Starting phenix.real_space_refine on Thu Feb 15 11:17:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f7f_31487/02_2024/7f7f_31487.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f7f_31487/02_2024/7f7f_31487.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.81 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f7f_31487/02_2024/7f7f_31487.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f7f_31487/02_2024/7f7f_31487.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f7f_31487/02_2024/7f7f_31487.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f7f_31487/02_2024/7f7f_31487.pdb" } resolution = 3.81 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= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Mg 1 5.21 5 S 60 5.16 5 C 7766 2.51 5 N 1996 2.21 5 O 2253 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 168": "NH1" <-> "NH2" Residue "A ARG 193": "NH1" <-> "NH2" Residue "A ARG 264": "NH1" <-> "NH2" Residue "A ARG 265": "NH1" <-> "NH2" Residue "A ARG 408": "NH1" <-> "NH2" Residue "A TYR 432": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 447": "NH1" <-> "NH2" Residue "A ARG 457": "NH1" <-> "NH2" Residue "A ARG 464": "NH1" <-> "NH2" Residue "A ARG 488": "NH1" <-> "NH2" Residue "A ARG 496": "NH1" <-> "NH2" Residue "A ARG 544": "NH1" <-> "NH2" Residue "A ARG 547": "NH1" <-> "NH2" Residue "A PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 580": "NH1" <-> "NH2" Residue "A ARG 703": "NH1" <-> "NH2" Residue "A ARG 713": "NH1" <-> "NH2" Residue "A ARG 714": "NH1" <-> "NH2" Residue "A PHE 739": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 765": "NH1" <-> "NH2" Residue "A ARG 809": "NH1" <-> "NH2" Residue "A ARG 848": "NH1" <-> "NH2" Residue "A ARG 880": "NH1" <-> "NH2" Residue "A ARG 916": "NH1" <-> "NH2" Residue "A ARG 953": "NH1" <-> "NH2" Residue "A ARG 966": "NH1" <-> "NH2" Residue "A ARG 1087": "NH1" <-> "NH2" Residue "A ARG 1088": "NH1" <-> "NH2" Residue "A ARG 1104": "NH1" <-> "NH2" Residue "A ARG 1153": "NH1" <-> "NH2" Residue "A ARG 1167": "NH1" <-> "NH2" Residue "A ARG 1178": "NH1" <-> "NH2" Residue "A ARG 1257": "NH1" <-> "NH2" Residue "A ARG 1268": "NH1" <-> "NH2" Residue "A PHE 1287": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1308": "NH1" <-> "NH2" Residue "A PHE 1365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1371": "NH1" <-> "NH2" Residue "A PHE 1388": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1393": "NH1" <-> "NH2" Residue "B ARG 73": "NH1" <-> "NH2" Residue "B TYR 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 143": "NH1" <-> "NH2" Residue "B ARG 162": "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 ARG 199": "NH1" <-> "NH2" Residue "B ARG 328": "NH1" <-> "NH2" Residue "B PHE 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 12076 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 9046 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1135, 9046 Classifications: {'peptide': 1135} Link IDs: {'CIS': 2, 'PTRANS': 36, 'TRANS': 1096} Chain breaks: 3 Chain: "B" Number of atoms: 2934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 2934 Classifications: {'peptide': 362} Link IDs: {'PTRANS': 19, 'TRANS': 342} Chain: "C" 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: "D" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 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: "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: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.46, per 1000 atoms: 0.53 Number of scatterers: 12076 At special positions: 0 Unit cell: (148.755, 109.72, 128.71, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 60 16.00 Mg 1 11.99 O 2253 8.00 N 1996 7.00 C 7766 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS B 110 " - pdb=" SG CYS B 159 " distance=2.03 Simple disulfide: pdb=" SG CYS B 216 " - pdb=" SG CYS B 231 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=2, symmetry=0 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " BETA1-6 " NAG E 1 " - " NAG E 2 " NAG-ASN " NAG C 1 " - " ASN B 298 " " NAG D 1 " - " ASN B 240 " " NAG E 1 " - " ASN B 256 " Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 4.26 Conformation dependent library (CDL) restraints added in 2.0 seconds 2974 Ramachandran restraints generated. 1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2798 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 12 sheets defined 32.4% alpha, 6.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.17 Creating SS restraints... Processing helix chain 'A' and resid 186 through 190 Processing helix chain 'A' and resid 221 through 232 removed outlier: 4.596A pdb=" N PHE A 232 " --> pdb=" O ILE A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 255 removed outlier: 3.958A pdb=" N VAL A 251 " --> pdb=" O LEU A 247 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ILE A 252 " --> pdb=" O VAL A 248 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ILE A 253 " --> pdb=" O VAL A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 262 removed outlier: 3.512A pdb=" N ASP A 262 " --> pdb=" O ASP A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 430 removed outlier: 3.937A pdb=" N GLY A 429 " --> pdb=" O ASP A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 456 removed outlier: 3.510A pdb=" N THR A 455 " --> pdb=" O CYS A 452 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N ILE A 456 " --> pdb=" O THR A 453 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 452 through 456' Processing helix chain 'A' and resid 501 through 503 No H-bonds generated for 'chain 'A' and resid 501 through 503' Processing helix chain 'A' and resid 530 through 535 Processing helix chain 'A' and resid 548 through 576 removed outlier: 3.799A pdb=" N VAL A 554 " --> pdb=" O ASN A 550 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N LEU A 563 " --> pdb=" O LEU A 559 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N CYS A 564 " --> pdb=" O LEU A 560 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N SER A 567 " --> pdb=" O LEU A 563 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N VAL A 573 " --> pdb=" O ILE A 569 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N TYR A 574 " --> pdb=" O ALA A 570 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N TYR A 575 " --> pdb=" O ASN A 571 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ASP A 576 " --> pdb=" O GLY A 572 " (cutoff:3.500A) Processing helix chain 'A' and resid 599 through 604 removed outlier: 3.760A pdb=" N TRP A 603 " --> pdb=" O PHE A 599 " (cutoff:3.500A) Processing helix chain 'A' and resid 612 through 629 removed outlier: 3.509A pdb=" N GLU A 622 " --> pdb=" O TYR A 618 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ILE A 623 " --> pdb=" O ILE A 619 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ILE A 624 " --> pdb=" O SER A 620 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N THR A 626 " --> pdb=" O GLU A 622 " (cutoff:3.500A) Processing helix chain 'A' and resid 655 through 659 Processing helix chain 'A' and resid 667 through 672 removed outlier: 3.685A pdb=" N LEU A 672 " --> pdb=" O LYS A 668 " (cutoff:3.500A) Processing helix chain 'A' and resid 710 through 723 Processing helix chain 'A' and resid 761 through 766 Processing helix chain 'A' and resid 766 through 777 removed outlier: 4.004A pdb=" N PHE A 770 " --> pdb=" O CYS A 766 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ALA A 775 " --> pdb=" O MET A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 800 through 812 removed outlier: 3.663A pdb=" N VAL A 805 " --> pdb=" O GLU A 801 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ASP A 810 " --> pdb=" O ALA A 806 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLY A 812 " --> pdb=" O ALA A 808 " (cutoff:3.500A) Processing helix chain 'A' and resid 892 through 906 removed outlier: 3.849A pdb=" N TYR A 903 " --> pdb=" O HIS A 899 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ALA A 904 " --> pdb=" O LEU A 900 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N THR A 905 " --> pdb=" O GLU A 901 " (cutoff:3.500A) Processing helix chain 'A' and resid 921 through 929 removed outlier: 4.226A pdb=" N LYS A 925 " --> pdb=" O SER A 921 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N ASN A 927 " --> pdb=" O TYR A 923 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N LYS A 929 " --> pdb=" O LYS A 925 " (cutoff:3.500A) Processing helix chain 'A' and resid 929 through 934 Processing helix chain 'A' and resid 943 through 951 removed outlier: 4.500A pdb=" N ILE A 951 " --> pdb=" O VAL A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 970 through 979 removed outlier: 3.717A pdb=" N GLU A 976 " --> pdb=" O PRO A 972 " (cutoff:3.500A) Processing helix chain 'A' and resid 996 through 1003 Processing helix chain 'A' and resid 1031 through 1047 removed outlier: 3.997A pdb=" N ALA A1035 " --> pdb=" O GLU A1031 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N SER A1038 " --> pdb=" O ASP A1034 " (cutoff:3.500A) Processing helix chain 'A' and resid 1074 through 1079 removed outlier: 3.754A pdb=" N LEU A1079 " --> pdb=" O ASP A1075 " (cutoff:3.500A) Processing helix chain 'A' and resid 1086 through 1095 removed outlier: 3.693A pdb=" N LEU A1092 " --> pdb=" O ARG A1088 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N LEU A1093 " --> pdb=" O LYS A1089 " (cutoff:3.500A) Processing helix chain 'A' and resid 1108 through 1121 removed outlier: 3.614A pdb=" N VAL A1114 " --> pdb=" O LYS A1110 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N VAL A1117 " --> pdb=" O VAL A1113 " (cutoff:3.500A) Processing helix chain 'A' and resid 1134 through 1141 Processing helix chain 'A' and resid 1153 through 1158 removed outlier: 3.672A pdb=" N MET A1157 " --> pdb=" O ARG A1153 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N CYS A1158 " --> pdb=" O GLN A1154 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1153 through 1158' Processing helix chain 'A' and resid 1165 through 1167 No H-bonds generated for 'chain 'A' and resid 1165 through 1167' Processing helix chain 'A' and resid 1168 through 1173 Processing helix chain 'A' and resid 1178 through 1183 Processing helix chain 'A' and resid 1183 through 1188 removed outlier: 3.590A pdb=" N ILE A1188 " --> pdb=" O LEU A1184 " (cutoff:3.500A) Processing helix chain 'A' and resid 1200 through 1205 Processing helix chain 'A' and resid 1232 through 1237 removed outlier: 3.628A pdb=" N PHE A1236 " --> pdb=" O LEU A1232 " (cutoff:3.500A) Processing helix chain 'A' and resid 1245 through 1250 removed outlier: 4.192A pdb=" N LEU A1250 " --> pdb=" O ASP A1246 " (cutoff:3.500A) Processing helix chain 'A' and resid 1252 through 1255 removed outlier: 3.756A pdb=" N LEU A1255 " --> pdb=" O VAL A1252 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1252 through 1255' Processing helix chain 'A' and resid 1256 through 1261 removed outlier: 3.666A pdb=" N ILE A1260 " --> pdb=" O TYR A1256 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEU A1261 " --> pdb=" O ARG A1257 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1256 through 1261' Processing helix chain 'A' and resid 1266 through 1287 removed outlier: 3.567A pdb=" N PHE A1270 " --> pdb=" O ASN A1266 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N TRP A1272 " --> pdb=" O ARG A1268 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N TYR A1273 " --> pdb=" O LYS A1269 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LEU A1275 " --> pdb=" O LEU A1271 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ASP A1276 " --> pdb=" O TRP A1272 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLY A1277 " --> pdb=" O TYR A1273 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ILE A1282 " --> pdb=" O LEU A1278 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N PHE A1285 " --> pdb=" O SER A1281 " (cutoff:3.500A) Processing helix chain 'A' and resid 1316 through 1321 removed outlier: 3.738A pdb=" N ILE A1321 " --> pdb=" O THR A1317 " (cutoff:3.500A) Processing helix chain 'A' and resid 1324 through 1331 Processing helix chain 'A' and resid 1348 through 1357 removed outlier: 3.507A pdb=" N THR A1353 " --> pdb=" O VAL A1349 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLY A1354 " --> pdb=" O PHE A1350 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ILE A1355 " --> pdb=" O ALA A1351 " (cutoff:3.500A) Processing helix chain 'A' and resid 1377 through 1382 removed outlier: 3.604A pdb=" N VAL A1381 " --> pdb=" O SER A1377 " (cutoff:3.500A) Processing helix chain 'A' and resid 1384 through 1395 Proline residue: A1392 - end of helix Processing helix chain 'A' and resid 1395 through 1404 removed outlier: 3.528A pdb=" N LYS A1401 " --> pdb=" O ASP A1397 " (cutoff:3.500A) Processing helix chain 'A' and resid 1406 through 1418 removed outlier: 3.550A pdb=" N ARG A1412 " --> pdb=" O VAL A1408 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N GLN A1416 " --> pdb=" O ARG A1412 " (cutoff:3.500A) Processing helix chain 'B' and resid 75 through 97 removed outlier: 4.126A pdb=" N LEU B 81 " --> pdb=" O PRO B 77 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ILE B 82 " --> pdb=" O LEU B 78 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N VAL B 87 " --> pdb=" O ALA B 83 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ILE B 88 " --> pdb=" O VAL B 84 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLY B 90 " --> pdb=" O PHE B 86 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N CYS B 92 " --> pdb=" O ILE B 88 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LEU B 94 " --> pdb=" O GLY B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 199 Processing helix chain 'B' and resid 205 through 210 removed outlier: 3.673A pdb=" N ASP B 210 " --> pdb=" O GLU B 206 " (cutoff:3.500A) Processing helix chain 'B' and resid 232 through 237 Processing helix chain 'B' and resid 266 through 270 removed outlier: 3.660A pdb=" N ASP B 269 " --> pdb=" O TRP B 266 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N LYS B 270 " --> pdb=" O GLU B 267 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 266 through 270' Processing helix chain 'B' and resid 308 through 313 removed outlier: 3.713A pdb=" N GLN B 312 " --> pdb=" O TRP B 308 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASN B 313 " --> pdb=" O GLU B 309 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 308 through 313' Processing helix chain 'B' and resid 350 through 354 removed outlier: 3.667A pdb=" N PHE B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 377 Processing helix chain 'B' and resid 377 through 383 Processing sheet with id=AA1, first strand: chain 'A' and resid 409 through 410 removed outlier: 3.610A pdb=" N ILE A 409 " --> pdb=" O ALA A 518 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 419 through 420 Processing sheet with id=AA3, first strand: chain 'A' and resid 487 through 488 Processing sheet with id=AA4, first strand: chain 'A' and resid 1071 through 1072 removed outlier: 8.227A pdb=" N CYS A1102 " --> pdb=" O LEU A 985 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N VAL A 987 " --> pdb=" O CYS A1102 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N ILE A 664 " --> pdb=" O TRP A 986 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N LEU A 988 " --> pdb=" O ILE A 664 " (cutoff:3.500A) removed outlier: 5.485A pdb=" N SER A 666 " --> pdb=" O LEU A 988 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N TYR A 663 " --> pdb=" O LEU A1126 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N ILE A1128 " --> pdb=" O TYR A 663 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N PHE A 665 " --> pdb=" O ILE A1128 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 673 through 683 removed outlier: 7.829A pdb=" N MET A 677 " --> pdb=" O ARG A 966 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N ARG A 966 " --> pdb=" O MET A 677 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N PHE A 679 " --> pdb=" O GLU A 964 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N GLU A 964 " --> pdb=" O PHE A 679 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LYS A 681 " --> pdb=" O ALA A 962 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLY A 960 " --> pdb=" O THR A 683 " (cutoff:3.500A) removed outlier: 5.310A pdb=" N LEU A 957 " --> pdb=" O GLN A 915 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N GLN A 915 " --> pdb=" O LEU A 957 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 823 through 824 Processing sheet with id=AA7, first strand: chain 'A' and resid 836 through 839 removed outlier: 3.851A pdb=" N ILE A 852 " --> pdb=" O ASN A 838 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 126 through 127 removed outlier: 3.769A pdb=" N VAL B 173 " --> pdb=" O ASN B 330 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 119 through 120 Processing sheet with id=AB1, first strand: chain 'B' and resid 159 through 161 Processing sheet with id=AB2, first strand: chain 'B' and resid 159 through 161 removed outlier: 6.021A pdb=" N ASP B 343 " --> pdb=" O GLN B 246 " (cutoff:3.500A) removed outlier: 8.384A pdb=" N GLN B 246 " --> pdb=" O ASP B 343 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 227 through 228 removed outlier: 6.612A pdb=" N ILE B 227 " --> pdb=" O ALA B 284 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 247 hydrogen bonds defined for protein. 690 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.45 Time building geometry restraints manager: 4.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3684 1.34 - 1.46: 2798 1.46 - 1.58: 5781 1.58 - 1.70: 1 1.70 - 1.82: 89 Bond restraints: 12353 Sorted by residual: bond pdb=" N GLU A1409 " pdb=" CA GLU A1409 " ideal model delta sigma weight residual 1.457 1.495 -0.038 1.29e-02 6.01e+03 8.64e+00 bond pdb=" N GLY B 399 " pdb=" CA GLY B 399 " ideal model delta sigma weight residual 1.449 1.488 -0.039 1.45e-02 4.76e+03 7.26e+00 bond pdb=" C VAL A1408 " pdb=" N GLU A1409 " ideal model delta sigma weight residual 1.333 1.369 -0.036 1.50e-02 4.44e+03 5.88e+00 bond pdb=" CD LYS A 542 " pdb=" CE LYS A 542 " ideal model delta sigma weight residual 1.520 1.451 0.069 3.00e-02 1.11e+03 5.30e+00 bond pdb=" CG LYS A 542 " pdb=" CD LYS A 542 " ideal model delta sigma weight residual 1.520 1.454 0.066 3.00e-02 1.11e+03 4.79e+00 ... (remaining 12348 not shown) Histogram of bond angle deviations from ideal: 96.84 - 104.52: 176 104.52 - 112.19: 5665 112.19 - 119.87: 5230 119.87 - 127.54: 5552 127.54 - 135.22: 129 Bond angle restraints: 16752 Sorted by residual: angle pdb=" N VAL A 604 " pdb=" CA VAL A 604 " pdb=" C VAL A 604 " ideal model delta sigma weight residual 112.29 105.99 6.30 9.40e-01 1.13e+00 4.49e+01 angle pdb=" N PHE A1366 " pdb=" CA PHE A1366 " pdb=" C PHE A1366 " ideal model delta sigma weight residual 114.56 107.61 6.95 1.27e+00 6.20e-01 3.00e+01 angle pdb=" C TYR A 172 " pdb=" N ASN A 173 " pdb=" CA ASN A 173 " ideal model delta sigma weight residual 121.54 131.42 -9.88 1.91e+00 2.74e-01 2.67e+01 angle pdb=" C ARG A1363 " pdb=" N GLU A1364 " pdb=" CA GLU A1364 " ideal model delta sigma weight residual 121.54 131.04 -9.50 1.91e+00 2.74e-01 2.48e+01 angle pdb=" C CYS A1003 " pdb=" N ASN A1004 " pdb=" CA ASN A1004 " ideal model delta sigma weight residual 121.54 130.39 -8.85 1.91e+00 2.74e-01 2.15e+01 ... (remaining 16747 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.39: 7018 21.39 - 42.78: 348 42.78 - 64.17: 31 64.17 - 85.56: 8 85.56 - 106.94: 12 Dihedral angle restraints: 7417 sinusoidal: 3053 harmonic: 4364 Sorted by residual: dihedral pdb=" CA GLU A1218 " pdb=" C GLU A1218 " pdb=" N TYR A1219 " pdb=" CA TYR A1219 " ideal model delta harmonic sigma weight residual -180.00 -137.75 -42.25 0 5.00e+00 4.00e-02 7.14e+01 dihedral pdb=" CA LYS A 541 " pdb=" C LYS A 541 " pdb=" N LYS A 542 " pdb=" CA LYS A 542 " ideal model delta harmonic sigma weight residual -180.00 -138.58 -41.42 0 5.00e+00 4.00e-02 6.86e+01 dihedral pdb=" CA GLN A 233 " pdb=" C GLN A 233 " pdb=" N ILE A 234 " pdb=" CA ILE A 234 " ideal model delta harmonic sigma weight residual 180.00 -138.98 -41.02 0 5.00e+00 4.00e-02 6.73e+01 ... (remaining 7414 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 1246 0.058 - 0.116: 482 0.116 - 0.174: 121 0.174 - 0.231: 18 0.231 - 0.289: 6 Chirality restraints: 1873 Sorted by residual: chirality pdb=" CB VAL A 245 " pdb=" CA VAL A 245 " pdb=" CG1 VAL A 245 " pdb=" CG2 VAL A 245 " both_signs ideal model delta sigma weight residual False -2.63 -2.34 -0.29 2.00e-01 2.50e+01 2.09e+00 chirality pdb=" C5 BMA D 3 " pdb=" C4 BMA D 3 " pdb=" C6 BMA D 3 " pdb=" O5 BMA D 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.27 2.00e-01 2.50e+01 1.84e+00 chirality pdb=" C4 NAG D 1 " pdb=" C3 NAG D 1 " pdb=" C5 NAG D 1 " pdb=" O4 NAG D 1 " both_signs ideal model delta sigma weight residual False -2.53 -2.27 -0.26 2.00e-01 2.50e+01 1.68e+00 ... (remaining 1870 not shown) Planarity restraints: 2126 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE B 398 " 0.029 2.00e-02 2.50e+03 5.76e-02 3.32e+01 pdb=" C PHE B 398 " -0.100 2.00e-02 2.50e+03 pdb=" O PHE B 398 " 0.037 2.00e-02 2.50e+03 pdb=" N GLY B 399 " 0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A1408 " 0.030 2.00e-02 2.50e+03 5.76e-02 3.31e+01 pdb=" C VAL A1408 " -0.100 2.00e-02 2.50e+03 pdb=" O VAL A1408 " 0.037 2.00e-02 2.50e+03 pdb=" N GLU A1409 " 0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE A1287 " -0.056 5.00e-02 4.00e+02 8.43e-02 1.14e+01 pdb=" N PRO A1288 " 0.146 5.00e-02 4.00e+02 pdb=" CA PRO A1288 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO A1288 " -0.047 5.00e-02 4.00e+02 ... (remaining 2123 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 292 2.68 - 3.23: 11016 3.23 - 3.79: 18973 3.79 - 4.34: 25164 4.34 - 4.90: 40361 Nonbonded interactions: 95806 Sorted by model distance: nonbonded pdb=" O THR A 669 " pdb="MG MG A1601 " model vdw 2.121 2.170 nonbonded pdb=" OH TYR A1193 " pdb=" OE1 GLN A1280 " model vdw 2.184 2.440 nonbonded pdb=" O ASP A 667 " pdb=" OG1 THR A 671 " model vdw 2.226 2.440 nonbonded pdb=" OH TYR A1221 " pdb=" OG1 THR A1353 " model vdw 2.229 2.440 nonbonded pdb=" OD2 ASP A 667 " pdb="MG MG A1601 " model vdw 2.262 2.170 ... (remaining 95801 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 'C' 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.500 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 6.040 Check model and map are aligned: 0.170 Set scattering table: 0.110 Process input model: 31.610 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6828 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 : 0.008 0.102 12353 Z= 0.495 Angle : 1.125 11.844 16752 Z= 0.593 Chirality : 0.064 0.289 1873 Planarity : 0.008 0.084 2123 Dihedral : 13.552 106.944 4613 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.62 % Favored : 90.32 % Rotamer: Outliers : 0.31 % Allowed : 6.69 % Favored : 93.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.42 % 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: -5.60 (0.16), residues: 1487 helix: -4.70 (0.10), residues: 493 sheet: -3.22 (0.37), residues: 128 loop : -3.29 (0.17), residues: 866 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.003 TRP A1415 HIS 0.012 0.002 HIS B 186 PHE 0.036 0.004 PHE A1287 TYR 0.045 0.003 TYR A1273 ARG 0.014 0.001 ARG A1412 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2974 Ramachandran restraints generated. 1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2974 Ramachandran restraints generated. 1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 184 time to evaluate : 1.393 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 189 MET cc_start: 0.5546 (mpm) cc_final: 0.4399 (mtt) REVERT: A 519 MET cc_start: -0.0530 (mtt) cc_final: -0.0964 (ttm) REVERT: A 633 TYR cc_start: 0.8188 (t80) cc_final: 0.7971 (t80) REVERT: A 652 TRP cc_start: 0.7261 (m100) cc_final: 0.7015 (m-10) REVERT: A 848 ARG cc_start: 0.4870 (mtt90) cc_final: 0.3017 (mtm110) REVERT: A 992 LYS cc_start: 0.6964 (pptt) cc_final: 0.6753 (ptmm) REVERT: B 123 SER cc_start: 0.8729 (m) cc_final: 0.8036 (p) REVERT: B 142 TRP cc_start: 0.7858 (m-10) cc_final: 0.7143 (m-10) REVERT: B 370 ARG cc_start: 0.8271 (ptm-80) cc_final: 0.7934 (ttt90) outliers start: 4 outliers final: 0 residues processed: 188 average time/residue: 0.3111 time to fit residues: 81.4247 Evaluate side-chains 115 residues out of total 1300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 115 time to evaluate : 1.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 125 optimal weight: 0.9980 chunk 112 optimal weight: 2.9990 chunk 62 optimal weight: 0.7980 chunk 38 optimal weight: 0.9990 chunk 76 optimal weight: 3.9990 chunk 60 optimal weight: 3.9990 chunk 116 optimal weight: 0.7980 chunk 45 optimal weight: 0.9990 chunk 71 optimal weight: 0.4980 chunk 86 optimal weight: 0.8980 chunk 135 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 411 ASN A 484 ASN A 556 ASN A 674 GLN A1046 ASN A1061 HIS A1067 ASN A1096 ASN A1209 ASN A1226 ASN A1301 ASN A1307 HIS ** A1330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 125 HIS B 171 ASN B 209 HIS B 330 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6827 moved from start: 0.1530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 12353 Z= 0.229 Angle : 0.697 7.586 16752 Z= 0.367 Chirality : 0.047 0.365 1873 Planarity : 0.005 0.064 2123 Dihedral : 10.866 84.830 1780 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 13.15 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.46 % Favored : 92.47 % Rotamer: Outliers : 2.23 % Allowed : 9.54 % Favored : 88.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.28 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.81 (0.18), residues: 1487 helix: -3.87 (0.15), residues: 501 sheet: -2.89 (0.40), residues: 133 loop : -2.87 (0.19), residues: 853 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A1415 HIS 0.005 0.001 HIS B 186 PHE 0.033 0.002 PHE A 565 TYR 0.016 0.002 TYR A1256 ARG 0.013 0.001 ARG B 187 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2974 Ramachandran restraints generated. 1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2974 Ramachandran restraints generated. 1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 143 time to evaluate : 1.304 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 188 ILE cc_start: 0.1739 (OUTLIER) cc_final: 0.1344 (mp) REVERT: A 189 MET cc_start: 0.5514 (mpm) cc_final: 0.4446 (mtt) REVERT: A 519 MET cc_start: -0.0164 (mtt) cc_final: -0.0962 (ttm) REVERT: A 633 TYR cc_start: 0.8100 (t80) cc_final: 0.7898 (t80) REVERT: A 643 LEU cc_start: 0.7222 (OUTLIER) cc_final: 0.6954 (tt) REVERT: A 652 TRP cc_start: 0.7443 (m100) cc_final: 0.7089 (m-10) REVERT: A 677 MET cc_start: 0.5481 (mmm) cc_final: 0.4717 (mtt) REVERT: A 848 ARG cc_start: 0.5198 (mtt90) cc_final: 0.3276 (mtm110) REVERT: B 123 SER cc_start: 0.8692 (m) cc_final: 0.8130 (p) REVERT: B 238 MET cc_start: 0.7234 (ttt) cc_final: 0.6990 (ttt) REVERT: B 321 ASP cc_start: 0.7178 (t0) cc_final: 0.6942 (t70) REVERT: B 370 ARG cc_start: 0.8295 (ptm-80) cc_final: 0.7868 (ttt180) outliers start: 29 outliers final: 13 residues processed: 162 average time/residue: 0.2455 time to fit residues: 58.0201 Evaluate side-chains 129 residues out of total 1300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 114 time to evaluate : 1.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 710 THR Chi-restraints excluded: chain A residue 798 SER Chi-restraints excluded: chain A residue 1037 LEU Chi-restraints excluded: chain A residue 1100 VAL Chi-restraints excluded: chain A residue 1219 TYR Chi-restraints excluded: chain A residue 1274 MET Chi-restraints excluded: chain A residue 1407 ASP Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 101 ASP Chi-restraints excluded: chain B residue 348 TRP Chi-restraints excluded: chain B residue 391 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 75 optimal weight: 2.9990 chunk 41 optimal weight: 0.0980 chunk 112 optimal weight: 3.9990 chunk 92 optimal weight: 0.9990 chunk 37 optimal weight: 0.0980 chunk 135 optimal weight: 0.3980 chunk 146 optimal weight: 2.9990 chunk 120 optimal weight: 4.9990 chunk 134 optimal weight: 0.0010 chunk 46 optimal weight: 1.9990 chunk 108 optimal weight: 0.0770 overall best weight: 0.1344 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 285 ASN A 778 HIS B 141 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6718 moved from start: 0.2153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 12353 Z= 0.149 Angle : 0.642 14.105 16752 Z= 0.327 Chirality : 0.044 0.309 1873 Planarity : 0.004 0.051 2123 Dihedral : 8.499 66.913 1780 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer: Outliers : 2.69 % Allowed : 11.00 % Favored : 86.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.05 (0.19), residues: 1487 helix: -3.10 (0.18), residues: 496 sheet: -2.44 (0.41), residues: 139 loop : -2.52 (0.20), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 468 HIS 0.005 0.001 HIS B 186 PHE 0.019 0.001 PHE A 565 TYR 0.031 0.001 TYR A1256 ARG 0.003 0.000 ARG A1308 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2974 Ramachandran restraints generated. 1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2974 Ramachandran restraints generated. 1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 145 time to evaluate : 1.347 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 188 ILE cc_start: 0.1821 (OUTLIER) cc_final: 0.1386 (mp) REVERT: A 189 MET cc_start: 0.5387 (mpm) cc_final: 0.4305 (mtt) REVERT: A 229 LEU cc_start: 0.4395 (OUTLIER) cc_final: 0.4157 (mm) REVERT: A 519 MET cc_start: -0.0410 (mtt) cc_final: -0.1374 (ttm) REVERT: A 633 TYR cc_start: 0.7901 (t80) cc_final: 0.7666 (t80) REVERT: A 643 LEU cc_start: 0.7263 (OUTLIER) cc_final: 0.7033 (tt) REVERT: A 677 MET cc_start: 0.5640 (mmm) cc_final: 0.4818 (mtt) REVERT: A 684 ILE cc_start: 0.5491 (OUTLIER) cc_final: 0.5243 (pt) REVERT: A 706 ILE cc_start: 0.6637 (OUTLIER) cc_final: 0.6305 (pp) REVERT: A 848 ARG cc_start: 0.4852 (mtt90) cc_final: 0.3087 (mtm110) REVERT: A 901 GLU cc_start: 0.5975 (pt0) cc_final: 0.5072 (tt0) REVERT: A 1040 TYR cc_start: 0.3578 (t80) cc_final: 0.2976 (t80) REVERT: B 123 SER cc_start: 0.8222 (m) cc_final: 0.8005 (p) REVERT: B 142 TRP cc_start: 0.7606 (m-10) cc_final: 0.7327 (m-10) REVERT: B 238 MET cc_start: 0.6920 (ttt) cc_final: 0.6710 (ttt) REVERT: B 321 ASP cc_start: 0.6940 (t0) cc_final: 0.6664 (t70) REVERT: B 370 ARG cc_start: 0.8154 (ptm-80) cc_final: 0.7766 (ttt180) REVERT: B 383 CYS cc_start: 0.6854 (m) cc_final: 0.6378 (t) outliers start: 35 outliers final: 16 residues processed: 168 average time/residue: 0.2670 time to fit residues: 65.7883 Evaluate side-chains 146 residues out of total 1300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 125 time to evaluate : 1.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 684 ILE Chi-restraints excluded: chain A residue 706 ILE Chi-restraints excluded: chain A residue 999 ILE Chi-restraints excluded: chain A residue 1013 LEU Chi-restraints excluded: chain A residue 1077 LEU Chi-restraints excluded: chain A residue 1092 LEU Chi-restraints excluded: chain A residue 1116 LEU Chi-restraints excluded: chain A residue 1227 LEU Chi-restraints excluded: chain A residue 1274 MET Chi-restraints excluded: chain A residue 1305 LEU Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 101 ASP Chi-restraints excluded: chain B residue 111 MET Chi-restraints excluded: chain B residue 348 TRP Chi-restraints excluded: chain B residue 391 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 133 optimal weight: 6.9990 chunk 101 optimal weight: 0.4980 chunk 70 optimal weight: 1.9990 chunk 15 optimal weight: 0.6980 chunk 64 optimal weight: 5.9990 chunk 91 optimal weight: 2.9990 chunk 136 optimal weight: 0.7980 chunk 144 optimal weight: 3.9990 chunk 71 optimal weight: 5.9990 chunk 128 optimal weight: 0.8980 chunk 38 optimal weight: 0.4980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 ASN A 674 GLN A 763 GLN ** A1330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 141 GLN B 341 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6804 moved from start: 0.2386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12353 Z= 0.204 Angle : 0.629 8.885 16752 Z= 0.323 Chirality : 0.046 0.338 1873 Planarity : 0.004 0.056 2123 Dihedral : 7.582 55.556 1780 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 12.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.93 % Favored : 93.07 % Rotamer: Outliers : 3.00 % Allowed : 12.38 % Favored : 84.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.77 (0.20), residues: 1487 helix: -2.84 (0.19), residues: 506 sheet: -2.47 (0.42), residues: 133 loop : -2.32 (0.20), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1415 HIS 0.003 0.001 HIS A1293 PHE 0.025 0.002 PHE A 565 TYR 0.028 0.001 TYR A1256 ARG 0.007 0.000 ARG A 447 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2974 Ramachandran restraints generated. 1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2974 Ramachandran restraints generated. 1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 130 time to evaluate : 1.403 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 188 ILE cc_start: 0.1800 (OUTLIER) cc_final: 0.1369 (mp) REVERT: A 189 MET cc_start: 0.5546 (OUTLIER) cc_final: 0.4445 (mtm) REVERT: A 224 LEU cc_start: 0.4388 (OUTLIER) cc_final: 0.3152 (pp) REVERT: A 519 MET cc_start: -0.0076 (mtt) cc_final: -0.1114 (ttm) REVERT: A 633 TYR cc_start: 0.7991 (t80) cc_final: 0.7775 (t80) REVERT: A 643 LEU cc_start: 0.7315 (OUTLIER) cc_final: 0.7042 (tt) REVERT: A 677 MET cc_start: 0.5668 (mmm) cc_final: 0.4822 (mtt) REVERT: A 684 ILE cc_start: 0.5499 (OUTLIER) cc_final: 0.5232 (pt) REVERT: A 706 ILE cc_start: 0.6674 (OUTLIER) cc_final: 0.6384 (pp) REVERT: A 848 ARG cc_start: 0.4959 (mtt90) cc_final: 0.3156 (mtm110) REVERT: A 1040 TYR cc_start: 0.3891 (t80) cc_final: 0.2804 (t80) REVERT: A 1072 ILE cc_start: 0.7894 (tp) cc_final: 0.7647 (tp) REVERT: A 1108 SER cc_start: 0.8015 (p) cc_final: 0.7595 (t) REVERT: A 1137 MET cc_start: 0.7555 (ttp) cc_final: 0.7350 (ttp) REVERT: B 123 SER cc_start: 0.8272 (m) cc_final: 0.8068 (p) REVERT: B 238 MET cc_start: 0.7185 (ttt) cc_final: 0.6979 (ttt) REVERT: B 321 ASP cc_start: 0.6901 (t0) cc_final: 0.6572 (t70) REVERT: B 370 ARG cc_start: 0.8241 (ptm-80) cc_final: 0.7849 (ttt180) REVERT: B 383 CYS cc_start: 0.6878 (m) cc_final: 0.6372 (t) outliers start: 39 outliers final: 23 residues processed: 157 average time/residue: 0.2653 time to fit residues: 61.7244 Evaluate side-chains 149 residues out of total 1300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 120 time to evaluate : 1.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 189 MET Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 684 ILE Chi-restraints excluded: chain A residue 706 ILE Chi-restraints excluded: chain A residue 999 ILE Chi-restraints excluded: chain A residue 1013 LEU Chi-restraints excluded: chain A residue 1092 LEU Chi-restraints excluded: chain A residue 1100 VAL Chi-restraints excluded: chain A residue 1219 TYR Chi-restraints excluded: chain A residue 1274 MET Chi-restraints excluded: chain A residue 1282 ILE Chi-restraints excluded: chain A residue 1381 VAL Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 101 ASP Chi-restraints excluded: chain B residue 111 MET Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 198 ILE Chi-restraints excluded: chain B residue 226 LYS Chi-restraints excluded: chain B residue 348 TRP Chi-restraints excluded: chain B residue 359 ILE Chi-restraints excluded: chain B residue 391 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 119 optimal weight: 5.9990 chunk 81 optimal weight: 0.0970 chunk 2 optimal weight: 0.9990 chunk 107 optimal weight: 0.8980 chunk 59 optimal weight: 0.9980 chunk 122 optimal weight: 2.9990 chunk 99 optimal weight: 0.4980 chunk 0 optimal weight: 10.0000 chunk 73 optimal weight: 0.9990 chunk 129 optimal weight: 0.9990 chunk 36 optimal weight: 0.0470 overall best weight: 0.5076 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 674 GLN ** A1330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6787 moved from start: 0.2593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12353 Z= 0.174 Angle : 0.602 9.023 16752 Z= 0.309 Chirality : 0.044 0.331 1873 Planarity : 0.004 0.055 2123 Dihedral : 7.000 54.947 1780 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 12.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.93 % Favored : 93.07 % Rotamer: Outliers : 2.69 % Allowed : 12.85 % Favored : 84.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.54 (0.20), residues: 1487 helix: -2.57 (0.20), residues: 506 sheet: -2.46 (0.40), residues: 144 loop : -2.19 (0.21), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1415 HIS 0.003 0.001 HIS A1293 PHE 0.021 0.001 PHE A1055 TYR 0.031 0.001 TYR A1256 ARG 0.003 0.000 ARG A 447 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2974 Ramachandran restraints generated. 1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2974 Ramachandran restraints generated. 1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 130 time to evaluate : 1.309 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 188 ILE cc_start: 0.1847 (OUTLIER) cc_final: 0.1403 (mp) REVERT: A 189 MET cc_start: 0.5591 (OUTLIER) cc_final: 0.4493 (mtm) REVERT: A 224 LEU cc_start: 0.4383 (OUTLIER) cc_final: 0.3146 (pp) REVERT: A 229 LEU cc_start: 0.4185 (OUTLIER) cc_final: 0.3917 (mm) REVERT: A 519 MET cc_start: -0.0131 (mtt) cc_final: -0.1146 (ttm) REVERT: A 633 TYR cc_start: 0.7932 (t80) cc_final: 0.7718 (t80) REVERT: A 643 LEU cc_start: 0.7278 (OUTLIER) cc_final: 0.7054 (tt) REVERT: A 677 MET cc_start: 0.5624 (mmm) cc_final: 0.4841 (mtt) REVERT: A 684 ILE cc_start: 0.5486 (OUTLIER) cc_final: 0.5243 (pt) REVERT: A 706 ILE cc_start: 0.6581 (OUTLIER) cc_final: 0.6256 (pp) REVERT: A 848 ARG cc_start: 0.4794 (mtt90) cc_final: 0.3114 (mtm110) REVERT: A 1040 TYR cc_start: 0.4017 (t80) cc_final: 0.3072 (t80) REVERT: A 1108 SER cc_start: 0.7966 (p) cc_final: 0.7554 (t) REVERT: B 321 ASP cc_start: 0.6787 (t0) cc_final: 0.6452 (t70) REVERT: B 343 ASP cc_start: 0.7205 (m-30) cc_final: 0.6588 (p0) outliers start: 35 outliers final: 24 residues processed: 152 average time/residue: 0.2303 time to fit residues: 52.4150 Evaluate side-chains 148 residues out of total 1300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 117 time to evaluate : 1.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 189 MET Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 684 ILE Chi-restraints excluded: chain A residue 706 ILE Chi-restraints excluded: chain A residue 710 THR Chi-restraints excluded: chain A residue 999 ILE Chi-restraints excluded: chain A residue 1013 LEU Chi-restraints excluded: chain A residue 1077 LEU Chi-restraints excluded: chain A residue 1100 VAL Chi-restraints excluded: chain A residue 1219 TYR Chi-restraints excluded: chain A residue 1258 VAL Chi-restraints excluded: chain A residue 1274 MET Chi-restraints excluded: chain A residue 1282 ILE Chi-restraints excluded: chain A residue 1305 LEU Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 101 ASP Chi-restraints excluded: chain B residue 226 LYS Chi-restraints excluded: chain B residue 348 TRP Chi-restraints excluded: chain B residue 359 ILE Chi-restraints excluded: chain B residue 391 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 48 optimal weight: 0.0770 chunk 129 optimal weight: 0.6980 chunk 28 optimal weight: 2.9990 chunk 84 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 144 optimal weight: 3.9990 chunk 119 optimal weight: 5.9990 chunk 66 optimal weight: 3.9990 chunk 11 optimal weight: 0.6980 chunk 47 optimal weight: 4.9990 chunk 75 optimal weight: 0.6980 overall best weight: 1.0340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1330 HIS B 96 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6870 moved from start: 0.2803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 12353 Z= 0.263 Angle : 0.649 8.845 16752 Z= 0.334 Chirality : 0.046 0.356 1873 Planarity : 0.004 0.056 2123 Dihedral : 7.023 53.855 1780 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 13.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.74 % Favored : 91.26 % Rotamer: Outliers : 3.62 % Allowed : 13.08 % Favored : 83.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.49 (0.20), residues: 1487 helix: -2.49 (0.20), residues: 510 sheet: -2.33 (0.41), residues: 134 loop : -2.21 (0.21), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A1415 HIS 0.005 0.001 HIS A1293 PHE 0.017 0.002 PHE A 565 TYR 0.031 0.002 TYR A1256 ARG 0.003 0.000 ARG A 447 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2974 Ramachandran restraints generated. 1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2974 Ramachandran restraints generated. 1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 132 time to evaluate : 1.213 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 188 ILE cc_start: 0.2300 (OUTLIER) cc_final: 0.1795 (mp) REVERT: A 189 MET cc_start: 0.5543 (OUTLIER) cc_final: 0.4469 (mtp) REVERT: A 196 ILE cc_start: 0.1076 (OUTLIER) cc_final: 0.0295 (tp) REVERT: A 224 LEU cc_start: 0.4442 (OUTLIER) cc_final: 0.3070 (pp) REVERT: A 229 LEU cc_start: 0.3947 (OUTLIER) cc_final: 0.3633 (mm) REVERT: A 519 MET cc_start: -0.0051 (mtt) cc_final: -0.1096 (ttm) REVERT: A 643 LEU cc_start: 0.7415 (OUTLIER) cc_final: 0.7130 (tt) REVERT: A 684 ILE cc_start: 0.5431 (OUTLIER) cc_final: 0.5159 (pt) REVERT: A 706 ILE cc_start: 0.6506 (OUTLIER) cc_final: 0.6196 (pp) REVERT: A 848 ARG cc_start: 0.4871 (mtt90) cc_final: 0.3146 (mtm110) REVERT: A 965 ASP cc_start: 0.7346 (t0) cc_final: 0.6794 (m-30) REVERT: A 1040 TYR cc_start: 0.4169 (t80) cc_final: 0.2986 (t80) REVERT: A 1072 ILE cc_start: 0.7851 (tp) cc_final: 0.7646 (tp) REVERT: A 1108 SER cc_start: 0.7937 (p) cc_final: 0.7538 (t) REVERT: A 1270 PHE cc_start: 0.8374 (OUTLIER) cc_final: 0.7836 (t80) REVERT: B 238 MET cc_start: 0.7206 (ttt) cc_final: 0.6829 (ttt) REVERT: B 321 ASP cc_start: 0.6865 (t0) cc_final: 0.6517 (t70) REVERT: B 343 ASP cc_start: 0.7162 (m-30) cc_final: 0.6524 (p0) outliers start: 47 outliers final: 29 residues processed: 163 average time/residue: 0.2241 time to fit residues: 54.9979 Evaluate side-chains 158 residues out of total 1300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 120 time to evaluate : 1.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 189 MET Chi-restraints excluded: chain A residue 196 ILE Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 684 ILE Chi-restraints excluded: chain A residue 706 ILE Chi-restraints excluded: chain A residue 710 THR Chi-restraints excluded: chain A residue 901 GLU Chi-restraints excluded: chain A residue 999 ILE Chi-restraints excluded: chain A residue 1013 LEU Chi-restraints excluded: chain A residue 1100 VAL Chi-restraints excluded: chain A residue 1219 TYR Chi-restraints excluded: chain A residue 1258 VAL Chi-restraints excluded: chain A residue 1266 ASN Chi-restraints excluded: chain A residue 1270 PHE Chi-restraints excluded: chain A residue 1274 MET Chi-restraints excluded: chain A residue 1282 ILE Chi-restraints excluded: chain A residue 1330 HIS Chi-restraints excluded: chain A residue 1381 VAL Chi-restraints excluded: chain A residue 1407 ASP Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 101 ASP Chi-restraints excluded: chain B residue 111 MET Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 198 ILE Chi-restraints excluded: chain B residue 348 TRP Chi-restraints excluded: chain B residue 359 ILE Chi-restraints excluded: chain B residue 391 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 138 optimal weight: 0.0030 chunk 16 optimal weight: 0.7980 chunk 82 optimal weight: 0.9980 chunk 105 optimal weight: 2.9990 chunk 81 optimal weight: 0.9990 chunk 121 optimal weight: 0.6980 chunk 80 optimal weight: 2.9990 chunk 143 optimal weight: 0.0020 chunk 89 optimal weight: 1.9990 chunk 87 optimal weight: 0.4980 chunk 66 optimal weight: 3.9990 overall best weight: 0.3998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1330 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6803 moved from start: 0.2937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12353 Z= 0.169 Angle : 0.608 9.477 16752 Z= 0.311 Chirality : 0.044 0.328 1873 Planarity : 0.004 0.057 2123 Dihedral : 6.678 54.635 1780 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 12.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.59 % Favored : 93.41 % Rotamer: Outliers : 3.77 % Allowed : 13.62 % Favored : 82.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.26 (0.21), residues: 1487 helix: -2.26 (0.21), residues: 511 sheet: -2.20 (0.41), residues: 134 loop : -2.11 (0.21), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 652 HIS 0.017 0.001 HIS A1330 PHE 0.013 0.001 PHE B 128 TYR 0.028 0.001 TYR A1256 ARG 0.004 0.000 ARG A 447 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2974 Ramachandran restraints generated. 1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2974 Ramachandran restraints generated. 1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 127 time to evaluate : 1.438 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 188 ILE cc_start: 0.2444 (OUTLIER) cc_final: 0.1985 (mp) REVERT: A 189 MET cc_start: 0.5495 (OUTLIER) cc_final: 0.4403 (mtm) REVERT: A 224 LEU cc_start: 0.4368 (OUTLIER) cc_final: 0.3164 (pp) REVERT: A 229 LEU cc_start: 0.4012 (OUTLIER) cc_final: 0.3700 (mm) REVERT: A 519 MET cc_start: -0.0124 (mtt) cc_final: -0.1136 (ttm) REVERT: A 523 MET cc_start: 0.2991 (tpt) cc_final: 0.2135 (mpp) REVERT: A 684 ILE cc_start: 0.5428 (OUTLIER) cc_final: 0.5155 (pt) REVERT: A 706 ILE cc_start: 0.6404 (OUTLIER) cc_final: 0.6100 (pp) REVERT: A 848 ARG cc_start: 0.4856 (mtt90) cc_final: 0.3135 (mtm110) REVERT: A 1040 TYR cc_start: 0.4088 (t80) cc_final: 0.2993 (t80) REVERT: A 1108 SER cc_start: 0.7964 (p) cc_final: 0.7563 (t) REVERT: A 1270 PHE cc_start: 0.8324 (OUTLIER) cc_final: 0.7791 (t80) REVERT: B 238 MET cc_start: 0.6930 (ttt) cc_final: 0.6608 (ttt) REVERT: B 321 ASP cc_start: 0.6855 (t0) cc_final: 0.6588 (t70) REVERT: B 343 ASP cc_start: 0.7051 (m-30) cc_final: 0.6478 (p0) outliers start: 49 outliers final: 32 residues processed: 157 average time/residue: 0.2319 time to fit residues: 54.6402 Evaluate side-chains 156 residues out of total 1300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 117 time to evaluate : 1.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 189 MET Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 684 ILE Chi-restraints excluded: chain A residue 706 ILE Chi-restraints excluded: chain A residue 710 THR Chi-restraints excluded: chain A residue 901 GLU Chi-restraints excluded: chain A residue 937 LEU Chi-restraints excluded: chain A residue 999 ILE Chi-restraints excluded: chain A residue 1013 LEU Chi-restraints excluded: chain A residue 1077 LEU Chi-restraints excluded: chain A residue 1100 VAL Chi-restraints excluded: chain A residue 1187 MET Chi-restraints excluded: chain A residue 1219 TYR Chi-restraints excluded: chain A residue 1266 ASN Chi-restraints excluded: chain A residue 1270 PHE Chi-restraints excluded: chain A residue 1274 MET Chi-restraints excluded: chain A residue 1282 ILE Chi-restraints excluded: chain A residue 1305 LEU Chi-restraints excluded: chain A residue 1330 HIS Chi-restraints excluded: chain A residue 1357 SER Chi-restraints excluded: chain A residue 1381 VAL Chi-restraints excluded: chain A residue 1407 ASP Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 101 ASP Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 185 ASN Chi-restraints excluded: chain B residue 198 ILE Chi-restraints excluded: chain B residue 348 TRP Chi-restraints excluded: chain B residue 359 ILE Chi-restraints excluded: chain B residue 391 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 88 optimal weight: 1.9990 chunk 57 optimal weight: 0.2980 chunk 85 optimal weight: 0.0010 chunk 43 optimal weight: 2.9990 chunk 28 optimal weight: 0.0370 chunk 27 optimal weight: 2.9990 chunk 91 optimal weight: 0.5980 chunk 97 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 13 optimal weight: 4.9990 chunk 112 optimal weight: 0.0970 overall best weight: 0.2062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 482 GLN A 674 GLN A1330 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6760 moved from start: 0.3100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 12353 Z= 0.150 Angle : 0.605 14.170 16752 Z= 0.304 Chirality : 0.043 0.308 1873 Planarity : 0.003 0.056 2123 Dihedral : 6.381 54.793 1780 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 11.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.72 % Favored : 93.28 % Rotamer: Outliers : 3.46 % Allowed : 14.54 % Favored : 82.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.08 (0.21), residues: 1487 helix: -2.01 (0.22), residues: 502 sheet: -2.09 (0.40), residues: 152 loop : -2.07 (0.22), residues: 833 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 348 HIS 0.017 0.001 HIS A1330 PHE 0.023 0.001 PHE A1055 TYR 0.028 0.001 TYR A1256 ARG 0.004 0.000 ARG B 62 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2974 Ramachandran restraints generated. 1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2974 Ramachandran restraints generated. 1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 134 time to evaluate : 1.315 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 188 ILE cc_start: 0.2496 (OUTLIER) cc_final: 0.2032 (mp) REVERT: A 189 MET cc_start: 0.5369 (OUTLIER) cc_final: 0.4455 (mtm) REVERT: A 224 LEU cc_start: 0.4244 (OUTLIER) cc_final: 0.3183 (pp) REVERT: A 229 LEU cc_start: 0.3981 (OUTLIER) cc_final: 0.3710 (mm) REVERT: A 519 MET cc_start: -0.0199 (mtt) cc_final: -0.1123 (ttm) REVERT: A 523 MET cc_start: 0.2937 (tpt) cc_final: 0.2106 (mpp) REVERT: A 684 ILE cc_start: 0.5411 (OUTLIER) cc_final: 0.5134 (pt) REVERT: A 706 ILE cc_start: 0.6245 (OUTLIER) cc_final: 0.5935 (pp) REVERT: A 848 ARG cc_start: 0.4894 (mtt90) cc_final: 0.3163 (mtm110) REVERT: A 1040 TYR cc_start: 0.4045 (t80) cc_final: 0.3180 (t80) REVERT: A 1108 SER cc_start: 0.7975 (p) cc_final: 0.7577 (t) REVERT: A 1186 GLU cc_start: 0.7766 (tp30) cc_final: 0.7543 (tp30) REVERT: A 1270 PHE cc_start: 0.8320 (OUTLIER) cc_final: 0.7852 (t80) REVERT: B 238 MET cc_start: 0.6742 (ttt) cc_final: 0.6445 (ttt) REVERT: B 321 ASP cc_start: 0.6802 (t0) cc_final: 0.6538 (t70) REVERT: B 343 ASP cc_start: 0.7004 (m-30) cc_final: 0.6430 (p0) REVERT: B 354 ASN cc_start: 0.7675 (t0) cc_final: 0.7202 (t0) outliers start: 45 outliers final: 32 residues processed: 160 average time/residue: 0.2338 time to fit residues: 56.0758 Evaluate side-chains 158 residues out of total 1300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 119 time to evaluate : 1.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 189 MET Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 684 ILE Chi-restraints excluded: chain A residue 706 ILE Chi-restraints excluded: chain A residue 710 THR Chi-restraints excluded: chain A residue 723 ARG Chi-restraints excluded: chain A residue 901 GLU Chi-restraints excluded: chain A residue 999 ILE Chi-restraints excluded: chain A residue 1013 LEU Chi-restraints excluded: chain A residue 1077 LEU Chi-restraints excluded: chain A residue 1100 VAL Chi-restraints excluded: chain A residue 1187 MET Chi-restraints excluded: chain A residue 1219 TYR Chi-restraints excluded: chain A residue 1266 ASN Chi-restraints excluded: chain A residue 1270 PHE Chi-restraints excluded: chain A residue 1274 MET Chi-restraints excluded: chain A residue 1282 ILE Chi-restraints excluded: chain A residue 1305 LEU Chi-restraints excluded: chain A residue 1330 HIS Chi-restraints excluded: chain A residue 1357 SER Chi-restraints excluded: chain A residue 1381 VAL Chi-restraints excluded: chain A residue 1407 ASP Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 101 ASP Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 185 ASN Chi-restraints excluded: chain B residue 198 ILE Chi-restraints excluded: chain B residue 348 TRP Chi-restraints excluded: chain B residue 359 ILE Chi-restraints excluded: chain B residue 391 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 130 optimal weight: 2.9990 chunk 137 optimal weight: 3.9990 chunk 125 optimal weight: 2.9990 chunk 133 optimal weight: 0.7980 chunk 80 optimal weight: 0.8980 chunk 58 optimal weight: 9.9990 chunk 105 optimal weight: 2.9990 chunk 41 optimal weight: 8.9990 chunk 120 optimal weight: 3.9990 chunk 126 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 764 GLN A1330 HIS B 96 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6957 moved from start: 0.3160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 12353 Z= 0.397 Angle : 0.763 13.382 16752 Z= 0.389 Chirality : 0.051 0.402 1873 Planarity : 0.005 0.061 2123 Dihedral : 7.256 54.825 1780 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 16.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.22 % Favored : 89.78 % Rotamer: Outliers : 3.77 % Allowed : 14.69 % Favored : 81.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.36 (0.20), residues: 1487 helix: -2.34 (0.21), residues: 503 sheet: -2.16 (0.43), residues: 128 loop : -2.21 (0.21), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A1415 HIS 0.029 0.002 HIS A1330 PHE 0.022 0.003 PHE A1365 TYR 0.027 0.002 TYR A1040 ARG 0.006 0.001 ARG A1153 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2974 Ramachandran restraints generated. 1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2974 Ramachandran restraints generated. 1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 126 time to evaluate : 1.301 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 188 ILE cc_start: 0.2479 (OUTLIER) cc_final: 0.1980 (mp) REVERT: A 189 MET cc_start: 0.5592 (OUTLIER) cc_final: 0.4506 (mtp) REVERT: A 196 ILE cc_start: 0.0662 (OUTLIER) cc_final: -0.0091 (tp) REVERT: A 224 LEU cc_start: 0.4601 (OUTLIER) cc_final: 0.3061 (pp) REVERT: A 229 LEU cc_start: 0.3927 (OUTLIER) cc_final: 0.3665 (mm) REVERT: A 258 ASP cc_start: 0.6716 (p0) cc_final: 0.6486 (p0) REVERT: A 519 MET cc_start: -0.0004 (mtt) cc_final: -0.1138 (ttm) REVERT: A 684 ILE cc_start: 0.5428 (OUTLIER) cc_final: 0.5190 (pt) REVERT: A 706 ILE cc_start: 0.6576 (OUTLIER) cc_final: 0.6224 (pp) REVERT: A 848 ARG cc_start: 0.5066 (mtt90) cc_final: 0.3211 (mtm110) REVERT: A 1037 LEU cc_start: 0.6535 (OUTLIER) cc_final: 0.6225 (pt) REVERT: A 1040 TYR cc_start: 0.4337 (t80) cc_final: 0.2839 (t80) REVERT: A 1108 SER cc_start: 0.7885 (p) cc_final: 0.7524 (t) REVERT: A 1270 PHE cc_start: 0.8492 (OUTLIER) cc_final: 0.7975 (t80) REVERT: B 238 MET cc_start: 0.7400 (ttt) cc_final: 0.7043 (ttt) REVERT: B 343 ASP cc_start: 0.7076 (m-30) cc_final: 0.6643 (p0) outliers start: 49 outliers final: 34 residues processed: 158 average time/residue: 0.2445 time to fit residues: 57.2598 Evaluate side-chains 162 residues out of total 1300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 119 time to evaluate : 1.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 189 MET Chi-restraints excluded: chain A residue 196 ILE Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 684 ILE Chi-restraints excluded: chain A residue 706 ILE Chi-restraints excluded: chain A residue 710 THR Chi-restraints excluded: chain A residue 723 ARG Chi-restraints excluded: chain A residue 901 GLU Chi-restraints excluded: chain A residue 937 LEU Chi-restraints excluded: chain A residue 999 ILE Chi-restraints excluded: chain A residue 1013 LEU Chi-restraints excluded: chain A residue 1037 LEU Chi-restraints excluded: chain A residue 1100 VAL Chi-restraints excluded: chain A residue 1219 TYR Chi-restraints excluded: chain A residue 1243 ASP Chi-restraints excluded: chain A residue 1266 ASN Chi-restraints excluded: chain A residue 1270 PHE Chi-restraints excluded: chain A residue 1274 MET Chi-restraints excluded: chain A residue 1282 ILE Chi-restraints excluded: chain A residue 1299 THR Chi-restraints excluded: chain A residue 1330 HIS Chi-restraints excluded: chain A residue 1381 VAL Chi-restraints excluded: chain A residue 1407 ASP Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 101 ASP Chi-restraints excluded: chain B residue 111 MET Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 185 ASN Chi-restraints excluded: chain B residue 198 ILE Chi-restraints excluded: chain B residue 264 ILE Chi-restraints excluded: chain B residue 348 TRP Chi-restraints excluded: chain B residue 359 ILE Chi-restraints excluded: chain B residue 391 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 141 optimal weight: 0.0980 chunk 86 optimal weight: 0.6980 chunk 67 optimal weight: 0.5980 chunk 98 optimal weight: 0.5980 chunk 148 optimal weight: 6.9990 chunk 136 optimal weight: 0.0970 chunk 118 optimal weight: 0.7980 chunk 12 optimal weight: 6.9990 chunk 91 optimal weight: 0.6980 chunk 72 optimal weight: 3.9990 chunk 93 optimal weight: 0.9980 overall best weight: 0.4178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1330 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6830 moved from start: 0.3240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12353 Z= 0.176 Angle : 0.648 13.702 16752 Z= 0.326 Chirality : 0.044 0.330 1873 Planarity : 0.004 0.057 2123 Dihedral : 6.695 54.359 1780 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 13.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.86 % Favored : 93.14 % Rotamer: Outliers : 3.08 % Allowed : 15.54 % Favored : 81.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.04 (0.21), residues: 1487 helix: -2.03 (0.22), residues: 503 sheet: -1.73 (0.44), residues: 140 loop : -2.08 (0.21), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 142 HIS 0.020 0.001 HIS A1330 PHE 0.012 0.001 PHE A 467 TYR 0.015 0.001 TYR A1040 ARG 0.003 0.000 ARG B 62 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2974 Ramachandran restraints generated. 1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2974 Ramachandran restraints generated. 1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 123 time to evaluate : 1.477 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 188 ILE cc_start: 0.2486 (OUTLIER) cc_final: 0.1979 (mp) REVERT: A 189 MET cc_start: 0.5299 (OUTLIER) cc_final: 0.4247 (mtt) REVERT: A 224 LEU cc_start: 0.4317 (OUTLIER) cc_final: 0.3145 (pp) REVERT: A 229 LEU cc_start: 0.4428 (OUTLIER) cc_final: 0.4098 (mm) REVERT: A 258 ASP cc_start: 0.6633 (p0) cc_final: 0.6387 (p0) REVERT: A 519 MET cc_start: -0.0313 (mtt) cc_final: -0.1265 (ttm) REVERT: A 523 MET cc_start: 0.3180 (tpt) cc_final: 0.2234 (mpp) REVERT: A 676 VAL cc_start: 0.6978 (m) cc_final: 0.6589 (t) REVERT: A 684 ILE cc_start: 0.5397 (OUTLIER) cc_final: 0.5163 (pt) REVERT: A 706 ILE cc_start: 0.6332 (OUTLIER) cc_final: 0.5998 (pp) REVERT: A 848 ARG cc_start: 0.4975 (mtt90) cc_final: 0.3189 (mtm110) REVERT: A 999 ILE cc_start: 0.7996 (OUTLIER) cc_final: 0.7650 (tt) REVERT: A 1037 LEU cc_start: 0.6444 (OUTLIER) cc_final: 0.6122 (pt) REVERT: A 1040 TYR cc_start: 0.4238 (t80) cc_final: 0.2993 (t80) REVERT: A 1108 SER cc_start: 0.7954 (p) cc_final: 0.7535 (t) REVERT: A 1270 PHE cc_start: 0.8383 (OUTLIER) cc_final: 0.7888 (t80) REVERT: B 238 MET cc_start: 0.7007 (ttt) cc_final: 0.6680 (ttt) REVERT: B 321 ASP cc_start: 0.6973 (t0) cc_final: 0.6739 (t70) REVERT: B 343 ASP cc_start: 0.6967 (m-30) cc_final: 0.6538 (p0) REVERT: B 359 ILE cc_start: 0.8802 (OUTLIER) cc_final: 0.8598 (pt) outliers start: 40 outliers final: 25 residues processed: 150 average time/residue: 0.2413 time to fit residues: 53.7449 Evaluate side-chains 154 residues out of total 1300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 119 time to evaluate : 1.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 189 MET Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 684 ILE Chi-restraints excluded: chain A residue 706 ILE Chi-restraints excluded: chain A residue 723 ARG Chi-restraints excluded: chain A residue 901 GLU Chi-restraints excluded: chain A residue 937 LEU Chi-restraints excluded: chain A residue 999 ILE Chi-restraints excluded: chain A residue 1037 LEU Chi-restraints excluded: chain A residue 1219 TYR Chi-restraints excluded: chain A residue 1243 ASP Chi-restraints excluded: chain A residue 1266 ASN Chi-restraints excluded: chain A residue 1270 PHE Chi-restraints excluded: chain A residue 1274 MET Chi-restraints excluded: chain A residue 1282 ILE Chi-restraints excluded: chain A residue 1299 THR Chi-restraints excluded: chain A residue 1330 HIS Chi-restraints excluded: chain A residue 1381 VAL Chi-restraints excluded: chain A residue 1407 ASP Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 101 ASP Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 185 ASN Chi-restraints excluded: chain B residue 198 ILE Chi-restraints excluded: chain B residue 348 TRP Chi-restraints excluded: chain B residue 359 ILE Chi-restraints excluded: chain B residue 391 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 125 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 108 optimal weight: 0.5980 chunk 17 optimal weight: 4.9990 chunk 32 optimal weight: 0.6980 chunk 118 optimal weight: 0.9990 chunk 49 optimal weight: 7.9990 chunk 121 optimal weight: 0.8980 chunk 14 optimal weight: 5.9990 chunk 21 optimal weight: 3.9990 chunk 103 optimal weight: 0.6980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 675 ASN A1330 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.193586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.169716 restraints weight = 14473.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 75)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.160183 restraints weight = 30144.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.157290 restraints weight = 37464.156| |-----------------------------------------------------------------------------| r_work (final): 0.3878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6895 moved from start: 0.3305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12353 Z= 0.224 Angle : 0.662 14.134 16752 Z= 0.332 Chirality : 0.045 0.341 1873 Planarity : 0.004 0.055 2123 Dihedral : 6.692 54.116 1780 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 13.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.27 % Favored : 91.73 % Rotamer: Outliers : 3.08 % Allowed : 16.08 % Favored : 80.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.06 (0.21), residues: 1487 helix: -2.00 (0.22), residues: 506 sheet: -1.72 (0.42), residues: 150 loop : -2.13 (0.21), residues: 831 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 142 HIS 0.016 0.002 HIS A 778 PHE 0.024 0.002 PHE A1055 TYR 0.017 0.001 TYR A1040 ARG 0.010 0.000 ARG A 447 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2469.88 seconds wall clock time: 46 minutes 9.39 seconds (2769.39 seconds total)