Starting phenix.real_space_refine on Thu Feb 15 15:36:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kyc_23075/02_2024/7kyc_23075_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kyc_23075/02_2024/7kyc_23075.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kyc_23075/02_2024/7kyc_23075.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kyc_23075/02_2024/7kyc_23075.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kyc_23075/02_2024/7kyc_23075_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kyc_23075/02_2024/7kyc_23075_updated.pdb" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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 P 3 5.49 5 Mg 1 5.21 5 S 61 5.16 5 Be 1 3.05 5 C 8188 2.51 5 N 2080 2.21 5 O 2360 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 183": "OE1" <-> "OE2" Residue "A PHE 206": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 235": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 258": "OD1" <-> "OD2" Residue "A ASP 262": "OD1" <-> "OD2" Residue "A ARG 264": "NH1" <-> "NH2" Residue "A ARG 265": "NH1" <-> "NH2" Residue "A ASP 382": "OD1" <-> "OD2" Residue "A ARG 388": "NH1" <-> "NH2" Residue "A ARG 408": "NH1" <-> "NH2" Residue "A GLU 414": "OE1" <-> "OE2" Residue "A ASP 418": "OD1" <-> "OD2" Residue "A ASP 428": "OD1" <-> "OD2" Residue "A ASP 439": "OD1" <-> "OD2" Residue "A GLU 441": "OE1" <-> "OE2" Residue "A ARG 457": "NH1" <-> "NH2" Residue "A ASP 461": "OD1" <-> "OD2" Residue "A ARG 464": "NH1" <-> "NH2" Residue "A PHE 467": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 472": "OE1" <-> "OE2" Residue "A TYR 479": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 481": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 488": "NH1" <-> "NH2" Residue "A ASP 492": "OD1" <-> "OD2" Residue "A GLU 494": "OE1" <-> "OE2" Residue "A GLU 548": "OE1" <-> "OE2" Residue "A PHE 561": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 TYR 633": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 644": "OD1" <-> "OD2" Residue "A TYR 663": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 665": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 667": "OD1" <-> "OD2" Residue "A TYR 693": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 701": "NH1" <-> "NH2" Residue "A ASP 707": "OD1" <-> "OD2" Residue "A GLU 711": "OE1" <-> "OE2" Residue "A GLU 715": "OE1" <-> "OE2" Residue "A ASP 722": "OD1" <-> "OD2" Residue "A ARG 723": "NH1" <-> "NH2" Residue "A ASP 724": "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 ASP 754": "OD1" <-> "OD2" Residue "A GLU 761": "OE1" <-> "OE2" Residue "A ASP 793": "OD1" <-> "OD2" Residue "A ARG 809": "NH1" <-> "NH2" 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 ARG 846": "NH1" <-> "NH2" Residue "A ARG 848": "NH1" <-> "NH2" Residue "A ARG 916": "NH1" <-> "NH2" Residue "A GLU 922": "OE1" <-> "OE2" Residue "A GLU 924": "OE1" <-> "OE2" Residue "A ARG 940": "NH1" <-> "NH2" Residue "A GLU 941": "OE1" <-> "OE2" Residue "A GLU 943": "OE1" <-> "OE2" Residue "A GLU 952": "OE1" <-> "OE2" 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 GLU 1009": "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 GLU 1051": "OE1" <-> "OE2" Residue "A PHE 1063": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1084": "OE1" <-> "OE2" Residue "A PHE 1090": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1104": "NH1" <-> "NH2" Residue "A ASP 1122": "OD1" <-> "OD2" Residue "A TYR 1161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1166": "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 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 TYR 1256": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 TYR 1292": "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 ASP 1335": "OD1" <-> "OD2" Residue "A PHE 1337": "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 TYR 1427": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1428": "OD1" <-> "OD2" Residue "B ARG 51": "NH1" <-> "NH2" Residue "B ARG 52": "NH1" <-> "NH2" Residue "B GLU 55": "OE1" <-> "OE2" 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 ARG 156": "NH1" <-> "NH2" Residue "B TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 187": "NH1" <-> "NH2" Residue "B PHE 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 196": "OD1" <-> "OD2" Residue "B GLU 201": "OE1" <-> "OE2" Residue "B ASP 210": "OD1" <-> "OD2" Residue "B ASP 252": "OD1" <-> "OD2" Residue "B TYR 280": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 290": "OE1" <-> "OE2" Residue "B TYR 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 299": "OE1" <-> "OE2" Residue "B ASP 321": "OD1" <-> "OD2" Residue "B ARG 328": "NH1" <-> "NH2" Residue "B ASP 333": "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" Residue "B ASP 405": "OD1" <-> "OD2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 12697 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 9409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1178, 9409 Classifications: {'peptide': 1178} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 39, 'TRANS': 1138} Chain breaks: 3 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 3004 Number of conformers: 1 Conformer: "" Number of residues, atoms: 374, 3004 Classifications: {'peptide': 374} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 19, 'TRANS': 354} Chain breaks: 1 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 4, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 25 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: 161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 161 Unusual residues: {' MG': 1, 'BEF': 1, 'POV': 3} 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: 7.09, per 1000 atoms: 0.56 Number of scatterers: 12697 At special positions: 0 Unit cell: (134.638, 121.422, 132.986, 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 61 16.00 P 3 15.00 Mg 1 11.99 F 3 9.00 O 2360 8.00 N 2080 7.00 C 8188 6.00 Be 1 4.00 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=2.02 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=1, 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 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 5.72 Conformation dependent library (CDL) restraints added in 2.4 seconds 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2910 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 58 helices and 9 sheets defined 42.9% alpha, 11.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.46 Creating SS restraints... Processing helix chain 'A' and resid 178 through 180 No H-bonds generated for 'chain 'A' and resid 178 through 180' Processing helix chain 'A' and resid 206 through 216 Processing helix chain 'A' and resid 218 through 233 Processing helix chain 'A' and resid 245 through 273 Processing helix chain 'A' and resid 459 through 464 Processing helix chain 'A' and resid 502 through 504 No H-bonds generated for 'chain 'A' and resid 502 through 504' Processing helix chain 'A' and resid 526 through 528 No H-bonds generated for 'chain 'A' and resid 526 through 528' Processing helix chain 'A' and resid 530 through 535 Processing helix chain 'A' and resid 544 through 576 Processing helix chain 'A' and resid 581 through 585 Processing helix chain 'A' and resid 594 through 608 removed outlier: 3.584A pdb=" N ILE A 607 " --> pdb=" O TRP A 603 " (cutoff:3.500A) Processing helix chain 'A' and resid 610 through 612 No H-bonds generated for 'chain 'A' and resid 610 through 612' Processing helix chain 'A' and resid 616 through 633 Processing helix chain 'A' and resid 655 through 659 Processing helix chain 'A' and resid 695 through 704 Processing helix chain 'A' and resid 708 through 733 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 removed outlier: 3.643A pdb=" N LYS A 756 " --> pdb=" O VAL A 752 " (cutoff:3.500A) 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 905 Processing helix chain 'A' and resid 920 through 935 Processing helix chain 'A' and resid 940 through 952 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: 3.984A pdb=" N GLU A1024 " --> pdb=" O ASP A1020 " (cutoff:3.500A) Processing helix chain 'A' and resid 1032 through 1043 Processing helix chain 'A' and resid 1051 through 1059 removed outlier: 3.739A pdb=" N LYS A1059 " --> pdb=" O PHE A1055 " (cutoff:3.500A) Processing helix chain 'A' and resid 1074 through 1082 removed outlier: 3.666A 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 1133 through 1139 Processing helix chain 'A' and resid 1154 through 1157 No H-bonds generated for 'chain 'A' and resid 1154 through 1157' Processing helix chain 'A' and resid 1166 through 1207 removed outlier: 3.623A pdb=" N ALA A1170 " --> pdb=" O ARG A1167 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU A1172 " --> pdb=" O LEU A1169 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N VAL A1173 " --> pdb=" O ALA A1170 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N LEU A1174 " --> pdb=" O ARG A1171 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N HIS A1176 " --> pdb=" O VAL A1173 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LEU A1184 " --> pdb=" O TYR A1181 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N GLU A1186 " --> pdb=" O ARG A1183 " (cutoff:3.500A) Proline residue: A1189 - end of helix removed outlier: 4.171A pdb=" N ASN A1195 " --> pdb=" O PHE A1192 " (cutoff:3.500A) Processing helix chain 'A' and resid 1219 through 1227 removed outlier: 5.096A 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: 3.904A 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 1329 Processing helix chain 'A' and resid 1336 through 1357 Processing helix chain 'A' and resid 1368 through 1373 Processing helix chain 'A' and resid 1376 through 1403 Proline residue: A1392 - end of helix Processing helix chain 'A' and resid 1407 through 1416 Processing helix chain 'B' and resid 37 through 43 Processing helix chain 'B' and resid 72 through 98 Proline residue: B 77 - end of helix Processing helix chain 'B' and resid 123 through 125 No H-bonds generated for 'chain 'B' and resid 123 through 125' 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 233 through 236 No H-bonds generated for 'chain 'B' and resid 233 through 236' Processing helix chain 'B' and resid 267 through 271 Processing helix chain 'B' and resid 287 through 289 No H-bonds generated for 'chain 'B' and resid 287 through 289' Processing helix chain 'B' and resid 309 through 314 Processing helix chain 'B' and resid 351 through 353 No H-bonds generated for 'chain 'B' and resid 351 through 353' Processing helix chain 'B' and resid 373 through 399 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 167 through 172 Processing sheet with id= B, first strand: chain 'A' and resid 276 through 280 Processing sheet with id= C, first strand: chain 'A' and resid 406 through 410 removed outlier: 7.094A pdb=" N ASP A 418 " --> pdb=" O MET A 523 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 444 through 448 removed outlier: 3.820A pdb=" N TYR A 432 " --> pdb=" O ARG A 513 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 1011 through 1014 removed outlier: 6.851A pdb=" N ALA A1099 " --> pdb=" O ILE A1070 " (cutoff:3.500A) removed outlier: 8.342A pdb=" N ILE A1072 " --> pdb=" O ALA A1099 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N LEU A1101 " --> pdb=" O ILE A1072 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N VAL A1100 " --> pdb=" O LEU A 985 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N MET A1124 " --> pdb=" O GLU A 662 " (cutoff:3.500A) removed outlier: 5.895A pdb=" N ILE A 664 " --> pdb=" O MET A1124 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N LEU A1126 " --> pdb=" O ILE A 664 " (cutoff:3.500A) removed outlier: 5.333A pdb=" N SER A 666 " --> pdb=" O LEU A1126 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N ILE A1128 " --> pdb=" O SER A 666 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N VAL A1143 " --> pdb=" O ALA A1127 " (cutoff:3.500A) removed outlier: 8.314A pdb=" N GLY A1129 " --> pdb=" O VAL A1143 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N ILE A1145 " --> pdb=" O GLY A1129 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N TYR A1161 " --> pdb=" O GLY A1146 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 687 through 689 removed outlier: 6.764A pdb=" N ALA A 962 " --> pdb=" O LYS A 680 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N CYS A 682 " --> pdb=" O GLY A 960 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N GLY A 960 " --> pdb=" O CYS A 682 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N ILE A 684 " --> pdb=" O LEU A 958 " (cutoff:3.500A) removed outlier: 8.752A pdb=" N LEU A 958 " --> pdb=" O ILE A 684 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N ILE A 913 " --> pdb=" O LEU A 958 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N GLY A 960 " --> pdb=" O LEU A 911 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N LEU A 911 " --> pdb=" O GLY A 960 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N ALA A 962 " --> pdb=" O ARG A 909 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N ARG A 909 " --> pdb=" O ALA A 962 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ASN A 838 " --> pdb=" O ILE A 852 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N LYS A 854 " --> pdb=" O ILE A 836 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N ILE A 836 " --> pdb=" O LYS A 854 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 813 through 816 removed outlier: 3.673A pdb=" N ILE A 824 " --> pdb=" O VAL A 816 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 126 through 129 removed outlier: 6.092A pdb=" N TYR B 177 " --> pdb=" O LEU B 326 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N LEU B 326 " --> pdb=" O TYR B 177 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N LEU B 179 " --> pdb=" O THR B 324 " (cutoff:3.500A) removed outlier: 5.460A pdb=" N THR B 324 " --> pdb=" O LEU B 179 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 141 through 145 534 hydrogen bonds defined for protein. 1449 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: 5.65 Time building geometry restraints manager: 5.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 2056 1.30 - 1.43: 3495 1.43 - 1.56: 7312 1.56 - 1.68: 25 1.68 - 1.81: 91 Bond restraints: 12979 Sorted by residual: bond pdb=" C31 POV A1603 " pdb=" O31 POV A1603 " ideal model delta sigma weight residual 1.327 1.429 -0.102 2.00e-02 2.50e+03 2.58e+01 bond pdb=" C31 POV A1604 " pdb=" O31 POV A1604 " ideal model delta sigma weight residual 1.327 1.427 -0.100 2.00e-02 2.50e+03 2.52e+01 bond pdb=" C31 POV A1605 " pdb=" O31 POV A1605 " ideal model delta sigma weight residual 1.327 1.423 -0.096 2.00e-02 2.50e+03 2.29e+01 bond pdb=" C21 POV A1603 " pdb=" O21 POV A1603 " ideal model delta sigma weight residual 1.330 1.421 -0.091 2.00e-02 2.50e+03 2.06e+01 bond pdb=" C21 POV A1604 " pdb=" O21 POV A1604 " ideal model delta sigma weight residual 1.330 1.420 -0.090 2.00e-02 2.50e+03 2.02e+01 ... (remaining 12974 not shown) Histogram of bond angle deviations from ideal: 98.23 - 105.49: 204 105.49 - 112.74: 6960 112.74 - 120.00: 4496 120.00 - 127.25: 5768 127.25 - 134.51: 140 Bond angle restraints: 17568 Sorted by residual: angle pdb=" N TYR B 136 " pdb=" CA TYR B 136 " pdb=" C TYR B 136 " ideal model delta sigma weight residual 110.97 121.70 -10.73 1.09e+00 8.42e-01 9.70e+01 angle pdb=" N ARG A1363 " pdb=" CA ARG A1363 " pdb=" C ARG A1363 " ideal model delta sigma weight residual 111.07 120.79 -9.72 1.07e+00 8.73e-01 8.25e+01 angle pdb=" N GLY A1304 " pdb=" CA GLY A1304 " pdb=" C GLY A1304 " ideal model delta sigma weight residual 111.03 121.45 -10.42 1.40e+00 5.10e-01 5.54e+01 angle pdb=" N LYS A 668 " pdb=" CA LYS A 668 " pdb=" C LYS A 668 " ideal model delta sigma weight residual 111.36 118.36 -7.00 1.09e+00 8.42e-01 4.13e+01 angle pdb="C212 POV A1605 " pdb="C213 POV A1605 " pdb="C214 POV A1605 " ideal model delta sigma weight residual 112.90 131.87 -18.97 3.00e+00 1.11e-01 4.00e+01 ... (remaining 17563 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.20: 7228 30.20 - 60.40: 586 60.40 - 90.61: 42 90.61 - 120.81: 3 120.81 - 151.01: 2 Dihedral angle restraints: 7861 sinusoidal: 3330 harmonic: 4531 Sorted by residual: dihedral pdb=" C ILE A 234 " pdb=" N ILE A 234 " pdb=" CA ILE A 234 " pdb=" CB ILE A 234 " ideal model delta harmonic sigma weight residual -122.00 -140.40 18.40 0 2.50e+00 1.60e-01 5.42e+01 dihedral pdb=" N ILE A 234 " pdb=" C ILE A 234 " pdb=" CA ILE A 234 " pdb=" CB ILE A 234 " ideal model delta harmonic sigma weight residual 123.40 139.11 -15.71 0 2.50e+00 1.60e-01 3.95e+01 dihedral pdb=" CA TYR A1292 " pdb=" C TYR A1292 " pdb=" N HIS A1293 " pdb=" CA HIS A1293 " ideal model delta harmonic sigma weight residual -180.00 -151.82 -28.18 0 5.00e+00 4.00e-02 3.18e+01 ... (remaining 7858 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.181: 1924 0.181 - 0.362: 28 0.362 - 0.544: 4 0.544 - 0.725: 0 0.725 - 0.906: 1 Chirality restraints: 1957 Sorted by residual: chirality pdb=" C1 NAG B1001 " pdb=" ND2 ASN B 298 " pdb=" C2 NAG B1001 " pdb=" O5 NAG B1001 " both_signs ideal model delta sigma weight residual False -2.40 -1.49 -0.91 2.00e-01 2.50e+01 2.05e+01 chirality pdb=" CA ILE A 234 " pdb=" N ILE A 234 " pdb=" C ILE A 234 " pdb=" CB ILE A 234 " both_signs ideal model delta sigma weight residual False 2.43 1.93 0.50 2.00e-01 2.50e+01 6.32e+00 chirality pdb=" CA HIS A1176 " pdb=" N HIS A1176 " pdb=" C HIS A1176 " pdb=" CB HIS A1176 " both_signs ideal model delta sigma weight residual False 2.51 2.02 0.49 2.00e-01 2.50e+01 6.08e+00 ... (remaining 1954 not shown) Planarity restraints: 2214 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE B 398 " 0.018 2.00e-02 2.50e+03 3.60e-02 1.29e+01 pdb=" C PHE B 398 " -0.062 2.00e-02 2.50e+03 pdb=" O PHE B 398 " 0.023 2.00e-02 2.50e+03 pdb=" N GLY B 399 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA A1170 " 0.017 2.00e-02 2.50e+03 3.40e-02 1.15e+01 pdb=" C ALA A1170 " -0.059 2.00e-02 2.50e+03 pdb=" O ALA A1170 " 0.023 2.00e-02 2.50e+03 pdb=" N ARG A1171 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A1174 " -0.017 2.00e-02 2.50e+03 3.35e-02 1.12e+01 pdb=" C LEU A1174 " 0.058 2.00e-02 2.50e+03 pdb=" O LEU A1174 " -0.021 2.00e-02 2.50e+03 pdb=" N VAL A1175 " -0.020 2.00e-02 2.50e+03 ... (remaining 2211 not shown) Histogram of nonbonded interaction distances: 1.82 - 2.44: 67 2.44 - 3.05: 8235 3.05 - 3.67: 19305 3.67 - 4.28: 31667 4.28 - 4.90: 51558 Nonbonded interactions: 110832 Sorted by model distance: nonbonded pdb=" OE2 GLU A 183 " pdb=" CG GLU A 184 " model vdw 1.822 3.440 nonbonded pdb=" O MET B 169 " pdb=" O LYS B 170 " model vdw 2.000 3.040 nonbonded pdb=" F2 BEF A1601 " pdb="MG MG A1602 " model vdw 2.080 2.120 nonbonded pdb=" OD2 ASP A 667 " pdb="MG MG A1602 " model vdw 2.099 2.170 nonbonded pdb=" O THR A 669 " pdb="MG MG A1602 " model vdw 2.140 2.170 ... (remaining 110827 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: 1.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 5.070 Check model and map are aligned: 0.190 Set scattering table: 0.110 Process input model: 39.570 Find NCS groups from input model: 0.340 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: 0.010 Load rotamer database and sin/cos tables:15.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8618 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 0.120 12979 Z= 0.797 Angle : 1.073 18.968 17568 Z= 0.612 Chirality : 0.067 0.906 1957 Planarity : 0.006 0.057 2209 Dihedral : 19.676 151.010 4945 Min Nonbonded Distance : 1.822 Molprobity Statistics. All-atom Clashscore : 16.02 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.03 % Favored : 95.71 % Rotamer: Outliers : 12.05 % Allowed : 19.49 % Favored : 68.45 % Cbeta Deviations : 0.21 % 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: -1.91 (0.19), residues: 1540 helix: -1.28 (0.17), residues: 691 sheet: 0.13 (0.34), residues: 205 loop : -1.58 (0.22), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP A1379 HIS 0.007 0.002 HIS A1176 PHE 0.024 0.003 PHE A1285 TYR 0.026 0.003 TYR A1326 ARG 0.011 0.001 ARG A 388 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 1354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 162 poor density : 168 time to evaluate : 1.312 Fit side-chains revert: symmetry clash REVERT: A 178 LYS cc_start: 0.8278 (OUTLIER) cc_final: 0.7398 (ptmm) REVERT: A 239 ASN cc_start: 0.4259 (OUTLIER) cc_final: 0.3458 (t0) REVERT: A 439 ASP cc_start: 0.8105 (OUTLIER) cc_final: 0.7736 (p0) REVERT: A 445 LYS cc_start: 0.8400 (mmtp) cc_final: 0.7987 (mmtt) REVERT: A 498 GLU cc_start: 0.8506 (tp30) cc_final: 0.8274 (tt0) REVERT: A 548 GLU cc_start: 0.8316 (OUTLIER) cc_final: 0.7231 (mm-30) REVERT: A 677 MET cc_start: 0.8943 (mmt) cc_final: 0.8736 (mmp) REVERT: A 683 THR cc_start: 0.8842 (OUTLIER) cc_final: 0.8592 (t) REVERT: A 722 ASP cc_start: 0.7784 (m-30) cc_final: 0.7188 (t0) REVERT: A 723 ARG cc_start: 0.8394 (OUTLIER) cc_final: 0.8139 (ttt-90) REVERT: A 753 ARG cc_start: 0.8458 (ttm170) cc_final: 0.7873 (mtt180) REVERT: A 764 GLN cc_start: 0.7418 (OUTLIER) cc_final: 0.6766 (tm-30) REVERT: A 848 ARG cc_start: 0.8455 (OUTLIER) cc_final: 0.8082 (ptt-90) REVERT: A 954 GLU cc_start: 0.6157 (OUTLIER) cc_final: 0.5801 (tm-30) REVERT: A 965 ASP cc_start: 0.8173 (t0) cc_final: 0.7917 (t0) REVERT: A 1030 SER cc_start: 0.8766 (t) cc_final: 0.8095 (p) REVERT: A 1051 GLU cc_start: 0.7672 (mm-30) cc_final: 0.7237 (mp0) REVERT: A 1171 ARG cc_start: 0.8713 (OUTLIER) cc_final: 0.7697 (ttt180) REVERT: A 1190 GLU cc_start: 0.8991 (OUTLIER) cc_final: 0.8539 (tp30) REVERT: A 1436 LYS cc_start: 0.7868 (ttpp) cc_final: 0.7613 (tttm) REVERT: B 262 LYS cc_start: 0.9110 (OUTLIER) cc_final: 0.8079 (mttt) REVERT: B 267 GLU cc_start: 0.7284 (tp30) cc_final: 0.7075 (mm-30) REVERT: B 271 LYS cc_start: 0.8815 (mttm) cc_final: 0.8614 (mttt) outliers start: 162 outliers final: 77 residues processed: 309 average time/residue: 1.1128 time to fit residues: 377.1595 Evaluate side-chains 233 residues out of total 1354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 144 time to evaluate : 1.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 LYS Chi-restraints excluded: chain A residue 183 GLU Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 399 LYS Chi-restraints excluded: chain A residue 419 ILE Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 439 ASP Chi-restraints excluded: chain A residue 452 CYS Chi-restraints excluded: chain A residue 471 SER Chi-restraints excluded: chain A residue 513 ARG Chi-restraints excluded: chain A residue 548 GLU Chi-restraints excluded: chain A residue 581 SER Chi-restraints excluded: chain A residue 584 SER Chi-restraints excluded: chain A residue 622 GLU Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 671 THR Chi-restraints excluded: chain A residue 683 THR Chi-restraints excluded: chain A residue 687 VAL Chi-restraints excluded: chain A residue 723 ARG Chi-restraints excluded: chain A residue 764 GLN Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 821 LYS Chi-restraints excluded: chain A residue 823 LEU Chi-restraints excluded: chain A residue 830 ILE Chi-restraints excluded: chain A residue 848 ARG Chi-restraints excluded: chain A residue 854 LYS Chi-restraints excluded: chain A residue 863 GLU Chi-restraints excluded: chain A residue 869 ILE Chi-restraints excluded: chain A residue 874 ASP Chi-restraints excluded: chain A residue 909 ARG Chi-restraints excluded: chain A residue 920 TRP Chi-restraints excluded: chain A residue 954 GLU Chi-restraints excluded: chain A residue 964 GLU Chi-restraints excluded: chain A residue 989 THR Chi-restraints excluded: chain A residue 999 ILE Chi-restraints excluded: chain A residue 1002 SER Chi-restraints excluded: chain A residue 1017 THR Chi-restraints excluded: chain A residue 1048 THR Chi-restraints excluded: chain A residue 1052 GLU Chi-restraints excluded: chain A residue 1060 ASP Chi-restraints excluded: chain A residue 1072 ILE Chi-restraints excluded: chain A residue 1085 ASP Chi-restraints excluded: chain A residue 1105 VAL Chi-restraints excluded: chain A residue 1123 VAL Chi-restraints excluded: chain A residue 1133 ASN Chi-restraints excluded: chain A residue 1138 ILE Chi-restraints excluded: chain A residue 1171 ARG Chi-restraints excluded: chain A residue 1172 LEU Chi-restraints excluded: chain A residue 1184 LEU Chi-restraints excluded: chain A residue 1190 GLU Chi-restraints excluded: chain A residue 1214 SER Chi-restraints excluded: chain A residue 1234 VAL Chi-restraints excluded: chain A residue 1258 VAL Chi-restraints excluded: chain A residue 1266 ASN Chi-restraints excluded: chain A residue 1300 SER Chi-restraints excluded: chain A residue 1301 ASN Chi-restraints excluded: chain A residue 1360 ILE Chi-restraints excluded: chain A residue 1363 ARG Chi-restraints excluded: chain A residue 1381 VAL Chi-restraints excluded: chain A residue 1387 LEU Chi-restraints excluded: chain A residue 1391 LEU Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 113 ASN Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 124 GLU Chi-restraints excluded: chain B residue 149 SER Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 170 LYS Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 192 SER Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 220 SER Chi-restraints excluded: chain B residue 258 SER Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 262 LYS Chi-restraints excluded: chain B residue 280 TYR Chi-restraints excluded: chain B residue 298 ASN Chi-restraints excluded: chain B residue 348 TRP Chi-restraints excluded: chain B residue 352 GLU Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain B residue 377 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 130 optimal weight: 0.7980 chunk 116 optimal weight: 0.2980 chunk 64 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 62 optimal weight: 20.0000 chunk 120 optimal weight: 6.9990 chunk 46 optimal weight: 7.9990 chunk 73 optimal weight: 1.9990 chunk 89 optimal weight: 0.8980 chunk 139 optimal weight: 1.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 186 ASN A 239 ASN A 273 ASN A 278 HIS A 285 ASN A 287 ASN A 379 ASN A 448 GLN A 454 ASN A 504 ASN A 640 ASN A 888 ASN A 902 GLN A 939 ASN A1096 ASN ** A1139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1154 GLN A1195 ASN A1293 HIS A1295 ASN B 60 GLN B 67 ASN B 97 ASN B 155 GLN B 186 HIS B 246 GLN B 282 GLN B 341 GLN B 347 HIS Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8560 moved from start: 0.1299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 12979 Z= 0.238 Angle : 0.604 11.226 17568 Z= 0.317 Chirality : 0.043 0.200 1957 Planarity : 0.004 0.043 2209 Dihedral : 14.604 116.587 2188 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 7.14 % Allowed : 23.81 % Favored : 69.05 % 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: -0.77 (0.20), residues: 1540 helix: -0.19 (0.19), residues: 709 sheet: 0.71 (0.34), residues: 206 loop : -1.21 (0.24), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1379 HIS 0.003 0.001 HIS A1176 PHE 0.014 0.002 PHE A1403 TYR 0.022 0.002 TYR A 923 ARG 0.007 0.000 ARG A 193 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 157 time to evaluate : 1.298 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 193 ARG cc_start: 0.7977 (mtp85) cc_final: 0.7777 (mtp180) REVERT: A 439 ASP cc_start: 0.8145 (OUTLIER) cc_final: 0.7921 (p0) REVERT: A 445 LYS cc_start: 0.8314 (mmtp) cc_final: 0.7887 (mmtt) REVERT: A 488 ARG cc_start: 0.8295 (mmt90) cc_final: 0.8052 (mmt90) REVERT: A 498 GLU cc_start: 0.8447 (OUTLIER) cc_final: 0.8218 (tt0) REVERT: A 523 MET cc_start: 0.8232 (mmm) cc_final: 0.8014 (tpp) REVERT: A 691 ARG cc_start: 0.8409 (OUTLIER) cc_final: 0.7723 (mtm180) REVERT: A 711 GLU cc_start: 0.7447 (OUTLIER) cc_final: 0.6607 (tt0) REVERT: A 722 ASP cc_start: 0.7809 (m-30) cc_final: 0.7060 (t0) REVERT: A 740 TYR cc_start: 0.8334 (m-80) cc_final: 0.8047 (m-80) REVERT: A 742 GLU cc_start: 0.8036 (mp0) cc_final: 0.7708 (pm20) REVERT: A 753 ARG cc_start: 0.8222 (ttm170) cc_final: 0.7953 (ttm170) REVERT: A 813 PHE cc_start: 0.8699 (m-80) cc_final: 0.8428 (m-80) REVERT: A 848 ARG cc_start: 0.8372 (OUTLIER) cc_final: 0.8054 (ptt-90) REVERT: A 965 ASP cc_start: 0.8230 (t0) cc_final: 0.7953 (t0) REVERT: A 1008 ASN cc_start: 0.7905 (m-40) cc_final: 0.7452 (m-40) REVERT: A 1016 LYS cc_start: 0.7267 (OUTLIER) cc_final: 0.6793 (pttt) REVERT: A 1030 SER cc_start: 0.8459 (t) cc_final: 0.8069 (p) REVERT: A 1051 GLU cc_start: 0.7542 (mm-30) cc_final: 0.7106 (mp0) REVERT: A 1190 GLU cc_start: 0.8833 (OUTLIER) cc_final: 0.8563 (tp30) REVERT: A 1218 GLU cc_start: 0.8516 (OUTLIER) cc_final: 0.8022 (tm-30) REVERT: A 1436 LYS cc_start: 0.7873 (ttpp) cc_final: 0.7560 (tttm) REVERT: B 138 THR cc_start: 0.7816 (m) cc_final: 0.7543 (m) outliers start: 96 outliers final: 47 residues processed: 238 average time/residue: 1.2941 time to fit residues: 335.7936 Evaluate side-chains 204 residues out of total 1354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 149 time to evaluate : 1.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 399 LYS Chi-restraints excluded: chain A residue 434 GLU Chi-restraints excluded: chain A residue 439 ASP Chi-restraints excluded: chain A residue 455 THR Chi-restraints excluded: chain A residue 498 GLU Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain A residue 584 SER Chi-restraints excluded: chain A residue 622 GLU Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 671 THR Chi-restraints excluded: chain A residue 691 ARG Chi-restraints excluded: chain A residue 704 GLN Chi-restraints excluded: chain A residue 711 GLU Chi-restraints excluded: chain A residue 737 SER Chi-restraints excluded: chain A residue 766 CYS Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 821 LYS Chi-restraints excluded: chain A residue 823 LEU Chi-restraints excluded: chain A residue 830 ILE Chi-restraints excluded: chain A residue 848 ARG Chi-restraints excluded: chain A residue 874 ASP Chi-restraints excluded: chain A residue 882 SER Chi-restraints excluded: chain A residue 901 GLU Chi-restraints excluded: chain A residue 909 ARG Chi-restraints excluded: chain A residue 920 TRP Chi-restraints excluded: chain A residue 964 GLU Chi-restraints excluded: chain A residue 1016 LYS Chi-restraints excluded: chain A residue 1020 ASP Chi-restraints excluded: chain A residue 1052 GLU Chi-restraints excluded: chain A residue 1060 ASP Chi-restraints excluded: chain A residue 1065 LYS Chi-restraints excluded: chain A residue 1072 ILE Chi-restraints excluded: chain A residue 1085 ASP Chi-restraints excluded: chain A residue 1103 CYS Chi-restraints excluded: chain A residue 1133 ASN Chi-restraints excluded: chain A residue 1190 GLU Chi-restraints excluded: chain A residue 1218 GLU Chi-restraints excluded: chain A residue 1234 VAL Chi-restraints excluded: chain A residue 1258 VAL Chi-restraints excluded: chain A residue 1266 ASN Chi-restraints excluded: chain A residue 1360 ILE Chi-restraints excluded: chain A residue 1363 ARG Chi-restraints excluded: chain A residue 1391 LEU Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 196 ASP Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 280 TYR Chi-restraints excluded: chain B residue 298 ASN Chi-restraints excluded: chain B residue 352 GLU Chi-restraints excluded: chain B residue 362 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 77 optimal weight: 4.9990 chunk 43 optimal weight: 7.9990 chunk 116 optimal weight: 3.9990 chunk 95 optimal weight: 3.9990 chunk 38 optimal weight: 0.0970 chunk 140 optimal weight: 4.9990 chunk 151 optimal weight: 6.9990 chunk 124 optimal weight: 0.8980 chunk 138 optimal weight: 0.2980 chunk 47 optimal weight: 10.0000 chunk 112 optimal weight: 0.7980 overall best weight: 1.2180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 410 HIS A 412 ASN A 899 HIS A 902 GLN ** A1139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1195 ASN B 131 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8558 moved from start: 0.1597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 12979 Z= 0.236 Angle : 0.575 9.552 17568 Z= 0.301 Chirality : 0.044 0.361 1957 Planarity : 0.004 0.036 2209 Dihedral : 12.860 110.817 2091 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 6.40 % Allowed : 24.26 % Favored : 69.35 % 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: -0.22 (0.21), residues: 1540 helix: 0.35 (0.19), residues: 693 sheet: 0.71 (0.34), residues: 216 loop : -0.93 (0.25), residues: 631 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 603 HIS 0.003 0.001 HIS B 131 PHE 0.014 0.001 PHE A1403 TYR 0.021 0.001 TYR B 280 ARG 0.004 0.000 ARG A 916 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 162 time to evaluate : 1.724 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 193 ARG cc_start: 0.7966 (mtp85) cc_final: 0.7713 (mtp180) REVERT: A 224 LEU cc_start: 0.8767 (OUTLIER) cc_final: 0.8564 (tp) REVERT: A 439 ASP cc_start: 0.8088 (OUTLIER) cc_final: 0.7876 (p0) REVERT: A 445 LYS cc_start: 0.8347 (mmtp) cc_final: 0.7914 (mmtt) REVERT: A 523 MET cc_start: 0.8164 (mmm) cc_final: 0.7902 (tpp) REVERT: A 677 MET cc_start: 0.8846 (OUTLIER) cc_final: 0.8561 (mmm) REVERT: A 704 GLN cc_start: 0.6599 (OUTLIER) cc_final: 0.6083 (tt0) REVERT: A 711 GLU cc_start: 0.7354 (OUTLIER) cc_final: 0.6570 (tt0) REVERT: A 722 ASP cc_start: 0.7848 (m-30) cc_final: 0.7160 (t0) REVERT: A 740 TYR cc_start: 0.8362 (m-80) cc_final: 0.8088 (m-80) REVERT: A 742 GLU cc_start: 0.7975 (mp0) cc_final: 0.7667 (pm20) REVERT: A 753 ARG cc_start: 0.8201 (ttm170) cc_final: 0.7850 (ttm170) REVERT: A 764 GLN cc_start: 0.7507 (OUTLIER) cc_final: 0.7036 (tt0) REVERT: A 813 PHE cc_start: 0.8726 (m-80) cc_final: 0.8439 (m-80) REVERT: A 909 ARG cc_start: 0.8492 (OUTLIER) cc_final: 0.7711 (mtt-85) REVERT: A 1016 LYS cc_start: 0.7221 (OUTLIER) cc_final: 0.6808 (pttt) REVERT: A 1020 ASP cc_start: 0.4231 (OUTLIER) cc_final: 0.3992 (p0) REVERT: A 1030 SER cc_start: 0.8423 (t) cc_final: 0.8035 (p) REVERT: A 1051 GLU cc_start: 0.7508 (mm-30) cc_final: 0.7113 (mp0) REVERT: A 1073 ASP cc_start: 0.7495 (OUTLIER) cc_final: 0.7295 (p0) REVERT: A 1190 GLU cc_start: 0.8842 (OUTLIER) cc_final: 0.8584 (tp30) REVERT: A 1391 LEU cc_start: 0.8936 (OUTLIER) cc_final: 0.8703 (tm) REVERT: A 1436 LYS cc_start: 0.7871 (ttpp) cc_final: 0.7546 (tttm) outliers start: 86 outliers final: 41 residues processed: 229 average time/residue: 1.2093 time to fit residues: 303.5983 Evaluate side-chains 203 residues out of total 1354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 150 time to evaluate : 1.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 399 LYS Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 439 ASP Chi-restraints excluded: chain A residue 455 THR Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain A residue 622 GLU Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 671 THR Chi-restraints excluded: chain A residue 677 MET Chi-restraints excluded: chain A residue 687 VAL Chi-restraints excluded: chain A residue 704 GLN Chi-restraints excluded: chain A residue 711 GLU Chi-restraints excluded: chain A residue 764 GLN Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 821 LYS Chi-restraints excluded: chain A residue 823 LEU Chi-restraints excluded: chain A residue 830 ILE Chi-restraints excluded: chain A residue 854 LYS Chi-restraints excluded: chain A residue 874 ASP Chi-restraints excluded: chain A residue 901 GLU Chi-restraints excluded: chain A residue 909 ARG Chi-restraints excluded: chain A residue 920 TRP Chi-restraints excluded: chain A residue 964 GLU Chi-restraints excluded: chain A residue 1016 LYS Chi-restraints excluded: chain A residue 1020 ASP Chi-restraints excluded: chain A residue 1052 GLU Chi-restraints excluded: chain A residue 1060 ASP Chi-restraints excluded: chain A residue 1065 LYS Chi-restraints excluded: chain A residue 1072 ILE Chi-restraints excluded: chain A residue 1073 ASP Chi-restraints excluded: chain A residue 1085 ASP Chi-restraints excluded: chain A residue 1103 CYS Chi-restraints excluded: chain A residue 1133 ASN Chi-restraints excluded: chain A residue 1190 GLU Chi-restraints excluded: chain A residue 1234 VAL Chi-restraints excluded: chain A residue 1258 VAL Chi-restraints excluded: chain A residue 1266 ASN Chi-restraints excluded: chain A residue 1311 VAL Chi-restraints excluded: chain A residue 1360 ILE Chi-restraints excluded: chain A residue 1387 LEU Chi-restraints excluded: chain A residue 1391 LEU Chi-restraints excluded: chain B residue 149 SER Chi-restraints excluded: chain B residue 151 ASP Chi-restraints excluded: chain B residue 176 ASN Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 196 ASP Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 352 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 138 optimal weight: 0.8980 chunk 105 optimal weight: 0.8980 chunk 72 optimal weight: 3.9990 chunk 15 optimal weight: 5.9990 chunk 66 optimal weight: 4.9990 chunk 94 optimal weight: 1.9990 chunk 140 optimal weight: 0.9980 chunk 148 optimal weight: 0.6980 chunk 73 optimal weight: 7.9990 chunk 133 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 410 HIS A 902 GLN ** A1139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.1814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12979 Z= 0.213 Angle : 0.556 8.718 17568 Z= 0.289 Chirality : 0.043 0.381 1957 Planarity : 0.004 0.033 2209 Dihedral : 11.958 104.657 2075 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.90 % Favored : 96.04 % Rotamer: Outliers : 6.10 % Allowed : 25.22 % Favored : 68.68 % 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: 0.04 (0.21), residues: 1540 helix: 0.56 (0.20), residues: 698 sheet: 0.78 (0.34), residues: 219 loop : -0.79 (0.25), residues: 623 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 603 HIS 0.003 0.001 HIS A1417 PHE 0.013 0.001 PHE A1403 TYR 0.020 0.001 TYR B 280 ARG 0.006 0.000 ARG A 488 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 156 time to evaluate : 1.391 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 224 LEU cc_start: 0.8773 (OUTLIER) cc_final: 0.8552 (tp) REVERT: A 445 LYS cc_start: 0.8364 (mmtp) cc_final: 0.7938 (mmtt) REVERT: A 523 MET cc_start: 0.8114 (mmm) cc_final: 0.7862 (tpp) REVERT: A 691 ARG cc_start: 0.8379 (OUTLIER) cc_final: 0.8041 (mmm160) REVERT: A 704 GLN cc_start: 0.6549 (OUTLIER) cc_final: 0.6006 (tt0) REVERT: A 711 GLU cc_start: 0.7299 (OUTLIER) cc_final: 0.6542 (tt0) REVERT: A 722 ASP cc_start: 0.7836 (m-30) cc_final: 0.7147 (t0) REVERT: A 740 TYR cc_start: 0.8351 (m-80) cc_final: 0.8082 (m-80) REVERT: A 742 GLU cc_start: 0.7959 (mp0) cc_final: 0.7651 (pm20) REVERT: A 764 GLN cc_start: 0.7506 (OUTLIER) cc_final: 0.7056 (tt0) REVERT: A 813 PHE cc_start: 0.8807 (m-80) cc_final: 0.8530 (m-80) REVERT: A 1016 LYS cc_start: 0.7109 (OUTLIER) cc_final: 0.6852 (pttt) REVERT: A 1020 ASP cc_start: 0.4193 (OUTLIER) cc_final: 0.3937 (p0) REVERT: A 1051 GLU cc_start: 0.7535 (mm-30) cc_final: 0.7097 (mp0) REVERT: A 1190 GLU cc_start: 0.8817 (OUTLIER) cc_final: 0.8512 (tp30) REVERT: A 1218 GLU cc_start: 0.8497 (OUTLIER) cc_final: 0.7981 (tm-30) REVERT: A 1436 LYS cc_start: 0.7848 (ttpp) cc_final: 0.7509 (tttm) REVERT: B 150 ASP cc_start: 0.8290 (t0) cc_final: 0.7986 (t0) REVERT: B 217 LYS cc_start: 0.6798 (OUTLIER) cc_final: 0.6405 (tppt) REVERT: B 280 TYR cc_start: 0.8423 (OUTLIER) cc_final: 0.8065 (p90) outliers start: 82 outliers final: 36 residues processed: 223 average time/residue: 1.2488 time to fit residues: 305.5903 Evaluate side-chains 198 residues out of total 1354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 151 time to evaluate : 1.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 399 LYS Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 455 THR Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain A residue 622 GLU Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 671 THR Chi-restraints excluded: chain A residue 687 VAL Chi-restraints excluded: chain A residue 691 ARG Chi-restraints excluded: chain A residue 704 GLN Chi-restraints excluded: chain A residue 711 GLU Chi-restraints excluded: chain A residue 737 SER Chi-restraints excluded: chain A residue 764 GLN Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 821 LYS Chi-restraints excluded: chain A residue 823 LEU Chi-restraints excluded: chain A residue 830 ILE Chi-restraints excluded: chain A residue 901 GLU Chi-restraints excluded: chain A residue 920 TRP Chi-restraints excluded: chain A residue 1016 LYS Chi-restraints excluded: chain A residue 1020 ASP Chi-restraints excluded: chain A residue 1065 LYS Chi-restraints excluded: chain A residue 1072 ILE Chi-restraints excluded: chain A residue 1085 ASP Chi-restraints excluded: chain A residue 1103 CYS Chi-restraints excluded: chain A residue 1133 ASN Chi-restraints excluded: chain A residue 1190 GLU Chi-restraints excluded: chain A residue 1218 GLU Chi-restraints excluded: chain A residue 1234 VAL Chi-restraints excluded: chain A residue 1258 VAL Chi-restraints excluded: chain A residue 1266 ASN Chi-restraints excluded: chain A residue 1311 VAL Chi-restraints excluded: chain A residue 1360 ILE Chi-restraints excluded: chain A residue 1387 LEU Chi-restraints excluded: chain A residue 1391 LEU Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 149 SER Chi-restraints excluded: chain B residue 151 ASP 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 217 LYS Chi-restraints excluded: chain B residue 280 TYR Chi-restraints excluded: chain B residue 352 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 123 optimal weight: 2.9990 chunk 84 optimal weight: 0.0050 chunk 2 optimal weight: 0.8980 chunk 110 optimal weight: 0.8980 chunk 61 optimal weight: 9.9990 chunk 127 optimal weight: 3.9990 chunk 102 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 76 optimal weight: 6.9990 chunk 133 optimal weight: 0.5980 chunk 37 optimal weight: 2.9990 overall best weight: 0.8796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 396 ASN A 410 HIS A 902 GLN ** A1139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 moved from start: 0.2018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12979 Z= 0.189 Angle : 0.532 8.385 17568 Z= 0.278 Chirality : 0.042 0.293 1957 Planarity : 0.004 0.042 2209 Dihedral : 11.191 95.233 2058 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.09 % Favored : 95.84 % Rotamer: Outliers : 5.73 % Allowed : 26.12 % Favored : 68.15 % 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: 0.22 (0.22), residues: 1540 helix: 0.73 (0.20), residues: 700 sheet: 0.69 (0.34), residues: 227 loop : -0.66 (0.25), residues: 613 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 603 HIS 0.003 0.001 HIS A1417 PHE 0.013 0.001 PHE A 842 TYR 0.019 0.001 TYR B 280 ARG 0.009 0.000 ARG A 193 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 162 time to evaluate : 1.411 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 445 LYS cc_start: 0.8378 (mmtp) cc_final: 0.7945 (mmtt) REVERT: A 677 MET cc_start: 0.8916 (mmt) cc_final: 0.8597 (mmt) REVERT: A 704 GLN cc_start: 0.6626 (OUTLIER) cc_final: 0.6152 (tt0) REVERT: A 742 GLU cc_start: 0.7966 (mp0) cc_final: 0.7648 (pm20) REVERT: A 764 GLN cc_start: 0.7500 (OUTLIER) cc_final: 0.7086 (tt0) REVERT: A 813 PHE cc_start: 0.8777 (m-80) cc_final: 0.8511 (m-80) REVERT: A 1020 ASP cc_start: 0.4185 (OUTLIER) cc_final: 0.3913 (p0) REVERT: A 1051 GLU cc_start: 0.7540 (mm-30) cc_final: 0.7127 (mp0) REVERT: A 1072 ILE cc_start: 0.8845 (OUTLIER) cc_final: 0.8641 (tt) REVERT: A 1073 ASP cc_start: 0.7441 (OUTLIER) cc_final: 0.7191 (p0) REVERT: A 1190 GLU cc_start: 0.8750 (OUTLIER) cc_final: 0.8512 (tp30) REVERT: A 1218 GLU cc_start: 0.8462 (OUTLIER) cc_final: 0.8046 (tm-30) REVERT: A 1436 LYS cc_start: 0.7857 (ttpp) cc_final: 0.7509 (tttm) REVERT: B 150 ASP cc_start: 0.8362 (t0) cc_final: 0.8036 (t0) outliers start: 77 outliers final: 38 residues processed: 223 average time/residue: 1.1909 time to fit residues: 291.5012 Evaluate side-chains 198 residues out of total 1354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 153 time to evaluate : 1.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 399 LYS Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 455 THR Chi-restraints excluded: chain A residue 471 SER Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 671 THR Chi-restraints excluded: chain A residue 704 GLN Chi-restraints excluded: chain A residue 737 SER Chi-restraints excluded: chain A residue 764 GLN Chi-restraints excluded: chain A residue 821 LYS Chi-restraints excluded: chain A residue 823 LEU Chi-restraints excluded: chain A residue 830 ILE Chi-restraints excluded: chain A residue 874 ASP Chi-restraints excluded: chain A residue 901 GLU Chi-restraints excluded: chain A residue 920 TRP Chi-restraints excluded: chain A residue 957 LEU Chi-restraints excluded: chain A residue 964 GLU Chi-restraints excluded: chain A residue 1020 ASP Chi-restraints excluded: chain A residue 1046 ASN Chi-restraints excluded: chain A residue 1065 LYS Chi-restraints excluded: chain A residue 1072 ILE Chi-restraints excluded: chain A residue 1073 ASP Chi-restraints excluded: chain A residue 1085 ASP Chi-restraints excluded: chain A residue 1133 ASN Chi-restraints excluded: chain A residue 1184 LEU Chi-restraints excluded: chain A residue 1190 GLU Chi-restraints excluded: chain A residue 1214 SER Chi-restraints excluded: chain A residue 1218 GLU Chi-restraints excluded: chain A residue 1223 MET Chi-restraints excluded: chain A residue 1234 VAL Chi-restraints excluded: chain A residue 1266 ASN Chi-restraints excluded: chain A residue 1311 VAL Chi-restraints excluded: chain A residue 1360 ILE Chi-restraints excluded: chain A residue 1387 LEU Chi-restraints excluded: chain A residue 1391 LEU Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 151 ASP Chi-restraints excluded: chain B residue 176 ASN Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 196 ASP Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 260 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 50 optimal weight: 8.9990 chunk 134 optimal weight: 2.9990 chunk 29 optimal weight: 0.8980 chunk 87 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 149 optimal weight: 7.9990 chunk 123 optimal weight: 2.9990 chunk 68 optimal weight: 20.0000 chunk 12 optimal weight: 20.0000 chunk 49 optimal weight: 5.9990 chunk 78 optimal weight: 5.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 396 ASN A 410 HIS A 902 GLN ** A1139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8581 moved from start: 0.1908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 12979 Z= 0.320 Angle : 0.595 8.253 17568 Z= 0.308 Chirality : 0.045 0.363 1957 Planarity : 0.004 0.044 2209 Dihedral : 10.939 88.727 2048 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.90 % Favored : 96.04 % Rotamer: Outliers : 5.58 % Allowed : 26.64 % Favored : 67.78 % 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: 0.19 (0.21), residues: 1540 helix: 0.70 (0.20), residues: 691 sheet: 0.77 (0.34), residues: 221 loop : -0.66 (0.25), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 314 HIS 0.003 0.001 HIS B 131 PHE 0.016 0.002 PHE A1341 TYR 0.020 0.002 TYR B 280 ARG 0.008 0.000 ARG A 193 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 150 time to evaluate : 1.405 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 445 LYS cc_start: 0.8407 (mmtp) cc_final: 0.7969 (mmtt) REVERT: A 691 ARG cc_start: 0.8394 (OUTLIER) cc_final: 0.7656 (mtm180) REVERT: A 704 GLN cc_start: 0.6639 (OUTLIER) cc_final: 0.6137 (tt0) REVERT: A 742 GLU cc_start: 0.7975 (mp0) cc_final: 0.7648 (pm20) REVERT: A 749 LYS cc_start: 0.7583 (OUTLIER) cc_final: 0.7307 (pttt) REVERT: A 764 GLN cc_start: 0.7517 (OUTLIER) cc_final: 0.7043 (tt0) REVERT: A 813 PHE cc_start: 0.8826 (m-80) cc_final: 0.8618 (m-80) REVERT: A 1020 ASP cc_start: 0.4207 (OUTLIER) cc_final: 0.3935 (p0) REVERT: A 1051 GLU cc_start: 0.7533 (mm-30) cc_final: 0.7153 (mp0) REVERT: A 1073 ASP cc_start: 0.7473 (OUTLIER) cc_final: 0.7248 (p0) REVERT: A 1190 GLU cc_start: 0.8872 (OUTLIER) cc_final: 0.8571 (tp30) REVERT: A 1218 GLU cc_start: 0.8564 (OUTLIER) cc_final: 0.8122 (tm-30) REVERT: A 1436 LYS cc_start: 0.7882 (ttpp) cc_final: 0.7531 (tttm) REVERT: B 150 ASP cc_start: 0.8431 (t0) cc_final: 0.8080 (t0) outliers start: 75 outliers final: 47 residues processed: 210 average time/residue: 1.1701 time to fit residues: 269.1809 Evaluate side-chains 200 residues out of total 1354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 145 time to evaluate : 1.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 399 LYS Chi-restraints excluded: chain A residue 427 THR Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 471 SER Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain A residue 590 ILE Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 671 THR Chi-restraints excluded: chain A residue 687 VAL Chi-restraints excluded: chain A residue 691 ARG Chi-restraints excluded: chain A residue 704 GLN Chi-restraints excluded: chain A residue 710 THR Chi-restraints excluded: chain A residue 749 LYS Chi-restraints excluded: chain A residue 764 GLN Chi-restraints excluded: chain A residue 821 LYS Chi-restraints excluded: chain A residue 823 LEU Chi-restraints excluded: chain A residue 830 ILE Chi-restraints excluded: chain A residue 874 ASP Chi-restraints excluded: chain A residue 901 GLU Chi-restraints excluded: chain A residue 920 TRP Chi-restraints excluded: chain A residue 957 LEU Chi-restraints excluded: chain A residue 964 GLU Chi-restraints excluded: chain A residue 1017 THR Chi-restraints excluded: chain A residue 1020 ASP Chi-restraints excluded: chain A residue 1046 ASN Chi-restraints excluded: chain A residue 1052 GLU Chi-restraints excluded: chain A residue 1065 LYS Chi-restraints excluded: chain A residue 1072 ILE Chi-restraints excluded: chain A residue 1073 ASP Chi-restraints excluded: chain A residue 1085 ASP Chi-restraints excluded: chain A residue 1133 ASN Chi-restraints excluded: chain A residue 1184 LEU Chi-restraints excluded: chain A residue 1190 GLU Chi-restraints excluded: chain A residue 1214 SER Chi-restraints excluded: chain A residue 1218 GLU Chi-restraints excluded: chain A residue 1223 MET Chi-restraints excluded: chain A residue 1234 VAL Chi-restraints excluded: chain A residue 1266 ASN Chi-restraints excluded: chain A residue 1360 ILE Chi-restraints excluded: chain A residue 1387 LEU Chi-restraints excluded: chain A residue 1391 LEU Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 149 SER Chi-restraints excluded: chain B residue 151 ASP Chi-restraints excluded: chain B residue 176 ASN Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 196 ASP Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 352 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 143 optimal weight: 0.0470 chunk 16 optimal weight: 6.9990 chunk 84 optimal weight: 0.1980 chunk 108 optimal weight: 0.7980 chunk 125 optimal weight: 2.9990 chunk 83 optimal weight: 4.9990 chunk 148 optimal weight: 0.1980 chunk 92 optimal weight: 0.9980 chunk 90 optimal weight: 3.9990 chunk 68 optimal weight: 20.0000 chunk 91 optimal weight: 1.9990 overall best weight: 0.4478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 396 ASN A 410 HIS A 902 GLN ** A1139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.2309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 12979 Z= 0.152 Angle : 0.512 9.284 17568 Z= 0.267 Chirality : 0.041 0.338 1957 Planarity : 0.004 0.037 2209 Dihedral : 10.339 89.973 2048 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.90 % Favored : 96.04 % Rotamer: Outliers : 4.17 % Allowed : 28.12 % Favored : 67.71 % 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: 0.32 (0.22), residues: 1540 helix: 0.79 (0.20), residues: 706 sheet: 0.71 (0.34), residues: 227 loop : -0.56 (0.26), residues: 607 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1352 HIS 0.002 0.000 HIS A1417 PHE 0.013 0.001 PHE A1403 TYR 0.020 0.001 TYR B 280 ARG 0.009 0.000 ARG A 193 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 162 time to evaluate : 1.541 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 445 LYS cc_start: 0.8396 (mmtp) cc_final: 0.7950 (mmtt) REVERT: A 447 ARG cc_start: 0.8898 (OUTLIER) cc_final: 0.8018 (mmt90) REVERT: A 691 ARG cc_start: 0.8374 (OUTLIER) cc_final: 0.8062 (mmm160) REVERT: A 704 GLN cc_start: 0.6559 (OUTLIER) cc_final: 0.6108 (tt0) REVERT: A 740 TYR cc_start: 0.8345 (m-80) cc_final: 0.8113 (m-80) REVERT: A 742 GLU cc_start: 0.7966 (mp0) cc_final: 0.7645 (pm20) REVERT: A 764 GLN cc_start: 0.7455 (OUTLIER) cc_final: 0.7161 (tt0) REVERT: A 813 PHE cc_start: 0.8735 (m-80) cc_final: 0.8502 (m-80) REVERT: A 1020 ASP cc_start: 0.4146 (OUTLIER) cc_final: 0.3863 (p0) REVERT: A 1051 GLU cc_start: 0.7486 (mm-30) cc_final: 0.7116 (mp0) REVERT: A 1073 ASP cc_start: 0.7340 (OUTLIER) cc_final: 0.7088 (p0) REVERT: A 1190 GLU cc_start: 0.8695 (OUTLIER) cc_final: 0.8442 (tp30) REVERT: A 1218 GLU cc_start: 0.8390 (OUTLIER) cc_final: 0.7810 (tm-30) REVERT: A 1436 LYS cc_start: 0.7856 (ttpp) cc_final: 0.7495 (tttm) REVERT: B 56 ASP cc_start: 0.7227 (m-30) cc_final: 0.6904 (m-30) REVERT: B 134 LYS cc_start: 0.8456 (mmtt) cc_final: 0.8202 (mmtm) REVERT: B 150 ASP cc_start: 0.8359 (t0) cc_final: 0.8018 (t0) outliers start: 56 outliers final: 25 residues processed: 207 average time/residue: 1.2492 time to fit residues: 282.8112 Evaluate side-chains 185 residues out of total 1354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 152 time to evaluate : 1.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 399 LYS Chi-restraints excluded: chain A residue 447 ARG Chi-restraints excluded: chain A residue 671 THR Chi-restraints excluded: chain A residue 691 ARG Chi-restraints excluded: chain A residue 704 GLN Chi-restraints excluded: chain A residue 764 GLN Chi-restraints excluded: chain A residue 821 LYS Chi-restraints excluded: chain A residue 823 LEU Chi-restraints excluded: chain A residue 830 ILE Chi-restraints excluded: chain A residue 850 SER Chi-restraints excluded: chain A residue 901 GLU Chi-restraints excluded: chain A residue 920 TRP Chi-restraints excluded: chain A residue 964 GLU Chi-restraints excluded: chain A residue 1020 ASP Chi-restraints excluded: chain A residue 1046 ASN Chi-restraints excluded: chain A residue 1073 ASP Chi-restraints excluded: chain A residue 1085 ASP Chi-restraints excluded: chain A residue 1133 ASN Chi-restraints excluded: chain A residue 1190 GLU Chi-restraints excluded: chain A residue 1218 GLU Chi-restraints excluded: chain A residue 1223 MET Chi-restraints excluded: chain A residue 1234 VAL Chi-restraints excluded: chain A residue 1266 ASN Chi-restraints excluded: chain A residue 1360 ILE Chi-restraints excluded: chain A residue 1391 LEU Chi-restraints excluded: chain B residue 149 SER Chi-restraints excluded: chain B residue 151 ASP Chi-restraints excluded: chain B residue 176 ASN Chi-restraints excluded: chain B residue 196 ASP Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 348 TRP Chi-restraints excluded: chain B residue 352 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 59 optimal weight: 9.9990 chunk 88 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 chunk 94 optimal weight: 2.9990 chunk 101 optimal weight: 3.9990 chunk 73 optimal weight: 7.9990 chunk 13 optimal weight: 0.1980 chunk 116 optimal weight: 0.8980 chunk 135 optimal weight: 0.3980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 410 HIS A 902 GLN ** A1139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 moved from start: 0.2326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 12979 Z= 0.190 Angle : 0.528 9.474 17568 Z= 0.273 Chirality : 0.042 0.306 1957 Planarity : 0.004 0.041 2209 Dihedral : 9.962 89.811 2042 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.90 % Favored : 95.97 % Rotamer: Outliers : 3.27 % Allowed : 28.79 % Favored : 67.93 % 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 (0.22), residues: 1540 helix: 0.90 (0.20), residues: 698 sheet: 0.73 (0.34), residues: 227 loop : -0.54 (0.26), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 314 HIS 0.002 0.001 HIS B 131 PHE 0.013 0.001 PHE A1403 TYR 0.020 0.001 TYR B 280 ARG 0.008 0.000 ARG A 193 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 153 time to evaluate : 1.464 Fit side-chains revert: symmetry clash REVERT: A 445 LYS cc_start: 0.8424 (mmtp) cc_final: 0.7985 (mmtt) REVERT: A 704 GLN cc_start: 0.6600 (OUTLIER) cc_final: 0.6165 (tt0) REVERT: A 742 GLU cc_start: 0.7954 (mp0) cc_final: 0.7626 (pm20) REVERT: A 813 PHE cc_start: 0.8786 (m-80) cc_final: 0.8563 (m-80) REVERT: A 1020 ASP cc_start: 0.4200 (OUTLIER) cc_final: 0.3657 (p0) REVERT: A 1051 GLU cc_start: 0.7514 (mm-30) cc_final: 0.7132 (mp0) REVERT: A 1073 ASP cc_start: 0.7309 (OUTLIER) cc_final: 0.7071 (p0) REVERT: A 1190 GLU cc_start: 0.8715 (OUTLIER) cc_final: 0.8505 (tp30) REVERT: A 1218 GLU cc_start: 0.8452 (OUTLIER) cc_final: 0.8031 (tm-30) REVERT: A 1436 LYS cc_start: 0.7871 (ttpp) cc_final: 0.7513 (tttm) REVERT: B 56 ASP cc_start: 0.7259 (m-30) cc_final: 0.6956 (m-30) REVERT: B 134 LYS cc_start: 0.8456 (mmtt) cc_final: 0.8201 (mmtm) REVERT: B 150 ASP cc_start: 0.8378 (t0) cc_final: 0.8063 (t0) outliers start: 44 outliers final: 26 residues processed: 186 average time/residue: 1.2990 time to fit residues: 264.4719 Evaluate side-chains 178 residues out of total 1354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 147 time to evaluate : 1.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 399 LYS Chi-restraints excluded: chain A residue 671 THR Chi-restraints excluded: chain A residue 687 VAL Chi-restraints excluded: chain A residue 704 GLN Chi-restraints excluded: chain A residue 721 LYS Chi-restraints excluded: chain A residue 821 LYS Chi-restraints excluded: chain A residue 830 ILE Chi-restraints excluded: chain A residue 850 SER Chi-restraints excluded: chain A residue 920 TRP Chi-restraints excluded: chain A residue 964 GLU Chi-restraints excluded: chain A residue 1017 THR Chi-restraints excluded: chain A residue 1020 ASP Chi-restraints excluded: chain A residue 1046 ASN Chi-restraints excluded: chain A residue 1073 ASP Chi-restraints excluded: chain A residue 1085 ASP Chi-restraints excluded: chain A residue 1133 ASN Chi-restraints excluded: chain A residue 1190 GLU Chi-restraints excluded: chain A residue 1214 SER Chi-restraints excluded: chain A residue 1218 GLU Chi-restraints excluded: chain A residue 1223 MET Chi-restraints excluded: chain A residue 1227 LEU Chi-restraints excluded: chain A residue 1266 ASN Chi-restraints excluded: chain A residue 1360 ILE Chi-restraints excluded: chain A residue 1391 LEU Chi-restraints excluded: chain B residue 149 SER Chi-restraints excluded: chain B residue 151 ASP Chi-restraints excluded: chain B residue 176 ASN Chi-restraints excluded: chain B residue 196 ASP Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 352 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 142 optimal weight: 3.9990 chunk 129 optimal weight: 3.9990 chunk 138 optimal weight: 3.9990 chunk 83 optimal weight: 4.9990 chunk 60 optimal weight: 4.9990 chunk 108 optimal weight: 2.9990 chunk 42 optimal weight: 6.9990 chunk 124 optimal weight: 8.9990 chunk 130 optimal weight: 3.9990 chunk 137 optimal weight: 0.5980 chunk 90 optimal weight: 1.9990 overall best weight: 2.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 764 GLN A 902 GLN A1139 GLN A1266 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8598 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 : 0.006 0.080 12979 Z= 0.413 Angle : 0.632 9.747 17568 Z= 0.327 Chirality : 0.047 0.291 1957 Planarity : 0.004 0.045 2209 Dihedral : 10.249 89.553 2039 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.16 % Favored : 95.71 % Rotamer: Outliers : 4.39 % Allowed : 27.75 % Favored : 67.86 % 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: 0.24 (0.21), residues: 1540 helix: 0.70 (0.20), residues: 695 sheet: 0.89 (0.34), residues: 215 loop : -0.62 (0.25), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 314 HIS 0.003 0.001 HIS A1176 PHE 0.017 0.002 PHE A1341 TYR 0.022 0.002 TYR B 280 ARG 0.009 0.001 ARG A 457 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 148 time to evaluate : 1.537 Fit side-chains REVERT: A 224 LEU cc_start: 0.8784 (OUTLIER) cc_final: 0.8519 (tp) REVERT: A 445 LYS cc_start: 0.8448 (mmtp) cc_final: 0.8002 (mmtt) REVERT: A 704 GLN cc_start: 0.6619 (OUTLIER) cc_final: 0.6109 (tt0) REVERT: A 742 GLU cc_start: 0.7987 (mp0) cc_final: 0.7661 (pm20) REVERT: A 761 GLU cc_start: 0.8017 (tp30) cc_final: 0.7647 (mm-30) REVERT: A 901 GLU cc_start: 0.7871 (OUTLIER) cc_final: 0.7668 (mp0) REVERT: A 902 GLN cc_start: 0.8116 (tt0) cc_final: 0.7698 (tm-30) REVERT: A 1020 ASP cc_start: 0.4310 (OUTLIER) cc_final: 0.4045 (p0) REVERT: A 1051 GLU cc_start: 0.7540 (mm-30) cc_final: 0.7155 (mp0) REVERT: A 1073 ASP cc_start: 0.7292 (OUTLIER) cc_final: 0.7059 (p0) REVERT: A 1190 GLU cc_start: 0.8917 (OUTLIER) cc_final: 0.8583 (tp30) REVERT: A 1218 GLU cc_start: 0.8630 (OUTLIER) cc_final: 0.8121 (tm-30) REVERT: A 1266 ASN cc_start: 0.9049 (OUTLIER) cc_final: 0.8735 (p0) REVERT: A 1436 LYS cc_start: 0.7895 (ttpp) cc_final: 0.7543 (tttm) REVERT: B 56 ASP cc_start: 0.7358 (m-30) cc_final: 0.7003 (m-30) REVERT: B 280 TYR cc_start: 0.8385 (OUTLIER) cc_final: 0.8031 (p90) REVERT: B 401 ARG cc_start: 0.8603 (OUTLIER) cc_final: 0.6726 (ptt90) outliers start: 59 outliers final: 33 residues processed: 195 average time/residue: 1.2477 time to fit residues: 265.4648 Evaluate side-chains 188 residues out of total 1354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 145 time to evaluate : 1.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 399 LYS Chi-restraints excluded: chain A residue 427 THR Chi-restraints excluded: chain A residue 671 THR Chi-restraints excluded: chain A residue 687 VAL Chi-restraints excluded: chain A residue 704 GLN Chi-restraints excluded: chain A residue 710 THR Chi-restraints excluded: chain A residue 721 LYS Chi-restraints excluded: chain A residue 737 SER Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 821 LYS Chi-restraints excluded: chain A residue 830 ILE Chi-restraints excluded: chain A residue 850 SER Chi-restraints excluded: chain A residue 893 LEU Chi-restraints excluded: chain A residue 901 GLU Chi-restraints excluded: chain A residue 920 TRP Chi-restraints excluded: chain A residue 964 GLU Chi-restraints excluded: chain A residue 1017 THR Chi-restraints excluded: chain A residue 1020 ASP Chi-restraints excluded: chain A residue 1073 ASP Chi-restraints excluded: chain A residue 1085 ASP Chi-restraints excluded: chain A residue 1133 ASN Chi-restraints excluded: chain A residue 1184 LEU Chi-restraints excluded: chain A residue 1190 GLU Chi-restraints excluded: chain A residue 1214 SER Chi-restraints excluded: chain A residue 1218 GLU Chi-restraints excluded: chain A residue 1223 MET Chi-restraints excluded: chain A residue 1227 LEU Chi-restraints excluded: chain A residue 1258 VAL Chi-restraints excluded: chain A residue 1266 ASN Chi-restraints excluded: chain A residue 1360 ILE Chi-restraints excluded: chain A residue 1387 LEU Chi-restraints excluded: chain A residue 1391 LEU Chi-restraints excluded: chain B residue 151 ASP Chi-restraints excluded: chain B residue 196 ASP Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 280 TYR Chi-restraints excluded: chain B residue 352 GLU Chi-restraints excluded: chain B residue 401 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 146 optimal weight: 0.9990 chunk 89 optimal weight: 4.9990 chunk 69 optimal weight: 0.7980 chunk 101 optimal weight: 0.7980 chunk 153 optimal weight: 0.5980 chunk 141 optimal weight: 0.5980 chunk 122 optimal weight: 4.9990 chunk 12 optimal weight: 4.9990 chunk 94 optimal weight: 0.9990 chunk 74 optimal weight: 0.6980 chunk 97 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 410 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8526 moved from start: 0.2377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 12979 Z= 0.174 Angle : 0.530 7.576 17568 Z= 0.275 Chirality : 0.042 0.294 1957 Planarity : 0.004 0.039 2209 Dihedral : 9.660 89.235 2039 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.51 % Favored : 96.36 % Rotamer: Outliers : 3.20 % Allowed : 29.02 % Favored : 67.78 % 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: 0.34 (0.22), residues: 1540 helix: 0.82 (0.20), residues: 702 sheet: 0.64 (0.33), residues: 227 loop : -0.54 (0.26), residues: 611 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1352 HIS 0.004 0.001 HIS B 131 PHE 0.014 0.001 PHE A1403 TYR 0.021 0.001 TYR B 280 ARG 0.009 0.000 ARG A 193 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 152 time to evaluate : 1.477 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 224 LEU cc_start: 0.8720 (OUTLIER) cc_final: 0.8507 (tp) REVERT: A 445 LYS cc_start: 0.8434 (mmtp) cc_final: 0.7991 (mmtt) REVERT: A 704 GLN cc_start: 0.6594 (OUTLIER) cc_final: 0.6118 (tt0) REVERT: A 742 GLU cc_start: 0.7951 (mp0) cc_final: 0.7640 (pm20) REVERT: A 761 GLU cc_start: 0.7880 (tp30) cc_final: 0.7538 (mm-30) REVERT: A 902 GLN cc_start: 0.8141 (tt0) cc_final: 0.7749 (tm-30) REVERT: A 1020 ASP cc_start: 0.4303 (OUTLIER) cc_final: 0.4025 (p0) REVERT: A 1051 GLU cc_start: 0.7492 (mm-30) cc_final: 0.7117 (mp0) REVERT: A 1073 ASP cc_start: 0.7211 (OUTLIER) cc_final: 0.6960 (p0) REVERT: A 1190 GLU cc_start: 0.8779 (OUTLIER) cc_final: 0.8181 (tp30) REVERT: A 1218 GLU cc_start: 0.8452 (OUTLIER) cc_final: 0.7934 (tm-30) REVERT: A 1436 LYS cc_start: 0.7868 (ttpp) cc_final: 0.7507 (tttm) outliers start: 43 outliers final: 28 residues processed: 186 average time/residue: 1.2317 time to fit residues: 250.5135 Evaluate side-chains 180 residues out of total 1354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 146 time to evaluate : 1.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 399 LYS Chi-restraints excluded: chain A residue 671 THR Chi-restraints excluded: chain A residue 687 VAL Chi-restraints excluded: chain A residue 704 GLN Chi-restraints excluded: chain A residue 710 THR Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 821 LYS Chi-restraints excluded: chain A residue 830 ILE Chi-restraints excluded: chain A residue 850 SER Chi-restraints excluded: chain A residue 893 LEU Chi-restraints excluded: chain A residue 901 GLU Chi-restraints excluded: chain A residue 920 TRP Chi-restraints excluded: chain A residue 964 GLU Chi-restraints excluded: chain A residue 1017 THR Chi-restraints excluded: chain A residue 1020 ASP Chi-restraints excluded: chain A residue 1073 ASP Chi-restraints excluded: chain A residue 1085 ASP Chi-restraints excluded: chain A residue 1133 ASN Chi-restraints excluded: chain A residue 1184 LEU Chi-restraints excluded: chain A residue 1190 GLU Chi-restraints excluded: chain A residue 1214 SER Chi-restraints excluded: chain A residue 1218 GLU Chi-restraints excluded: chain A residue 1223 MET Chi-restraints excluded: chain A residue 1360 ILE Chi-restraints excluded: chain A residue 1391 LEU Chi-restraints excluded: chain B residue 151 ASP Chi-restraints excluded: chain B residue 176 ASN Chi-restraints excluded: chain B residue 196 ASP Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 348 TRP Chi-restraints excluded: chain B residue 352 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 130 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 chunk 112 optimal weight: 3.9990 chunk 18 optimal weight: 3.9990 chunk 33 optimal weight: 0.5980 chunk 122 optimal weight: 5.9990 chunk 51 optimal weight: 1.9990 chunk 125 optimal weight: 3.9990 chunk 15 optimal weight: 0.9980 chunk 22 optimal weight: 0.8980 chunk 107 optimal weight: 2.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 410 HIS A1266 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.145920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.106338 restraints weight = 14353.331| |-----------------------------------------------------------------------------| r_work (start): 0.3057 rms_B_bonded: 1.88 r_work: 0.2781 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2651 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.2651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8772 moved from start: 0.2297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 12979 Z= 0.261 Angle : 0.562 8.875 17568 Z= 0.291 Chirality : 0.043 0.279 1957 Planarity : 0.004 0.044 2209 Dihedral : 9.594 89.347 2037 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.03 % Favored : 95.84 % Rotamer: Outliers : 3.57 % Allowed : 28.57 % Favored : 67.86 % 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: 0.32 (0.21), residues: 1540 helix: 0.80 (0.20), residues: 695 sheet: 0.76 (0.34), residues: 221 loop : -0.57 (0.25), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 314 HIS 0.003 0.001 HIS A1417 PHE 0.013 0.001 PHE A1341 TYR 0.019 0.001 TYR B 280 ARG 0.009 0.001 ARG A 193 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5324.20 seconds wall clock time: 95 minutes 47.16 seconds (5747.16 seconds total)