER) cc_final: 0.6376 (m-40) REVERT: A 695 GLU cc_start: 0.6700 (OUTLIER) cc_final: 0.6208 (tm-30) REVERT: A 795 LYS cc_start: 0.8388 (mtpt) cc_final: 0.8103 (mmtp) REVERT: A 824 ILE cc_start: 0.8054 (OUTLIER) cc_final: 0.7652 (tp) REVERT: A 849 MET cc_start: 0.7755 (ttm) cc_final: 0.7503 (ttt) REVERT: A 954 GLU cc_start: 0.6534 (OUTLIER) cc_final: 0.5778 (tp30) REVERT: A 1087 ARG cc_start: 0.7855 (mtm180) cc_final: 0.7272 (mtm-85) REVERT: A 1153 ARG cc_start: 0.8385 (OUTLIER) cc_final: 0.7430 (mtp85) REVERT: A 1190 GLU cc_start: 0.8123 (OUTLIER) cc_final: 0.6956 (mt-10) REVERT: A 1227 LEU cc_start: 0.7876 (OUTLIER) cc_final: 0.7467 (mp) REVERT: B 181 LYS cc_start: 0.8415 (mttt) cc_final: 0.8125 (mttm) REVERT: B 188 ARG cc_start: 0.8099 (tpm170) cc_final: 0.7730 (ttp-170) REVERT: B 190 VAL cc_start: 0.8990 (OUTLIER) cc_final: 0.8463 (m) outliers start: 54 outliers final: 43 residues processed: 157 average time/residue: 0.2530 time to fit residues: 56.2880 Evaluate side-chains 156 residues out of total 1144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 105 time to evaluate : 1.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 540 THR Chi-restraints excluded: chain A residue 597 ASN Chi-restraints excluded: chain A residue 612 LEU Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 695 GLU Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 823 LEU Chi-restraints excluded: chain A residue 824 ILE Chi-restraints excluded: chain A residue 893 LEU Chi-restraints excluded: chain A residue 954 GLU Chi-restraints excluded: chain A residue 957 LEU Chi-restraints excluded: chain A residue 985 LEU Chi-restraints excluded: chain A residue 1054 ILE Chi-restraints excluded: chain A residue 1133 ASN Chi-restraints excluded: chain A residue 1143 VAL Chi-restraints excluded: chain A residue 1151 GLU Chi-restraints excluded: chain A residue 1153 ARG Chi-restraints excluded: chain A residue 1169 LEU Chi-restraints excluded: chain A residue 1190 GLU Chi-restraints excluded: chain A residue 1218 GLU Chi-restraints excluded: chain A residue 1227 LEU Chi-restraints excluded: chain A residue 1246 ASP Chi-restraints excluded: chain A residue 1266 ASN Chi-restraints excluded: chain A residue 1274 MET Chi-restraints excluded: chain A residue 1291 VAL Chi-restraints excluded: chain A residue 1299 THR Chi-restraints excluded: chain A residue 1348 VAL Chi-restraints excluded: chain A residue 1387 LEU Chi-restraints excluded: chain A residue 1406 THR Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 113 ASN Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 176 ASN Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 195 GLU Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 216 CYS Chi-restraints excluded: chain B residue 224 ASP Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 280 TYR Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain B residue 298 ASN Chi-restraints excluded: chain B residue 300 THR Chi-restraints excluded: chain B residue 348 TRP Chi-restraints excluded: chain B residue 352 GLU Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 390 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 75 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 chunk 130 optimal weight: 9.9990 chunk 120 optimal weight: 1.9990 chunk 103 optimal weight: 5.9990 chunk 10 optimal weight: 2.9990 chunk 80 optimal weight: 0.2980 chunk 63 optimal weight: 0.9980 chunk 82 optimal weight: 0.5980 chunk 110 optimal weight: 2.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1417 HIS B 96 GLN B 97 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.2021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 11069 Z= 0.220 Angle : 0.563 14.920 15005 Z= 0.282 Chirality : 0.042 0.185 1672 Planarity : 0.004 0.038 1882 Dihedral : 10.221 153.986 1719 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 4.63 % Allowed : 21.77 % Favored : 73.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.33 (0.23), residues: 1314 helix: 0.74 (0.21), residues: 627 sheet: 0.17 (0.40), residues: 162 loop : -1.51 (0.27), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 926 HIS 0.002 0.001 HIS B 347 PHE 0.014 0.001 PHE A1285 TYR 0.018 0.001 TYR B 280 ARG 0.004 0.000 ARG A 880 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 105 time to evaluate : 1.171 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 597 ASN cc_start: 0.7023 (OUTLIER) cc_final: 0.6501 (m-40) REVERT: A 695 GLU cc_start: 0.6692 (OUTLIER) cc_final: 0.6203 (tm-30) REVERT: A 795 LYS cc_start: 0.8363 (mtpt) cc_final: 0.8078 (mmtp) REVERT: A 824 ILE cc_start: 0.8062 (OUTLIER) cc_final: 0.7811 (tp) REVERT: A 849 MET cc_start: 0.7809 (ttm) cc_final: 0.7547 (ttt) REVERT: A 1087 ARG cc_start: 0.7847 (mtm180) cc_final: 0.7268 (mtm-85) REVERT: A 1153 ARG cc_start: 0.8355 (OUTLIER) cc_final: 0.7231 (mtp85) REVERT: A 1190 GLU cc_start: 0.8143 (OUTLIER) cc_final: 0.6955 (mt-10) REVERT: A 1227 LEU cc_start: 0.7946 (OUTLIER) cc_final: 0.7553 (mp) REVERT: B 181 LYS cc_start: 0.8416 (mttt) cc_final: 0.8122 (mttm) REVERT: B 188 ARG cc_start: 0.8107 (tpm170) cc_final: 0.7733 (ttp-170) REVERT: B 190 VAL cc_start: 0.9003 (OUTLIER) cc_final: 0.8441 (m) outliers start: 53 outliers final: 44 residues processed: 151 average time/residue: 0.2383 time to fit residues: 52.8364 Evaluate side-chains 154 residues out of total 1144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 103 time to evaluate : 1.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 540 THR Chi-restraints excluded: chain A residue 597 ASN Chi-restraints excluded: chain A residue 612 LEU Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 695 GLU Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 823 LEU Chi-restraints excluded: chain A residue 824 ILE Chi-restraints excluded: chain A residue 893 LEU Chi-restraints excluded: chain A residue 920 TRP Chi-restraints excluded: chain A residue 957 LEU Chi-restraints excluded: chain A residue 985 LEU Chi-restraints excluded: chain A residue 1054 ILE Chi-restraints excluded: chain A residue 1133 ASN Chi-restraints excluded: chain A residue 1143 VAL Chi-restraints excluded: chain A residue 1151 GLU Chi-restraints excluded: chain A residue 1153 ARG Chi-restraints excluded: chain A residue 1169 LEU Chi-restraints excluded: chain A residue 1190 GLU Chi-restraints excluded: chain A residue 1218 GLU Chi-restraints excluded: chain A residue 1227 LEU Chi-restraints excluded: chain A residue 1246 ASP Chi-restraints excluded: chain A residue 1266 ASN Chi-restraints excluded: chain A residue 1274 MET Chi-restraints excluded: chain A residue 1291 VAL Chi-restraints excluded: chain A residue 1299 THR Chi-restraints excluded: chain A residue 1348 VAL Chi-restraints excluded: chain A residue 1387 LEU Chi-restraints excluded: chain A residue 1406 THR Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 113 ASN Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 176 ASN Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 195 GLU Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 216 CYS Chi-restraints excluded: chain B residue 224 ASP Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 280 TYR Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain B residue 298 ASN Chi-restraints excluded: chain B residue 300 THR Chi-restraints excluded: chain B residue 348 TRP Chi-restraints excluded: chain B residue 352 GLU Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 390 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 31 optimal weight: 0.9990 chunk 95 optimal weight: 0.5980 chunk 15 optimal weight: 0.9980 chunk 28 optimal weight: 10.0000 chunk 104 optimal weight: 0.9980 chunk 43 optimal weight: 10.0000 chunk 106 optimal weight: 1.9990 chunk 13 optimal weight: 0.7980 chunk 19 optimal weight: 0.8980 chunk 91 optimal weight: 0.7980 chunk 5 optimal weight: 6.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1417 HIS B 96 GLN ** B 97 ASN ** 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 = 0.3884 r_free = 0.3884 target = 0.172488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.133275 restraints weight = 11237.419| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 1.74 r_work: 0.2937 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2795 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.2124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11069 Z= 0.175 Angle : 0.548 14.846 15005 Z= 0.274 Chirality : 0.041 0.206 1672 Planarity : 0.003 0.038 1882 Dihedral : 10.005 152.076 1719 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 4.46 % Allowed : 21.85 % Favored : 73.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.27 (0.23), residues: 1314 helix: 0.77 (0.21), residues: 627 sheet: 0.24 (0.40), residues: 162 loop : -1.48 (0.27), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 926 HIS 0.002 0.001 HIS B 347 PHE 0.013 0.001 PHE A1285 TYR 0.018 0.001 TYR B 280 ARG 0.003 0.000 ARG A 264 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2560.30 seconds wall clock time: 47 minutes 32.92 seconds (2852.92 seconds total)