Starting phenix.real_space_refine on Sat Mar 16 06:49:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jb6_6408/03_2024/3jb6_6408_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jb6_6408/03_2024/3jb6_6408.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jb6_6408/03_2024/3jb6_6408.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jb6_6408/03_2024/3jb6_6408.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jb6_6408/03_2024/3jb6_6408_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jb6_6408/03_2024/3jb6_6408_updated.pdb" } resolution = 3.3 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 ------------------------------------------------------------------------------- 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= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 6 5.49 5 S 54 5.16 5 C 8821 2.51 5 N 2379 2.21 5 O 2644 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 147": "NH1" <-> "NH2" Residue "A TYR 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 317": "NH1" <-> "NH2" Residue "A TYR 385": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 460": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 578": "NH1" <-> "NH2" Residue "A ARG 867": "NH1" <-> "NH2" Residue "A ARG 873": "NH1" <-> "NH2" Residue "A ARG 997": "NH1" <-> "NH2" Residue "A ARG 1146": "NH1" <-> "NH2" Residue "A ARG 1175": "NH1" <-> "NH2" Residue "B TYR 13": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 491": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 548": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 123": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 13904 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 9556 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1196, 9556 Classifications: {'peptide': 1196} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 4, 'PCIS': 1, 'PTRANS': 36, 'TRANS': 1154} Chain breaks: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 3985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 498, 3985 Classifications: {'peptide': 498} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 17, 'TRANS': 478} Chain breaks: 2 Chain: "C" Number of atoms: 170 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 170 Classifications: {'peptide': 21} Link IDs: {'PTRANS': 1, 'TRANS': 19} Chain: "D" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 129 Classifications: {'peptide': 16} Link IDs: {'TRANS': 15} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GTP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GTP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.88, per 1000 atoms: 0.57 Number of scatterers: 13904 At special positions: 0 Unit cell: (104.03, 131.3, 110.09, 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 54 16.00 P 6 15.00 O 2644 8.00 N 2379 7.00 C 8821 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.06 Conformation dependent library (CDL) restraints added in 2.5 seconds 3434 Ramachandran restraints generated. 1717 Oldfield, 0 Emsley, 1717 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3284 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 77 helices and 14 sheets defined 46.3% alpha, 8.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.70 Creating SS restraints... Processing helix chain 'A' and resid 7 through 9 No H-bonds generated for 'chain 'A' and resid 7 through 9' Processing helix chain 'A' and resid 11 through 15 Processing helix chain 'A' and resid 20 through 33 removed outlier: 3.796A pdb=" N LYS A 24 " --> pdb=" O ARG A 20 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ILE A 26 " --> pdb=" O SER A 22 " (cutoff:3.500A) Processing helix chain 'A' and resid 37 through 44 removed outlier: 3.552A pdb=" N HIS A 41 " --> pdb=" O ARG A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 76 No H-bonds generated for 'chain 'A' and resid 73 through 76' Processing helix chain 'A' and resid 83 through 86 removed outlier: 3.541A pdb=" N TYR A 86 " --> pdb=" O PRO A 83 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 83 through 86' Processing helix chain 'A' and resid 121 through 134 Processing helix chain 'A' and resid 145 through 160 removed outlier: 3.661A pdb=" N VAL A 152 " --> pdb=" O GLU A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 175 removed outlier: 3.640A pdb=" N TYR A 170 " --> pdb=" O PRO A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 219 removed outlier: 3.933A pdb=" N VAL A 207 " --> pdb=" O PRO A 204 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N TYR A 208 " --> pdb=" O THR A 205 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N CYS A 210 " --> pdb=" O VAL A 207 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N VAL A 213 " --> pdb=" O CYS A 210 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N THR A 215 " --> pdb=" O GLN A 212 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE A 217 " --> pdb=" O GLY A 214 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N MET A 218 " --> pdb=" O THR A 215 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N SER A 219 " --> pdb=" O ALA A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 237 removed outlier: 3.588A pdb=" N ILE A 228 " --> pdb=" O HIS A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 263 removed outlier: 4.890A pdb=" N GLY A 251 " --> pdb=" O LEU A 247 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N ILE A 252 " --> pdb=" O LYS A 248 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ARG A 254 " --> pdb=" O LYS A 250 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N TRP A 256 " --> pdb=" O ILE A 252 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N TYR A 257 " --> pdb=" O GLY A 253 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N GLN A 258 " --> pdb=" O ARG A 254 " (cutoff:3.500A) removed outlier: 4.901A pdb=" N GLU A 259 " --> pdb=" O SER A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 306 removed outlier: 4.363A pdb=" N THR A 295 " --> pdb=" O PHE A 291 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N PHE A 296 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N ILE A 297 " --> pdb=" O SER A 293 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N SER A 298 " --> pdb=" O SER A 294 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLU A 305 " --> pdb=" O ALA A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 320 removed outlier: 3.692A pdb=" N GLN A 320 " --> pdb=" O ASN A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 338 Processing helix chain 'A' and resid 353 through 357 Processing helix chain 'A' and resid 389 through 410 removed outlier: 3.746A pdb=" N TYR A 396 " --> pdb=" O ILE A 392 " (cutoff:3.500A) removed outlier: 5.084A pdb=" N SER A 399 " --> pdb=" O SER A 395 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N PHE A 400 " --> pdb=" O TYR A 396 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N THR A 401 " --> pdb=" O LEU A 397 " (cutoff:3.500A) removed outlier: 5.397A pdb=" N ASP A 402 " --> pdb=" O SER A 398 " (cutoff:3.500A) removed outlier: 5.152A pdb=" N GLU A 403 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LYS A 406 " --> pdb=" O ASP A 402 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ARG A 407 " --> pdb=" O GLU A 403 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLY A 410 " --> pdb=" O LYS A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 423 Processing helix chain 'A' and resid 450 through 459 Processing helix chain 'A' and resid 463 through 470 removed outlier: 3.607A pdb=" N PHE A 467 " --> pdb=" O PRO A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 496 through 499 No H-bonds generated for 'chain 'A' and resid 496 through 499' Processing helix chain 'A' and resid 501 through 512 removed outlier: 4.056A pdb=" N GLN A 509 " --> pdb=" O THR A 505 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N ILE A 510 " --> pdb=" O ILE A 506 " (cutoff:3.500A) removed outlier: 4.917A pdb=" N TYR A 511 " --> pdb=" O GLY A 507 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N GLU A 512 " --> pdb=" O LYS A 508 " (cutoff:3.500A) Processing helix chain 'A' and resid 532 through 535 No H-bonds generated for 'chain 'A' and resid 532 through 535' Processing helix chain 'A' and resid 549 through 554 removed outlier: 4.513A pdb=" N ASP A 552 " --> pdb=" O ALA A 549 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ALA A 553 " --> pdb=" O GLY A 550 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 573 removed outlier: 3.767A pdb=" N ASN A 564 " --> pdb=" O ASP A 561 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N THR A 565 " --> pdb=" O ILE A 562 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N LEU A 568 " --> pdb=" O THR A 565 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ASP A 569 " --> pdb=" O PHE A 566 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ALA A 571 " --> pdb=" O LEU A 568 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N SER A 572 " --> pdb=" O ASP A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 604 through 614 removed outlier: 3.808A pdb=" N ALA A 610 " --> pdb=" O TRP A 606 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA A 613 " --> pdb=" O CYS A 609 " (cutoff:3.500A) Processing helix chain 'A' and resid 642 through 666 removed outlier: 3.595A pdb=" N HIS A 647 " --> pdb=" O ASP A 643 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N HIS A 648 " --> pdb=" O THR A 644 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU A 652 " --> pdb=" O HIS A 648 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLU A 660 " --> pdb=" O VAL A 656 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ALA A 664 " --> pdb=" O GLU A 660 " (cutoff:3.500A) Processing helix chain 'A' and resid 690 through 706 removed outlier: 3.517A pdb=" N TYR A 694 " --> pdb=" O GLU A 690 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU A 704 " --> pdb=" O ASN A 700 " (cutoff:3.500A) Processing helix chain 'A' and resid 736 through 738 No H-bonds generated for 'chain 'A' and resid 736 through 738' Processing helix chain 'A' and resid 753 through 770 removed outlier: 3.654A pdb=" N VAL A 768 " --> pdb=" O ILE A 764 " (cutoff:3.500A) removed outlier: 5.186A pdb=" N PHE A 769 " --> pdb=" O ASP A 765 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N ARG A 770 " --> pdb=" O ASP A 766 " (cutoff:3.500A) Processing helix chain 'A' and resid 774 through 787 removed outlier: 3.974A pdb=" N MET A 779 " --> pdb=" O GLU A 775 " (cutoff:3.500A) Processing helix chain 'A' and resid 801 through 810 removed outlier: 3.602A pdb=" N ASN A 807 " --> pdb=" O SER A 803 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N LYS A 810 " --> pdb=" O ASN A 806 " (cutoff:3.500A) Processing helix chain 'A' and resid 834 through 838 Processing helix chain 'A' and resid 868 through 877 removed outlier: 3.556A pdb=" N ASP A 877 " --> pdb=" O LEU A 874 " (cutoff:3.500A) Processing helix chain 'A' and resid 881 through 887 removed outlier: 3.622A pdb=" N GLN A 886 " --> pdb=" O GLY A 882 " (cutoff:3.500A) Processing helix chain 'A' and resid 894 through 899 Processing helix chain 'A' and resid 902 through 910 Processing helix chain 'A' and resid 919 through 923 Processing helix chain 'A' and resid 933 through 940 removed outlier: 4.092A pdb=" N GLN A 939 " --> pdb=" O THR A 935 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N LEU A 940 " --> pdb=" O SER A 936 " (cutoff:3.500A) Processing helix chain 'A' and resid 943 through 958 Processing helix chain 'A' and resid 969 through 981 removed outlier: 4.100A pdb=" N GLY A 972 " --> pdb=" O TYR A 969 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N GLU A 975 " --> pdb=" O GLY A 972 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N LYS A 976 " --> pdb=" O LEU A 973 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N LYS A 979 " --> pdb=" O LYS A 976 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N SER A 980 " --> pdb=" O ILE A 977 " (cutoff:3.500A) Processing helix chain 'A' and resid 996 through 1005 removed outlier: 3.533A pdb=" N ALA A1004 " --> pdb=" O ASP A1000 " (cutoff:3.500A) Processing helix chain 'A' and resid 1015 through 1020 Processing helix chain 'A' and resid 1035 through 1039 removed outlier: 3.540A pdb=" N LYS A1038 " --> pdb=" O PRO A1035 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N HIS A1039 " --> pdb=" O HIS A1036 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1035 through 1039' Processing helix chain 'A' and resid 1054 through 1061 Processing helix chain 'A' and resid 1067 through 1080 removed outlier: 3.510A pdb=" N LEU A1072 " --> pdb=" O SER A1068 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N ILE A1079 " --> pdb=" O ASP A1075 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ARG A1080 " --> pdb=" O VAL A1076 " (cutoff:3.500A) Processing helix chain 'A' and resid 1091 through 1102 Processing helix chain 'A' and resid 1104 through 1113 removed outlier: 4.520A pdb=" N ASN A1108 " --> pdb=" O THR A1105 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N PHE A1111 " --> pdb=" O ASN A1108 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N THR A1112 " --> pdb=" O ASP A1109 " (cutoff:3.500A) Processing helix chain 'A' and resid 1120 through 1134 removed outlier: 3.918A pdb=" N ALA A1129 " --> pdb=" O LEU A1125 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LEU A1133 " --> pdb=" O ALA A1129 " (cutoff:3.500A) Processing helix chain 'A' and resid 1155 through 1161 removed outlier: 4.524A pdb=" N ARG A1160 " --> pdb=" O SER A1157 " (cutoff:3.500A) Processing helix chain 'A' and resid 1166 through 1171 removed outlier: 4.006A pdb=" N VAL A1170 " --> pdb=" O LYS A1167 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N SER A1171 " --> pdb=" O TYR A1168 " (cutoff:3.500A) Processing helix chain 'A' and resid 1176 through 1192 removed outlier: 3.693A pdb=" N ILE A1180 " --> pdb=" O ALA A1176 " (cutoff:3.500A) removed outlier: 5.600A pdb=" N ALA A1191 " --> pdb=" O LEU A1187 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N ASN A1192 " --> pdb=" O ARG A1188 " (cutoff:3.500A) Processing helix chain 'A' and resid 1204 through 1212 removed outlier: 3.822A pdb=" N GLY A1212 " --> pdb=" O ALA A1208 " (cutoff:3.500A) Processing helix chain 'A' and resid 1215 through 1218 No H-bonds generated for 'chain 'A' and resid 1215 through 1218' Processing helix chain 'B' and resid 10 through 15 removed outlier: 3.819A pdb=" N GLU B 15 " --> pdb=" O LYS B 11 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 62 Processing helix chain 'B' and resid 70 through 78 Processing helix chain 'B' and resid 136 through 148 removed outlier: 3.549A pdb=" N LEU B 144 " --> pdb=" O GLU B 140 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N PHE B 148 " --> pdb=" O LEU B 144 " (cutoff:3.500A) Processing helix chain 'B' and resid 162 through 165 No H-bonds generated for 'chain 'B' and resid 162 through 165' Processing helix chain 'B' and resid 170 through 178 removed outlier: 3.835A pdb=" N LEU B 175 " --> pdb=" O TYR B 171 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N ALA B 177 " --> pdb=" O ASN B 173 " (cutoff:3.500A) removed outlier: 4.916A pdb=" N TYR B 178 " --> pdb=" O GLN B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 196 through 201 removed outlier: 3.574A pdb=" N TYR B 201 " --> pdb=" O TYR B 197 " (cutoff:3.500A) Processing helix chain 'B' and resid 236 through 242 Processing helix chain 'B' and resid 290 through 296 Processing helix chain 'B' and resid 328 through 340 removed outlier: 3.506A pdb=" N GLU B 337 " --> pdb=" O SER B 333 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ALA B 338 " --> pdb=" O LYS B 334 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL B 340 " --> pdb=" O LEU B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 374 removed outlier: 4.148A pdb=" N THR B 365 " --> pdb=" O SER B 361 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLU B 368 " --> pdb=" O SER B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 385 through 393 removed outlier: 3.773A pdb=" N LYS B 392 " --> pdb=" O ARG B 388 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 409 removed outlier: 3.512A pdb=" N SER B 408 " --> pdb=" O ASP B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 429 removed outlier: 3.728A pdb=" N HIS B 429 " --> pdb=" O LEU B 425 " (cutoff:3.500A) Processing helix chain 'B' and resid 434 through 439 removed outlier: 3.821A pdb=" N LEU B 439 " --> pdb=" O ALA B 435 " (cutoff:3.500A) Processing helix chain 'B' and resid 442 through 460 removed outlier: 3.811A pdb=" N GLU B 451 " --> pdb=" O LYS B 447 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLU B 454 " --> pdb=" O ASP B 450 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N VAL B 455 " --> pdb=" O GLU B 451 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ALA B 458 " --> pdb=" O GLU B 454 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N GLN B 459 " --> pdb=" O VAL B 455 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU B 460 " --> pdb=" O LEU B 456 " (cutoff:3.500A) Processing helix chain 'B' and resid 468 through 476 Processing helix chain 'B' and resid 492 through 496 removed outlier: 3.858A pdb=" N ALA B 496 " --> pdb=" O ALA B 493 " (cutoff:3.500A) Processing helix chain 'B' and resid 513 through 519 removed outlier: 3.524A pdb=" N ARG B 518 " --> pdb=" O THR B 514 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ASP B 519 " --> pdb=" O GLN B 515 " (cutoff:3.500A) Processing helix chain 'B' and resid 524 through 537 removed outlier: 3.807A pdb=" N PHE B 529 " --> pdb=" O VAL B 526 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ARG B 531 " --> pdb=" O LEU B 528 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ASP B 532 " --> pdb=" O PHE B 529 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N TYR B 535 " --> pdb=" O ASP B 532 " (cutoff:3.500A) Processing helix chain 'B' and resid 547 through 556 removed outlier: 3.685A pdb=" N ILE B 554 " --> pdb=" O MET B 550 " (cutoff:3.500A) Processing helix chain 'C' and resid 121 through 130 Processing helix chain 'D' and resid 113 through 125 removed outlier: 3.546A pdb=" N GLN D 124 " --> pdb=" O VAL D 120 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 54 through 58 Processing sheet with id= B, first strand: chain 'A' and resid 183 through 186 removed outlier: 3.517A pdb=" N ARG A 191 " --> pdb=" O SER A 186 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 598 through 602 removed outlier: 6.544A pdb=" N LYS A 382 " --> pdb=" O LEU A 372 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 477 through 479 removed outlier: 3.641A pdb=" N VAL A 477 " --> pdb=" O ILE A 489 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ARG A 487 " --> pdb=" O ARG A 479 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 714 through 716 removed outlier: 3.573A pdb=" N SER A 545 " --> pdb=" O GLU A 714 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N THR A 674 " --> pdb=" O ILE A 685 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N GLN A 687 " --> pdb=" O LEU A 672 " (cutoff:3.500A) removed outlier: 5.585A pdb=" N LEU A 672 " --> pdb=" O GLN A 687 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 621 through 624 Processing sheet with id= G, first strand: chain 'A' and resid 719 through 721 Processing sheet with id= H, first strand: chain 'A' and resid 992 through 994 removed outlier: 3.932A pdb=" N LYS A 992 " --> pdb=" O THR A 793 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ASP A 797 " --> pdb=" O VAL A 994 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'A' and resid 1022 through 1026 Processing sheet with id= J, first strand: chain 'A' and resid 266 through 272 removed outlier: 3.702A pdb=" N GLY A 280 " --> pdb=" O VAL A 271 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 157 through 159 removed outlier: 5.902A pdb=" N HIS B 182 " --> pdb=" O ILE B 158 " (cutoff:3.500A) No H-bonds generated for sheet with id= K Processing sheet with id= L, first strand: chain 'B' and resid 204 through 208 Processing sheet with id= M, first strand: chain 'B' and resid 297 through 299 removed outlier: 3.571A pdb=" N LYS B 315 " --> pdb=" O THR B 259 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'B' and resid 543 through 546 removed outlier: 4.321A pdb=" N THR B 543 " --> pdb=" O THR B 504 " (cutoff:3.500A) removed outlier: 8.513A pdb=" N VAL B 505 " --> pdb=" O THR B 348 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N VAL B 350 " --> pdb=" O VAL B 505 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N LEU B 507 " --> pdb=" O VAL B 350 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N TYR B 352 " --> pdb=" O LEU B 507 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ALA B 353 " --> pdb=" O GLY B 489 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLU B 488 " --> pdb=" O LEU B 381 " (cutoff:3.500A) 473 hydrogen bonds defined for protein. 1266 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: 4.40 Time building geometry restraints manager: 5.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.08 - 1.23: 87 1.23 - 1.38: 5536 1.38 - 1.53: 8088 1.53 - 1.68: 397 1.68 - 1.83: 95 Bond restraints: 14203 Sorted by residual: bond pdb=" N PRO D 111 " pdb=" CA PRO D 111 " ideal model delta sigma weight residual 1.466 1.113 0.353 1.50e-02 4.44e+03 5.55e+02 bond pdb=" C ALA C 129 " pdb=" O ALA C 129 " ideal model delta sigma weight residual 1.237 1.077 0.160 1.17e-02 7.31e+03 1.86e+02 bond pdb=" C ASN C 127 " pdb=" O ASN C 127 " ideal model delta sigma weight residual 1.237 1.075 0.161 1.19e-02 7.06e+03 1.84e+02 bond pdb=" C PRO C 132 " pdb=" O PRO C 132 " ideal model delta sigma weight residual 1.233 1.087 0.146 1.13e-02 7.83e+03 1.66e+02 bond pdb=" CA VAL C 120 " pdb=" CB VAL C 120 " ideal model delta sigma weight residual 1.540 1.402 0.138 1.10e-02 8.26e+03 1.58e+02 ... (remaining 14198 not shown) Histogram of bond angle deviations from ideal: 93.01 - 103.07: 131 103.07 - 113.13: 7878 113.13 - 123.19: 10691 123.19 - 133.25: 532 133.25 - 143.31: 18 Bond angle restraints: 19250 Sorted by residual: angle pdb=" N LEU C 130 " pdb=" CA LEU C 130 " pdb=" C LEU C 130 " ideal model delta sigma weight residual 113.17 133.79 -20.62 1.26e+00 6.30e-01 2.68e+02 angle pdb=" N ALA C 129 " pdb=" CA ALA C 129 " pdb=" C ALA C 129 " ideal model delta sigma weight residual 111.28 123.26 -11.98 1.09e+00 8.42e-01 1.21e+02 angle pdb=" CA PHE C 121 " pdb=" C PHE C 121 " pdb=" O PHE C 121 " ideal model delta sigma weight residual 120.42 110.93 9.49 1.06e+00 8.90e-01 8.01e+01 angle pdb=" N MET C 133 " pdb=" CA MET C 133 " pdb=" CB MET C 133 " ideal model delta sigma weight residual 110.42 98.63 11.79 1.66e+00 3.63e-01 5.04e+01 angle pdb=" CG1 VAL C 120 " pdb=" CB VAL C 120 " pdb=" CG2 VAL C 120 " ideal model delta sigma weight residual 110.80 95.32 15.48 2.20e+00 2.07e-01 4.95e+01 ... (remaining 19245 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.92: 8410 27.92 - 55.84: 88 55.84 - 83.75: 10 83.75 - 111.67: 0 111.67 - 139.59: 2 Dihedral angle restraints: 8510 sinusoidal: 3410 harmonic: 5100 Sorted by residual: dihedral pdb=" N LEU C 130 " pdb=" C LEU C 130 " pdb=" CA LEU C 130 " pdb=" CB LEU C 130 " ideal model delta harmonic sigma weight residual 122.80 145.12 -22.32 0 2.50e+00 1.60e-01 7.97e+01 dihedral pdb=" C LEU C 130 " pdb=" N LEU C 130 " pdb=" CA LEU C 130 " pdb=" CB LEU C 130 " ideal model delta harmonic sigma weight residual -122.60 -144.38 21.78 0 2.50e+00 1.60e-01 7.59e+01 dihedral pdb=" CA SER A 926 " pdb=" C SER A 926 " pdb=" N PRO A 927 " pdb=" CA PRO A 927 " ideal model delta harmonic sigma weight residual 180.00 144.58 35.42 0 5.00e+00 4.00e-02 5.02e+01 ... (remaining 8507 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.219: 2136 0.219 - 0.439: 6 0.439 - 0.658: 3 0.658 - 0.878: 1 0.878 - 1.097: 1 Chirality restraints: 2147 Sorted by residual: chirality pdb=" CA LEU C 130 " pdb=" N LEU C 130 " pdb=" C LEU C 130 " pdb=" CB LEU C 130 " both_signs ideal model delta sigma weight residual False 2.51 1.41 1.10 2.00e-01 2.50e+01 3.01e+01 chirality pdb=" CA PRO D 111 " pdb=" N PRO D 111 " pdb=" C PRO D 111 " pdb=" CB PRO D 111 " both_signs ideal model delta sigma weight residual False 2.72 1.94 0.78 2.00e-01 2.50e+01 1.53e+01 chirality pdb=" CA PHE C 121 " pdb=" N PHE C 121 " pdb=" C PHE C 121 " pdb=" CB PHE C 121 " both_signs ideal model delta sigma weight residual False 2.51 1.95 0.56 2.00e-01 2.50e+01 7.89e+00 ... (remaining 2144 not shown) Planarity restraints: 2451 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG C 117 " -0.599 9.50e-02 1.11e+02 2.68e-01 4.40e+01 pdb=" NE ARG C 117 " 0.036 2.00e-02 2.50e+03 pdb=" CZ ARG C 117 " 0.006 2.00e-02 2.50e+03 pdb=" NH1 ARG C 117 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG C 117 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 606 " 0.033 2.00e-02 2.50e+03 2.59e-02 1.68e+01 pdb=" CG TRP A 606 " -0.070 2.00e-02 2.50e+03 pdb=" CD1 TRP A 606 " 0.026 2.00e-02 2.50e+03 pdb=" CD2 TRP A 606 " -0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP A 606 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A 606 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP A 606 " 0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 606 " 0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 606 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP A 606 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 769 " 0.018 2.00e-02 2.50e+03 2.12e-02 7.87e+00 pdb=" CG PHE A 769 " -0.049 2.00e-02 2.50e+03 pdb=" CD1 PHE A 769 " 0.018 2.00e-02 2.50e+03 pdb=" CD2 PHE A 769 " 0.010 2.00e-02 2.50e+03 pdb=" CE1 PHE A 769 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE A 769 " 0.005 2.00e-02 2.50e+03 pdb=" CZ PHE A 769 " 0.001 2.00e-02 2.50e+03 ... (remaining 2448 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 269 2.68 - 3.23: 13834 3.23 - 3.79: 20445 3.79 - 4.34: 30185 4.34 - 4.90: 48796 Nonbonded interactions: 113529 Sorted by model distance: nonbonded pdb=" OH TYR B 352 " pdb=" OD1 ASP B 495 " model vdw 2.123 2.440 nonbonded pdb=" O CYS A 574 " pdb=" ND2 ASN A 603 " model vdw 2.150 2.520 nonbonded pdb=" O ILE A1190 " pdb=" NH2 ARG D 117 " model vdw 2.175 2.520 nonbonded pdb=" NE2 GLN A 617 " pdb=" OE1 GLU A 634 " model vdw 2.205 2.520 nonbonded pdb=" O CYS A 265 " pdb=" OG1 THR A 286 " model vdw 2.224 2.440 ... (remaining 113524 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.180 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: 1.520 Check model and map are aligned: 0.220 Set scattering table: 0.130 Process input model: 39.600 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8796 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 : 0.010 0.353 14203 Z= 0.679 Angle : 0.900 20.624 19250 Z= 0.550 Chirality : 0.062 1.097 2147 Planarity : 0.007 0.268 2451 Dihedral : 9.545 139.588 5226 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.45 % Favored : 97.44 % Rotamer: Outliers : 0.20 % Allowed : 1.13 % Favored : 98.67 % Cbeta Deviations : 0.24 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.30 % Twisted Proline : 1.79 % 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: -3.72 (0.16), residues: 1717 helix: -3.85 (0.11), residues: 805 sheet: -1.38 (0.35), residues: 143 loop : -0.80 (0.20), residues: 769 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.070 0.004 TRP A 606 HIS 0.013 0.002 HIS C 131 PHE 0.049 0.003 PHE A 769 TYR 0.033 0.002 TYR B 19 ARG 0.012 0.001 ARG A1175 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3434 Ramachandran restraints generated. 1717 Oldfield, 0 Emsley, 1717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3434 Ramachandran restraints generated. 1717 Oldfield, 0 Emsley, 1717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 440 residues out of total 1507 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 437 time to evaluate : 1.570 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 ASP cc_start: 0.9024 (p0) cc_final: 0.8530 (p0) REVERT: A 82 ASP cc_start: 0.9100 (t0) cc_final: 0.8873 (t0) REVERT: A 90 GLU cc_start: 0.8678 (mp0) cc_final: 0.8364 (mp0) REVERT: A 91 ASP cc_start: 0.6927 (t0) cc_final: 0.6503 (p0) REVERT: A 119 LYS cc_start: 0.8579 (mtmt) cc_final: 0.8358 (mtmm) REVERT: A 163 THR cc_start: 0.9278 (m) cc_final: 0.9077 (t) REVERT: A 473 PRO cc_start: 0.8956 (Cg_endo) cc_final: 0.8715 (Cg_exo) REVERT: A 480 GLN cc_start: 0.8466 (mt0) cc_final: 0.8148 (mt0) REVERT: A 596 GLN cc_start: 0.9053 (mt0) cc_final: 0.8664 (mp10) REVERT: A 623 GLU cc_start: 0.7850 (tm-30) cc_final: 0.7369 (tt0) REVERT: A 703 ILE cc_start: 0.9024 (tt) cc_final: 0.8701 (tt) REVERT: A 809 SER cc_start: 0.8908 (t) cc_final: 0.8632 (p) REVERT: A 884 MET cc_start: 0.9155 (mtp) cc_final: 0.8920 (mtm) REVERT: A 889 SER cc_start: 0.8683 (m) cc_final: 0.8313 (p) REVERT: A 950 ARG cc_start: 0.8493 (ttt-90) cc_final: 0.8164 (ttp80) REVERT: A 961 HIS cc_start: 0.8440 (m90) cc_final: 0.8184 (m90) REVERT: A 967 ILE cc_start: 0.8318 (mt) cc_final: 0.8116 (mt) REVERT: A 1010 LYS cc_start: 0.8627 (ptpt) cc_final: 0.8218 (pttt) REVERT: A 1138 GLU cc_start: 0.8523 (pm20) cc_final: 0.8151 (pt0) REVERT: B 136 LYS cc_start: 0.8569 (tttt) cc_final: 0.7969 (tmtt) REVERT: B 149 ARG cc_start: 0.8773 (mtt90) cc_final: 0.8537 (mtt-85) REVERT: B 235 GLU cc_start: 0.8678 (tt0) cc_final: 0.8326 (mp0) REVERT: B 277 ASP cc_start: 0.8686 (m-30) cc_final: 0.8376 (m-30) REVERT: B 395 ASP cc_start: 0.8587 (m-30) cc_final: 0.8330 (m-30) REVERT: B 431 ILE cc_start: 0.9106 (mm) cc_final: 0.8842 (mm) REVERT: B 443 ARG cc_start: 0.8957 (mtp85) cc_final: 0.8754 (mtp-110) REVERT: B 553 SER cc_start: 0.9563 (t) cc_final: 0.9349 (p) REVERT: B 558 LYS cc_start: 0.8815 (pttt) cc_final: 0.8384 (tttm) outliers start: 3 outliers final: 2 residues processed: 440 average time/residue: 0.3264 time to fit residues: 194.3879 Evaluate side-chains 285 residues out of total 1507 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 283 time to evaluate : 1.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 123 GLU Chi-restraints excluded: chain C residue 130 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 144 optimal weight: 0.0370 chunk 129 optimal weight: 8.9990 chunk 71 optimal weight: 6.9990 chunk 44 optimal weight: 5.9990 chunk 87 optimal weight: 2.9990 chunk 69 optimal weight: 6.9990 chunk 134 optimal weight: 7.9990 chunk 51 optimal weight: 4.9990 chunk 81 optimal weight: 7.9990 chunk 99 optimal weight: 8.9990 chunk 155 optimal weight: 5.9990 overall best weight: 4.0066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 161 GLN A 276 ASN A 413 HIS A 525 ASN A 696 HIS A 725 GLN A 898 HIS A1020 HIS A1070 ASN A1108 ASN A1147 GLN B 212 ASN B 369 GLN B 414 ASN C 127 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8819 moved from start: 0.2073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 14203 Z= 0.297 Angle : 0.600 8.159 19250 Z= 0.313 Chirality : 0.043 0.166 2147 Planarity : 0.004 0.060 2451 Dihedral : 7.611 136.624 1948 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 1.73 % Allowed : 7.24 % Favored : 91.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.30 % Twisted Proline : 1.79 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.27 (0.17), residues: 1717 helix: -2.12 (0.15), residues: 825 sheet: -1.01 (0.36), residues: 136 loop : -0.61 (0.21), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP A 606 HIS 0.008 0.001 HIS A 364 PHE 0.016 0.002 PHE A 902 TYR 0.021 0.002 TYR A 242 ARG 0.005 0.001 ARG A 946 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3434 Ramachandran restraints generated. 1717 Oldfield, 0 Emsley, 1717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3434 Ramachandran restraints generated. 1717 Oldfield, 0 Emsley, 1717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 1507 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 310 time to evaluate : 1.489 Fit side-chains revert: symmetry clash REVERT: A 24 LYS cc_start: 0.8456 (mttt) cc_final: 0.8245 (mtpt) REVERT: A 28 HIS cc_start: 0.8738 (t70) cc_final: 0.8522 (t70) REVERT: A 37 ARG cc_start: 0.8757 (ttp80) cc_final: 0.8517 (ttp80) REVERT: A 91 ASP cc_start: 0.6956 (t0) cc_final: 0.6472 (p0) REVERT: A 165 TYR cc_start: 0.9443 (p90) cc_final: 0.9234 (p90) REVERT: A 479 ARG cc_start: 0.8476 (ttp-170) cc_final: 0.7791 (mtp180) REVERT: A 596 GLN cc_start: 0.8995 (mt0) cc_final: 0.8639 (mp10) REVERT: A 623 GLU cc_start: 0.7913 (tm-30) cc_final: 0.7605 (tt0) REVERT: A 634 GLU cc_start: 0.8655 (tp30) cc_final: 0.8448 (tp30) REVERT: A 703 ILE cc_start: 0.9006 (tt) cc_final: 0.8739 (tt) REVERT: A 802 ASP cc_start: 0.7182 (t0) cc_final: 0.6597 (t0) REVERT: A 806 ASN cc_start: 0.8631 (m-40) cc_final: 0.8126 (m110) REVERT: A 807 ASN cc_start: 0.8026 (m-40) cc_final: 0.7787 (m-40) REVERT: A 809 SER cc_start: 0.8934 (t) cc_final: 0.8604 (p) REVERT: A 889 SER cc_start: 0.8726 (m) cc_final: 0.8513 (t) REVERT: A 910 ASP cc_start: 0.8799 (m-30) cc_final: 0.8447 (t0) REVERT: A 950 ARG cc_start: 0.8380 (ttt-90) cc_final: 0.7971 (ttp80) REVERT: A 951 ARG cc_start: 0.8096 (mtt180) cc_final: 0.7870 (ttt90) REVERT: A 961 HIS cc_start: 0.8292 (m90) cc_final: 0.8040 (m90) REVERT: A 966 ASP cc_start: 0.8536 (p0) cc_final: 0.8205 (p0) REVERT: A 996 SER cc_start: 0.8477 (m) cc_final: 0.8153 (p) REVERT: A 1010 LYS cc_start: 0.8590 (ptpt) cc_final: 0.8170 (pttp) REVERT: A 1138 GLU cc_start: 0.8645 (pm20) cc_final: 0.8186 (pt0) REVERT: B 149 ARG cc_start: 0.8776 (mtt90) cc_final: 0.8556 (mtt-85) REVERT: B 160 ASP cc_start: 0.9108 (t0) cc_final: 0.8885 (t0) REVERT: B 235 GLU cc_start: 0.8660 (tt0) cc_final: 0.8293 (mp0) REVERT: B 241 LYS cc_start: 0.8692 (tptt) cc_final: 0.8330 (tptt) REVERT: B 277 ASP cc_start: 0.8712 (m-30) cc_final: 0.8459 (m-30) REVERT: B 321 MET cc_start: 0.9098 (mtt) cc_final: 0.8758 (mmm) REVERT: B 558 LYS cc_start: 0.8788 (pttt) cc_final: 0.8331 (tttm) outliers start: 26 outliers final: 18 residues processed: 326 average time/residue: 0.2981 time to fit residues: 136.9637 Evaluate side-chains 288 residues out of total 1507 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 270 time to evaluate : 1.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 294 SER Chi-restraints excluded: chain A residue 354 ASP Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 680 ASP Chi-restraints excluded: chain A residue 712 THR Chi-restraints excluded: chain A residue 793 THR Chi-restraints excluded: chain A residue 794 LEU Chi-restraints excluded: chain A residue 803 SER Chi-restraints excluded: chain A residue 854 ASP Chi-restraints excluded: chain A residue 856 THR Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain A residue 1132 SER Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 200 SER Chi-restraints excluded: chain B residue 364 SER Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 123 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 86 optimal weight: 20.0000 chunk 48 optimal weight: 7.9990 chunk 129 optimal weight: 8.9990 chunk 105 optimal weight: 9.9990 chunk 42 optimal weight: 10.0000 chunk 155 optimal weight: 8.9990 chunk 168 optimal weight: 5.9990 chunk 138 optimal weight: 6.9990 chunk 154 optimal weight: 5.9990 chunk 53 optimal weight: 4.9990 chunk 124 optimal weight: 5.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 ASN A 64 GLN A 276 ASN A 525 ASN A 705 ASN A1108 ASN B 170 ASN B 212 ASN B 369 GLN C 131 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8864 moved from start: 0.2543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 14203 Z= 0.409 Angle : 0.612 8.791 19250 Z= 0.317 Chirality : 0.045 0.173 2147 Planarity : 0.004 0.060 2451 Dihedral : 7.522 139.773 1946 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 3.19 % Allowed : 8.23 % Favored : 88.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.30 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.56 (0.19), residues: 1717 helix: -1.31 (0.16), residues: 829 sheet: -0.89 (0.39), residues: 134 loop : -0.50 (0.21), residues: 754 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP A 606 HIS 0.007 0.001 HIS A 364 PHE 0.019 0.002 PHE A 902 TYR 0.025 0.002 TYR A 242 ARG 0.007 0.001 ARG A 168 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3434 Ramachandran restraints generated. 1717 Oldfield, 0 Emsley, 1717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3434 Ramachandran restraints generated. 1717 Oldfield, 0 Emsley, 1717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 1507 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 272 time to evaluate : 1.748 Fit side-chains REVERT: A 24 LYS cc_start: 0.8568 (mttt) cc_final: 0.8292 (mtpt) REVERT: A 28 HIS cc_start: 0.8767 (t70) cc_final: 0.8495 (t70) REVERT: A 37 ARG cc_start: 0.8861 (ttp80) cc_final: 0.8565 (ttp80) REVERT: A 91 ASP cc_start: 0.6672 (t0) cc_final: 0.6083 (p0) REVERT: A 248 LYS cc_start: 0.9128 (ttmm) cc_final: 0.8927 (ttpp) REVERT: A 320 GLN cc_start: 0.8551 (mm-40) cc_final: 0.8258 (pt0) REVERT: A 464 GLU cc_start: 0.9177 (tp30) cc_final: 0.8932 (mt-10) REVERT: A 473 PRO cc_start: 0.8975 (Cg_endo) cc_final: 0.8726 (Cg_exo) REVERT: A 596 GLN cc_start: 0.8968 (mt0) cc_final: 0.8589 (mp10) REVERT: A 623 GLU cc_start: 0.8152 (tm-30) cc_final: 0.7847 (tt0) REVERT: A 703 ILE cc_start: 0.9073 (tt) cc_final: 0.8743 (tt) REVERT: A 802 ASP cc_start: 0.7223 (t0) cc_final: 0.6841 (t0) REVERT: A 806 ASN cc_start: 0.8613 (m-40) cc_final: 0.8206 (m-40) REVERT: A 809 SER cc_start: 0.8919 (t) cc_final: 0.8531 (p) REVERT: A 910 ASP cc_start: 0.8798 (m-30) cc_final: 0.8465 (t0) REVERT: A 950 ARG cc_start: 0.8306 (ttt-90) cc_final: 0.7904 (ttp80) REVERT: A 951 ARG cc_start: 0.8074 (mtt180) cc_final: 0.7856 (ttt90) REVERT: A 961 HIS cc_start: 0.8220 (m90) cc_final: 0.7944 (m90) REVERT: A 966 ASP cc_start: 0.8602 (p0) cc_final: 0.8218 (p0) REVERT: A 996 SER cc_start: 0.8479 (m) cc_final: 0.8196 (p) REVERT: A 1010 LYS cc_start: 0.8632 (ptpt) cc_final: 0.8151 (pttp) REVERT: A 1023 GLU cc_start: 0.7667 (tt0) cc_final: 0.7180 (mm-30) REVERT: A 1082 ASN cc_start: 0.8208 (t0) cc_final: 0.7412 (p0) REVERT: A 1138 GLU cc_start: 0.8814 (pm20) cc_final: 0.8189 (pt0) REVERT: B 141 MET cc_start: 0.9373 (tpt) cc_final: 0.8983 (tpt) REVERT: B 149 ARG cc_start: 0.8759 (mtt90) cc_final: 0.8552 (mtt-85) REVERT: B 160 ASP cc_start: 0.9166 (t0) cc_final: 0.8899 (t0) REVERT: B 235 GLU cc_start: 0.8677 (tt0) cc_final: 0.8256 (mp0) REVERT: B 277 ASP cc_start: 0.8589 (m-30) cc_final: 0.8380 (m-30) REVERT: B 510 ILE cc_start: 0.9434 (OUTLIER) cc_final: 0.9166 (pt) REVERT: B 558 LYS cc_start: 0.8849 (pttt) cc_final: 0.8409 (tttm) outliers start: 48 outliers final: 33 residues processed: 300 average time/residue: 0.2786 time to fit residues: 119.0730 Evaluate side-chains 290 residues out of total 1507 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 256 time to evaluate : 1.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 179 ASP Chi-restraints excluded: chain A residue 180 GLU Chi-restraints excluded: chain A residue 252 ILE Chi-restraints excluded: chain A residue 294 SER Chi-restraints excluded: chain A residue 354 ASP Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 545 SER Chi-restraints excluded: chain A residue 589 VAL Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 680 ASP Chi-restraints excluded: chain A residue 681 ASP Chi-restraints excluded: chain A residue 712 THR Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 793 THR Chi-restraints excluded: chain A residue 794 LEU Chi-restraints excluded: chain A residue 803 SER Chi-restraints excluded: chain A residue 826 THR Chi-restraints excluded: chain A residue 854 ASP Chi-restraints excluded: chain A residue 856 THR Chi-restraints excluded: chain A residue 1044 SER Chi-restraints excluded: chain A residue 1068 SER Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain A residue 1132 SER Chi-restraints excluded: chain A residue 1189 SER Chi-restraints excluded: chain A residue 1201 VAL Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 200 SER Chi-restraints excluded: chain B residue 317 SER Chi-restraints excluded: chain B residue 364 SER Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain B residue 487 VAL Chi-restraints excluded: chain B residue 510 ILE Chi-restraints excluded: chain C residue 123 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 153 optimal weight: 8.9990 chunk 116 optimal weight: 10.0000 chunk 80 optimal weight: 5.9990 chunk 17 optimal weight: 6.9990 chunk 74 optimal weight: 3.9990 chunk 104 optimal weight: 0.9990 chunk 156 optimal weight: 7.9990 chunk 165 optimal weight: 2.9990 chunk 81 optimal weight: 0.7980 chunk 147 optimal weight: 8.9990 chunk 44 optimal weight: 7.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 276 ASN A 525 ASN A 807 ASN A1108 ASN B 369 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8830 moved from start: 0.2833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14203 Z= 0.218 Angle : 0.507 7.887 19250 Z= 0.263 Chirality : 0.041 0.162 2147 Planarity : 0.004 0.060 2451 Dihedral : 7.245 140.772 1946 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 2.52 % Allowed : 10.16 % Favored : 87.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.30 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.19), residues: 1717 helix: -0.65 (0.17), residues: 830 sheet: -0.72 (0.41), residues: 140 loop : -0.36 (0.22), residues: 747 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 606 HIS 0.003 0.001 HIS A1203 PHE 0.011 0.001 PHE A 902 TYR 0.016 0.001 TYR A 242 ARG 0.005 0.000 ARG B 252 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3434 Ramachandran restraints generated. 1717 Oldfield, 0 Emsley, 1717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3434 Ramachandran restraints generated. 1717 Oldfield, 0 Emsley, 1717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 1507 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 285 time to evaluate : 1.509 Fit side-chains REVERT: A 24 LYS cc_start: 0.8500 (mttt) cc_final: 0.8258 (mtpt) REVERT: A 28 HIS cc_start: 0.8762 (t70) cc_final: 0.8558 (t70) REVERT: A 37 ARG cc_start: 0.8780 (ttp80) cc_final: 0.8455 (ttp80) REVERT: A 91 ASP cc_start: 0.6934 (t0) cc_final: 0.6279 (p0) REVERT: A 248 LYS cc_start: 0.9115 (ttmm) cc_final: 0.8913 (ttpp) REVERT: A 464 GLU cc_start: 0.9136 (tp30) cc_final: 0.8901 (mt-10) REVERT: A 473 PRO cc_start: 0.8900 (Cg_endo) cc_final: 0.8624 (Cg_exo) REVERT: A 479 ARG cc_start: 0.8564 (ttp-170) cc_final: 0.7730 (mtp180) REVERT: A 596 GLN cc_start: 0.8955 (mt0) cc_final: 0.8547 (mp10) REVERT: A 623 GLU cc_start: 0.8101 (tm-30) cc_final: 0.7870 (tp30) REVERT: A 703 ILE cc_start: 0.9024 (tt) cc_final: 0.8693 (tt) REVERT: A 706 GLU cc_start: 0.8907 (mm-30) cc_final: 0.8519 (mm-30) REVERT: A 721 VAL cc_start: 0.9304 (OUTLIER) cc_final: 0.8865 (m) REVERT: A 802 ASP cc_start: 0.7038 (t0) cc_final: 0.6577 (t0) REVERT: A 806 ASN cc_start: 0.8645 (m-40) cc_final: 0.8202 (m-40) REVERT: A 809 SER cc_start: 0.8937 (t) cc_final: 0.8552 (p) REVERT: A 910 ASP cc_start: 0.8719 (m-30) cc_final: 0.8423 (t0) REVERT: A 950 ARG cc_start: 0.8358 (ttt-90) cc_final: 0.7952 (ttp80) REVERT: A 966 ASP cc_start: 0.8579 (p0) cc_final: 0.8201 (p0) REVERT: A 996 SER cc_start: 0.8447 (m) cc_final: 0.8149 (p) REVERT: A 1010 LYS cc_start: 0.8566 (ptpt) cc_final: 0.8364 (mttp) REVERT: A 1065 LEU cc_start: 0.8482 (OUTLIER) cc_final: 0.8238 (pp) REVERT: A 1082 ASN cc_start: 0.8134 (t0) cc_final: 0.7364 (p0) REVERT: A 1138 GLU cc_start: 0.8847 (pm20) cc_final: 0.8214 (pt0) REVERT: B 149 ARG cc_start: 0.8760 (mtt90) cc_final: 0.8538 (mtt-85) REVERT: B 160 ASP cc_start: 0.9172 (t0) cc_final: 0.8842 (t0) REVERT: B 235 GLU cc_start: 0.8679 (tt0) cc_final: 0.8276 (mp0) REVERT: B 242 LEU cc_start: 0.8814 (tp) cc_final: 0.8586 (mp) REVERT: B 277 ASP cc_start: 0.8590 (m-30) cc_final: 0.8383 (m-30) REVERT: B 364 SER cc_start: 0.9069 (OUTLIER) cc_final: 0.8847 (m) REVERT: B 510 ILE cc_start: 0.9384 (OUTLIER) cc_final: 0.9089 (pt) REVERT: B 525 VAL cc_start: 0.9045 (OUTLIER) cc_final: 0.8694 (p) REVERT: B 558 LYS cc_start: 0.8776 (pttt) cc_final: 0.8345 (tttm) REVERT: C 117 ARG cc_start: 0.8820 (ttt-90) cc_final: 0.8558 (ttt90) outliers start: 38 outliers final: 26 residues processed: 310 average time/residue: 0.2836 time to fit residues: 124.3592 Evaluate side-chains 302 residues out of total 1507 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 271 time to evaluate : 1.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 180 GLU Chi-restraints excluded: chain A residue 294 SER Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 354 ASP Chi-restraints excluded: chain A residue 402 ASP Chi-restraints excluded: chain A residue 589 VAL Chi-restraints excluded: chain A residue 680 ASP Chi-restraints excluded: chain A residue 681 ASP Chi-restraints excluded: chain A residue 721 VAL Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 794 LEU Chi-restraints excluded: chain A residue 796 VAL Chi-restraints excluded: chain A residue 803 SER Chi-restraints excluded: chain A residue 854 ASP Chi-restraints excluded: chain A residue 856 THR Chi-restraints excluded: chain A residue 889 SER Chi-restraints excluded: chain A residue 1065 LEU Chi-restraints excluded: chain A residue 1119 LYS Chi-restraints excluded: chain A residue 1132 SER Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 200 SER Chi-restraints excluded: chain B residue 317 SER Chi-restraints excluded: chain B residue 364 SER Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain B residue 510 ILE Chi-restraints excluded: chain B residue 525 VAL Chi-restraints excluded: chain C residue 123 GLU Chi-restraints excluded: chain C residue 125 PHE Chi-restraints excluded: chain D residue 123 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 137 optimal weight: 9.9990 chunk 93 optimal weight: 0.0770 chunk 2 optimal weight: 10.0000 chunk 123 optimal weight: 5.9990 chunk 68 optimal weight: 10.0000 chunk 141 optimal weight: 0.7980 chunk 114 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 84 optimal weight: 10.0000 chunk 148 optimal weight: 0.6980 chunk 41 optimal weight: 9.9990 overall best weight: 3.5142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 276 ASN A 525 ASN A1108 ASN B 63 HIS B 369 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8840 moved from start: 0.2982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 14203 Z= 0.254 Angle : 0.517 8.181 19250 Z= 0.266 Chirality : 0.041 0.162 2147 Planarity : 0.004 0.055 2451 Dihedral : 7.219 142.729 1946 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 3.12 % Allowed : 9.96 % Favored : 86.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.30 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.20), residues: 1717 helix: -0.32 (0.18), residues: 826 sheet: -0.61 (0.42), residues: 140 loop : -0.28 (0.22), residues: 751 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 606 HIS 0.004 0.001 HIS A 696 PHE 0.012 0.001 PHE A 902 TYR 0.017 0.001 TYR A 242 ARG 0.005 0.000 ARG A 168 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3434 Ramachandran restraints generated. 1717 Oldfield, 0 Emsley, 1717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3434 Ramachandran restraints generated. 1717 Oldfield, 0 Emsley, 1717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 1507 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 276 time to evaluate : 1.544 Fit side-chains REVERT: A 37 ARG cc_start: 0.8866 (ttp80) cc_final: 0.8590 (ttp80) REVERT: A 91 ASP cc_start: 0.6778 (t0) cc_final: 0.6072 (p0) REVERT: A 320 GLN cc_start: 0.8773 (mp10) cc_final: 0.8546 (mp10) REVERT: A 464 GLU cc_start: 0.9129 (tp30) cc_final: 0.8876 (mt-10) REVERT: A 473 PRO cc_start: 0.8864 (Cg_endo) cc_final: 0.8595 (Cg_exo) REVERT: A 479 ARG cc_start: 0.8539 (ttp-170) cc_final: 0.7680 (mtp180) REVERT: A 703 ILE cc_start: 0.9052 (tt) cc_final: 0.8730 (tt) REVERT: A 706 GLU cc_start: 0.8860 (mm-30) cc_final: 0.8452 (mm-30) REVERT: A 721 VAL cc_start: 0.9322 (OUTLIER) cc_final: 0.8873 (m) REVERT: A 809 SER cc_start: 0.8953 (t) cc_final: 0.8567 (p) REVERT: A 910 ASP cc_start: 0.8752 (m-30) cc_final: 0.8456 (t0) REVERT: A 950 ARG cc_start: 0.8427 (ttt-90) cc_final: 0.8053 (ttp80) REVERT: A 966 ASP cc_start: 0.8503 (p0) cc_final: 0.8194 (p0) REVERT: A 996 SER cc_start: 0.8451 (m) cc_final: 0.8153 (p) REVERT: A 1023 GLU cc_start: 0.7726 (tt0) cc_final: 0.7201 (mm-30) REVERT: A 1065 LEU cc_start: 0.8528 (OUTLIER) cc_final: 0.8277 (pp) REVERT: A 1082 ASN cc_start: 0.8171 (t0) cc_final: 0.7406 (p0) REVERT: A 1138 GLU cc_start: 0.8854 (pm20) cc_final: 0.8230 (pt0) REVERT: B 149 ARG cc_start: 0.8778 (mtt90) cc_final: 0.8548 (mtt-85) REVERT: B 160 ASP cc_start: 0.9178 (t0) cc_final: 0.8844 (t0) REVERT: B 235 GLU cc_start: 0.8629 (tt0) cc_final: 0.8122 (mp0) REVERT: B 241 LYS cc_start: 0.8811 (tptt) cc_final: 0.8352 (tptt) REVERT: B 242 LEU cc_start: 0.8849 (tp) cc_final: 0.8644 (mp) REVERT: B 364 SER cc_start: 0.9075 (OUTLIER) cc_final: 0.8854 (m) REVERT: B 510 ILE cc_start: 0.9391 (OUTLIER) cc_final: 0.9102 (pt) REVERT: B 525 VAL cc_start: 0.9041 (OUTLIER) cc_final: 0.8689 (p) REVERT: B 558 LYS cc_start: 0.8744 (pttt) cc_final: 0.8335 (tttm) REVERT: C 117 ARG cc_start: 0.8859 (ttt-90) cc_final: 0.8632 (ttt90) outliers start: 47 outliers final: 35 residues processed: 305 average time/residue: 0.2829 time to fit residues: 122.6266 Evaluate side-chains 301 residues out of total 1507 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 261 time to evaluate : 1.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 179 ASP Chi-restraints excluded: chain A residue 180 GLU Chi-restraints excluded: chain A residue 294 SER Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 354 ASP Chi-restraints excluded: chain A residue 402 ASP Chi-restraints excluded: chain A residue 589 VAL Chi-restraints excluded: chain A residue 680 ASP Chi-restraints excluded: chain A residue 681 ASP Chi-restraints excluded: chain A residue 712 THR Chi-restraints excluded: chain A residue 721 VAL Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 794 LEU Chi-restraints excluded: chain A residue 796 VAL Chi-restraints excluded: chain A residue 803 SER Chi-restraints excluded: chain A residue 826 THR Chi-restraints excluded: chain A residue 854 ASP Chi-restraints excluded: chain A residue 856 THR Chi-restraints excluded: chain A residue 889 SER Chi-restraints excluded: chain A residue 940 LEU Chi-restraints excluded: chain A residue 1065 LEU Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain A residue 1119 LYS Chi-restraints excluded: chain A residue 1132 SER Chi-restraints excluded: chain A residue 1153 ASP Chi-restraints excluded: chain A residue 1189 SER Chi-restraints excluded: chain A residue 1210 VAL Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 200 SER Chi-restraints excluded: chain B residue 317 SER Chi-restraints excluded: chain B residue 364 SER Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain B residue 510 ILE Chi-restraints excluded: chain B residue 525 VAL Chi-restraints excluded: chain C residue 123 GLU Chi-restraints excluded: chain C residue 125 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 55 optimal weight: 6.9990 chunk 148 optimal weight: 1.9990 chunk 32 optimal weight: 10.0000 chunk 97 optimal weight: 0.1980 chunk 40 optimal weight: 3.9990 chunk 165 optimal weight: 0.8980 chunk 137 optimal weight: 1.9990 chunk 76 optimal weight: 10.0000 chunk 13 optimal weight: 9.9990 chunk 54 optimal weight: 0.9980 chunk 86 optimal weight: 6.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 276 ASN A 525 ASN A 705 ASN A1108 ASN B 63 HIS B 369 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8789 moved from start: 0.3250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 14203 Z= 0.126 Angle : 0.457 9.892 19250 Z= 0.235 Chirality : 0.038 0.155 2147 Planarity : 0.003 0.052 2451 Dihedral : 6.866 140.956 1946 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 2.32 % Allowed : 11.29 % Favored : 86.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.30 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.20), residues: 1717 helix: 0.11 (0.18), residues: 833 sheet: -0.40 (0.41), residues: 150 loop : -0.24 (0.22), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 606 HIS 0.003 0.001 HIS A 236 PHE 0.008 0.001 PHE A 902 TYR 0.015 0.001 TYR A 805 ARG 0.008 0.000 ARG B 252 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3434 Ramachandran restraints generated. 1717 Oldfield, 0 Emsley, 1717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3434 Ramachandran restraints generated. 1717 Oldfield, 0 Emsley, 1717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 1507 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 289 time to evaluate : 1.471 Fit side-chains revert: symmetry clash REVERT: A 37 ARG cc_start: 0.8766 (ttp80) cc_final: 0.8353 (ttp80) REVERT: A 360 ARG cc_start: 0.8700 (ptt180) cc_final: 0.8378 (ptt90) REVERT: A 464 GLU cc_start: 0.9086 (tp30) cc_final: 0.8847 (mt-10) REVERT: A 479 ARG cc_start: 0.8484 (ttp-170) cc_final: 0.7620 (mtp180) REVERT: A 703 ILE cc_start: 0.8983 (tt) cc_final: 0.8566 (tt) REVERT: A 706 GLU cc_start: 0.8815 (mm-30) cc_final: 0.8433 (mm-30) REVERT: A 721 VAL cc_start: 0.9245 (OUTLIER) cc_final: 0.8753 (m) REVERT: A 809 SER cc_start: 0.8897 (t) cc_final: 0.8510 (p) REVERT: A 910 ASP cc_start: 0.8686 (m-30) cc_final: 0.8421 (t0) REVERT: A 950 ARG cc_start: 0.8363 (ttt-90) cc_final: 0.8039 (ttp80) REVERT: A 966 ASP cc_start: 0.8526 (p0) cc_final: 0.8308 (p0) REVERT: A 996 SER cc_start: 0.8386 (m) cc_final: 0.8072 (p) REVERT: A 1065 LEU cc_start: 0.8395 (OUTLIER) cc_final: 0.8187 (pp) REVERT: A 1082 ASN cc_start: 0.8125 (t0) cc_final: 0.7425 (p0) REVERT: A 1138 GLU cc_start: 0.8849 (pm20) cc_final: 0.8145 (pt0) REVERT: B 149 ARG cc_start: 0.8723 (mtt90) cc_final: 0.8523 (mtt-85) REVERT: B 160 ASP cc_start: 0.9154 (t0) cc_final: 0.8771 (t0) REVERT: B 201 TYR cc_start: 0.9299 (m-80) cc_final: 0.8642 (m-80) REVERT: B 235 GLU cc_start: 0.8612 (tt0) cc_final: 0.8127 (mp0) REVERT: B 242 LEU cc_start: 0.8852 (tp) cc_final: 0.8562 (mp) REVERT: B 321 MET cc_start: 0.9070 (mtt) cc_final: 0.8704 (mmm) REVERT: B 468 GLU cc_start: 0.9097 (tt0) cc_final: 0.8893 (mt-10) REVERT: B 510 ILE cc_start: 0.9330 (OUTLIER) cc_final: 0.9027 (pt) REVERT: B 558 LYS cc_start: 0.8681 (pttt) cc_final: 0.8278 (tttm) outliers start: 35 outliers final: 23 residues processed: 310 average time/residue: 0.2828 time to fit residues: 124.1716 Evaluate side-chains 290 residues out of total 1507 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 264 time to evaluate : 1.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 179 ASP Chi-restraints excluded: chain A residue 294 SER Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 354 ASP Chi-restraints excluded: chain A residue 402 ASP Chi-restraints excluded: chain A residue 712 THR Chi-restraints excluded: chain A residue 721 VAL Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 794 LEU Chi-restraints excluded: chain A residue 796 VAL Chi-restraints excluded: chain A residue 826 THR Chi-restraints excluded: chain A residue 854 ASP Chi-restraints excluded: chain A residue 940 LEU Chi-restraints excluded: chain A residue 1065 LEU Chi-restraints excluded: chain A residue 1119 LYS Chi-restraints excluded: chain A residue 1132 SER Chi-restraints excluded: chain A residue 1189 SER Chi-restraints excluded: chain A residue 1210 VAL Chi-restraints excluded: chain B residue 200 SER Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain B residue 510 ILE Chi-restraints excluded: chain C residue 123 GLU Chi-restraints excluded: chain C residue 125 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 159 optimal weight: 9.9990 chunk 18 optimal weight: 0.5980 chunk 94 optimal weight: 10.0000 chunk 120 optimal weight: 0.8980 chunk 93 optimal weight: 1.9990 chunk 139 optimal weight: 0.5980 chunk 92 optimal weight: 7.9990 chunk 164 optimal weight: 4.9990 chunk 103 optimal weight: 10.0000 chunk 100 optimal weight: 8.9990 chunk 76 optimal weight: 10.0000 overall best weight: 1.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 HIS A 276 ASN ** A 617 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 705 ASN A1108 ASN B 63 HIS B 69 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8799 moved from start: 0.3352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 14203 Z= 0.158 Angle : 0.471 9.973 19250 Z= 0.240 Chirality : 0.039 0.153 2147 Planarity : 0.003 0.050 2451 Dihedral : 6.768 140.733 1946 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 2.72 % Allowed : 11.49 % Favored : 85.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.30 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.20), residues: 1717 helix: 0.33 (0.19), residues: 830 sheet: -0.42 (0.41), residues: 139 loop : -0.16 (0.22), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 606 HIS 0.003 0.001 HIS A 236 PHE 0.009 0.001 PHE A1086 TYR 0.016 0.001 TYR A 805 ARG 0.008 0.000 ARG B 252 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3434 Ramachandran restraints generated. 1717 Oldfield, 0 Emsley, 1717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3434 Ramachandran restraints generated. 1717 Oldfield, 0 Emsley, 1717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 1507 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 269 time to evaluate : 1.713 Fit side-chains revert: symmetry clash REVERT: A 37 ARG cc_start: 0.8775 (ttp80) cc_final: 0.8251 (ttp80) REVERT: A 91 ASP cc_start: 0.6939 (t0) cc_final: 0.6201 (p0) REVERT: A 360 ARG cc_start: 0.8729 (ptt180) cc_final: 0.8411 (ptt90) REVERT: A 464 GLU cc_start: 0.9112 (tp30) cc_final: 0.8872 (mt-10) REVERT: A 478 GLU cc_start: 0.8768 (mt-10) cc_final: 0.8020 (pp20) REVERT: A 479 ARG cc_start: 0.8485 (ttp-170) cc_final: 0.7573 (mtp180) REVERT: A 703 ILE cc_start: 0.9023 (tt) cc_final: 0.8608 (tt) REVERT: A 706 GLU cc_start: 0.8796 (mm-30) cc_final: 0.8408 (mm-30) REVERT: A 721 VAL cc_start: 0.9265 (OUTLIER) cc_final: 0.8779 (m) REVERT: A 809 SER cc_start: 0.8869 (t) cc_final: 0.8490 (p) REVERT: A 910 ASP cc_start: 0.8672 (m-30) cc_final: 0.8414 (t0) REVERT: A 950 ARG cc_start: 0.8404 (ttt-90) cc_final: 0.8018 (ttp80) REVERT: A 996 SER cc_start: 0.8394 (m) cc_final: 0.8081 (p) REVERT: A 1065 LEU cc_start: 0.8437 (OUTLIER) cc_final: 0.8200 (pp) REVERT: A 1082 ASN cc_start: 0.8160 (t0) cc_final: 0.7436 (p0) REVERT: A 1138 GLU cc_start: 0.8838 (pm20) cc_final: 0.8176 (pt0) REVERT: B 149 ARG cc_start: 0.8722 (mtt90) cc_final: 0.8506 (mtt-85) REVERT: B 160 ASP cc_start: 0.9164 (t0) cc_final: 0.8803 (t0) REVERT: B 201 TYR cc_start: 0.9314 (m-80) cc_final: 0.8662 (m-80) REVERT: B 235 GLU cc_start: 0.8606 (tt0) cc_final: 0.8114 (mp0) REVERT: B 242 LEU cc_start: 0.8811 (tp) cc_final: 0.8523 (mp) REVERT: B 321 MET cc_start: 0.9055 (mtt) cc_final: 0.8702 (mmm) REVERT: B 510 ILE cc_start: 0.9331 (OUTLIER) cc_final: 0.9029 (pt) REVERT: B 525 VAL cc_start: 0.9036 (OUTLIER) cc_final: 0.8760 (p) REVERT: B 558 LYS cc_start: 0.8683 (pttt) cc_final: 0.8278 (tttm) outliers start: 41 outliers final: 30 residues processed: 296 average time/residue: 0.2864 time to fit residues: 120.2933 Evaluate side-chains 292 residues out of total 1507 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 258 time to evaluate : 1.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 179 ASP Chi-restraints excluded: chain A residue 180 GLU Chi-restraints excluded: chain A residue 294 SER Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 354 ASP Chi-restraints excluded: chain A residue 402 ASP Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 721 VAL Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 794 LEU Chi-restraints excluded: chain A residue 796 VAL Chi-restraints excluded: chain A residue 826 THR Chi-restraints excluded: chain A residue 854 ASP Chi-restraints excluded: chain A residue 889 SER Chi-restraints excluded: chain A residue 940 LEU Chi-restraints excluded: chain A residue 1065 LEU Chi-restraints excluded: chain A residue 1119 LYS Chi-restraints excluded: chain A residue 1132 SER Chi-restraints excluded: chain A residue 1153 ASP Chi-restraints excluded: chain A residue 1189 SER Chi-restraints excluded: chain A residue 1190 ILE Chi-restraints excluded: chain A residue 1210 VAL Chi-restraints excluded: chain B residue 200 SER Chi-restraints excluded: chain B residue 317 SER Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain B residue 510 ILE Chi-restraints excluded: chain B residue 525 VAL Chi-restraints excluded: chain C residue 123 GLU Chi-restraints excluded: chain C residue 125 PHE Chi-restraints excluded: chain D residue 123 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 101 optimal weight: 10.0000 chunk 65 optimal weight: 3.9990 chunk 98 optimal weight: 0.2980 chunk 49 optimal weight: 9.9990 chunk 32 optimal weight: 10.0000 chunk 31 optimal weight: 10.0000 chunk 104 optimal weight: 1.9990 chunk 112 optimal weight: 0.8980 chunk 81 optimal weight: 9.9990 chunk 15 optimal weight: 6.9990 chunk 129 optimal weight: 9.9990 overall best weight: 2.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 276 ASN ** A 617 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 705 ASN A1108 ASN B 63 HIS B 212 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8819 moved from start: 0.3353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14203 Z= 0.216 Angle : 0.500 9.585 19250 Z= 0.255 Chirality : 0.040 0.158 2147 Planarity : 0.003 0.049 2451 Dihedral : 6.816 140.931 1946 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 2.46 % Allowed : 12.28 % Favored : 85.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.30 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.20), residues: 1717 helix: 0.32 (0.19), residues: 824 sheet: -0.49 (0.40), residues: 139 loop : -0.17 (0.22), residues: 754 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 606 HIS 0.003 0.001 HIS A 236 PHE 0.010 0.001 PHE B 335 TYR 0.017 0.001 TYR A 805 ARG 0.008 0.000 ARG B 252 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3434 Ramachandran restraints generated. 1717 Oldfield, 0 Emsley, 1717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3434 Ramachandran restraints generated. 1717 Oldfield, 0 Emsley, 1717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 1507 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 264 time to evaluate : 1.669 Fit side-chains revert: symmetry clash REVERT: A 37 ARG cc_start: 0.8800 (ttp80) cc_final: 0.8292 (ttp80) REVERT: A 360 ARG cc_start: 0.8789 (ptt180) cc_final: 0.8487 (ptt90) REVERT: A 464 GLU cc_start: 0.9134 (tp30) cc_final: 0.8891 (mt-10) REVERT: A 478 GLU cc_start: 0.8766 (mt-10) cc_final: 0.8008 (pp20) REVERT: A 479 ARG cc_start: 0.8496 (ttp-170) cc_final: 0.7561 (mtp180) REVERT: A 703 ILE cc_start: 0.9041 (tt) cc_final: 0.8625 (tt) REVERT: A 706 GLU cc_start: 0.8860 (mm-30) cc_final: 0.8460 (mm-30) REVERT: A 809 SER cc_start: 0.8877 (t) cc_final: 0.8488 (p) REVERT: A 910 ASP cc_start: 0.8682 (m-30) cc_final: 0.8438 (t0) REVERT: A 950 ARG cc_start: 0.8493 (ttt-90) cc_final: 0.8002 (ttp80) REVERT: A 996 SER cc_start: 0.8415 (m) cc_final: 0.8112 (p) REVERT: A 1065 LEU cc_start: 0.8478 (OUTLIER) cc_final: 0.8241 (pp) REVERT: A 1082 ASN cc_start: 0.8147 (t0) cc_final: 0.7436 (p0) REVERT: A 1138 GLU cc_start: 0.8850 (pm20) cc_final: 0.8165 (pt0) REVERT: B 141 MET cc_start: 0.9342 (tpt) cc_final: 0.8958 (tpt) REVERT: B 149 ARG cc_start: 0.8734 (mtt90) cc_final: 0.8509 (mtt-85) REVERT: B 160 ASP cc_start: 0.9168 (t0) cc_final: 0.8811 (t0) REVERT: B 201 TYR cc_start: 0.9320 (m-80) cc_final: 0.8655 (m-80) REVERT: B 235 GLU cc_start: 0.8606 (tt0) cc_final: 0.8127 (mp0) REVERT: B 242 LEU cc_start: 0.8822 (tp) cc_final: 0.8505 (mp) REVERT: B 243 TYR cc_start: 0.8901 (m-80) cc_final: 0.8645 (m-80) REVERT: B 321 MET cc_start: 0.9095 (mtt) cc_final: 0.8773 (mmm) REVERT: B 510 ILE cc_start: 0.9352 (OUTLIER) cc_final: 0.9055 (pt) REVERT: B 525 VAL cc_start: 0.9026 (OUTLIER) cc_final: 0.8746 (p) REVERT: B 558 LYS cc_start: 0.8698 (pttt) cc_final: 0.8293 (tttm) outliers start: 37 outliers final: 29 residues processed: 289 average time/residue: 0.2751 time to fit residues: 113.0832 Evaluate side-chains 290 residues out of total 1507 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 258 time to evaluate : 1.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 179 ASP Chi-restraints excluded: chain A residue 277 GLU Chi-restraints excluded: chain A residue 294 SER Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 354 ASP Chi-restraints excluded: chain A residue 402 ASP Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 794 LEU Chi-restraints excluded: chain A residue 796 VAL Chi-restraints excluded: chain A residue 826 THR Chi-restraints excluded: chain A residue 854 ASP Chi-restraints excluded: chain A residue 889 SER Chi-restraints excluded: chain A residue 940 LEU Chi-restraints excluded: chain A residue 1065 LEU Chi-restraints excluded: chain A residue 1119 LYS Chi-restraints excluded: chain A residue 1132 SER Chi-restraints excluded: chain A residue 1153 ASP Chi-restraints excluded: chain A residue 1189 SER Chi-restraints excluded: chain A residue 1190 ILE Chi-restraints excluded: chain A residue 1210 VAL Chi-restraints excluded: chain B residue 200 SER Chi-restraints excluded: chain B residue 317 SER Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain B residue 498 ILE Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain B residue 510 ILE Chi-restraints excluded: chain B residue 525 VAL Chi-restraints excluded: chain C residue 125 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 149 optimal weight: 3.9990 chunk 157 optimal weight: 4.9990 chunk 144 optimal weight: 5.9990 chunk 153 optimal weight: 8.9990 chunk 92 optimal weight: 6.9990 chunk 66 optimal weight: 0.8980 chunk 120 optimal weight: 0.2980 chunk 47 optimal weight: 8.9990 chunk 138 optimal weight: 3.9990 chunk 145 optimal weight: 0.0770 chunk 100 optimal weight: 0.9990 overall best weight: 1.2542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 276 ASN ** A 617 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 705 ASN A1108 ASN B 63 HIS B 212 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8782 moved from start: 0.3505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 14203 Z= 0.131 Angle : 0.465 9.377 19250 Z= 0.237 Chirality : 0.039 0.149 2147 Planarity : 0.003 0.047 2451 Dihedral : 6.513 139.109 1943 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 2.12 % Allowed : 12.75 % Favored : 85.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.30 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.20), residues: 1717 helix: 0.56 (0.19), residues: 817 sheet: -0.41 (0.41), residues: 139 loop : -0.10 (0.22), residues: 761 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 606 HIS 0.003 0.001 HIS A 236 PHE 0.008 0.001 PHE A1086 TYR 0.016 0.001 TYR A 805 ARG 0.004 0.000 ARG A1188 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3434 Ramachandran restraints generated. 1717 Oldfield, 0 Emsley, 1717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3434 Ramachandran restraints generated. 1717 Oldfield, 0 Emsley, 1717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 1507 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 266 time to evaluate : 1.632 Fit side-chains revert: symmetry clash REVERT: A 37 ARG cc_start: 0.8761 (ttp80) cc_final: 0.8285 (ttp80) REVERT: A 464 GLU cc_start: 0.9104 (tp30) cc_final: 0.8860 (mt-10) REVERT: A 478 GLU cc_start: 0.8763 (mt-10) cc_final: 0.7978 (pp20) REVERT: A 479 ARG cc_start: 0.8456 (ttp-170) cc_final: 0.7540 (mtp180) REVERT: A 618 THR cc_start: 0.9199 (m) cc_final: 0.8877 (t) REVERT: A 703 ILE cc_start: 0.8979 (tt) cc_final: 0.8589 (tt) REVERT: A 706 GLU cc_start: 0.8826 (mm-30) cc_final: 0.8451 (mm-30) REVERT: A 809 SER cc_start: 0.8833 (t) cc_final: 0.8461 (p) REVERT: A 889 SER cc_start: 0.8909 (OUTLIER) cc_final: 0.8574 (p) REVERT: A 910 ASP cc_start: 0.8706 (m-30) cc_final: 0.8445 (t0) REVERT: A 950 ARG cc_start: 0.8460 (ttt-90) cc_final: 0.7972 (ttp80) REVERT: A 996 SER cc_start: 0.8363 (m) cc_final: 0.8049 (p) REVERT: A 1065 LEU cc_start: 0.8432 (OUTLIER) cc_final: 0.8211 (pp) REVERT: A 1082 ASN cc_start: 0.8108 (t0) cc_final: 0.7434 (p0) REVERT: A 1138 GLU cc_start: 0.8859 (pm20) cc_final: 0.8174 (pt0) REVERT: A 1192 ASN cc_start: 0.8789 (t0) cc_final: 0.8569 (t0) REVERT: B 160 ASP cc_start: 0.9173 (t0) cc_final: 0.8811 (t0) REVERT: B 201 TYR cc_start: 0.9291 (m-80) cc_final: 0.8640 (m-80) REVERT: B 235 GLU cc_start: 0.8602 (tt0) cc_final: 0.8092 (mp0) REVERT: B 242 LEU cc_start: 0.8785 (tp) cc_final: 0.8463 (mp) REVERT: B 321 MET cc_start: 0.9038 (mtt) cc_final: 0.8690 (mmm) REVERT: B 510 ILE cc_start: 0.9308 (OUTLIER) cc_final: 0.8959 (pt) REVERT: B 525 VAL cc_start: 0.9026 (OUTLIER) cc_final: 0.8751 (p) REVERT: B 558 LYS cc_start: 0.8658 (pttt) cc_final: 0.8255 (tttm) outliers start: 32 outliers final: 23 residues processed: 286 average time/residue: 0.2841 time to fit residues: 115.7833 Evaluate side-chains 283 residues out of total 1507 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 256 time to evaluate : 1.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 179 ASP Chi-restraints excluded: chain A residue 277 GLU Chi-restraints excluded: chain A residue 294 SER Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 354 ASP Chi-restraints excluded: chain A residue 402 ASP Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 794 LEU Chi-restraints excluded: chain A residue 796 VAL Chi-restraints excluded: chain A residue 826 THR Chi-restraints excluded: chain A residue 854 ASP Chi-restraints excluded: chain A residue 889 SER Chi-restraints excluded: chain A residue 940 LEU Chi-restraints excluded: chain A residue 1065 LEU Chi-restraints excluded: chain A residue 1119 LYS Chi-restraints excluded: chain A residue 1132 SER Chi-restraints excluded: chain A residue 1153 ASP Chi-restraints excluded: chain A residue 1190 ILE Chi-restraints excluded: chain A residue 1210 VAL Chi-restraints excluded: chain B residue 200 SER Chi-restraints excluded: chain B residue 498 ILE Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain B residue 510 ILE Chi-restraints excluded: chain B residue 525 VAL Chi-restraints excluded: chain C residue 125 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 162 optimal weight: 8.9990 chunk 99 optimal weight: 10.0000 chunk 77 optimal weight: 10.0000 chunk 112 optimal weight: 5.9990 chunk 170 optimal weight: 7.9990 chunk 156 optimal weight: 2.9990 chunk 135 optimal weight: 7.9990 chunk 14 optimal weight: 5.9990 chunk 104 optimal weight: 6.9990 chunk 83 optimal weight: 3.9990 chunk 107 optimal weight: 10.0000 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 276 ASN A 378 HIS A 514 ASN ** A 617 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 705 ASN A1095 GLN B 63 HIS B 69 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8853 moved from start: 0.3343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 14203 Z= 0.350 Angle : 0.571 9.213 19250 Z= 0.292 Chirality : 0.043 0.160 2147 Planarity : 0.004 0.049 2451 Dihedral : 6.894 141.411 1943 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.46 % Allowed : 12.28 % Favored : 85.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.30 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.20), residues: 1717 helix: 0.08 (0.18), residues: 833 sheet: -0.58 (0.41), residues: 132 loop : -0.26 (0.22), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 606 HIS 0.004 0.001 HIS A1036 PHE 0.015 0.002 PHE A 902 TYR 0.025 0.002 TYR B 243 ARG 0.005 0.001 ARG A 168 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3434 Ramachandran restraints generated. 1717 Oldfield, 0 Emsley, 1717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3434 Ramachandran restraints generated. 1717 Oldfield, 0 Emsley, 1717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 1507 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 257 time to evaluate : 1.553 Fit side-chains REVERT: A 37 ARG cc_start: 0.8870 (ttp80) cc_final: 0.8350 (ttp80) REVERT: A 91 ASP cc_start: 0.6814 (t0) cc_final: 0.6044 (p0) REVERT: A 464 GLU cc_start: 0.9164 (tp30) cc_final: 0.8914 (mt-10) REVERT: A 478 GLU cc_start: 0.8776 (mt-10) cc_final: 0.8015 (pp20) REVERT: A 479 ARG cc_start: 0.8529 (ttp-170) cc_final: 0.7549 (mtp180) REVERT: A 703 ILE cc_start: 0.9040 (tt) cc_final: 0.8775 (tt) REVERT: A 706 GLU cc_start: 0.8902 (mm-30) cc_final: 0.8462 (mm-30) REVERT: A 809 SER cc_start: 0.8983 (t) cc_final: 0.8558 (p) REVERT: A 910 ASP cc_start: 0.8681 (m-30) cc_final: 0.8452 (t0) REVERT: A 950 ARG cc_start: 0.8522 (ttt-90) cc_final: 0.7981 (ttp80) REVERT: A 996 SER cc_start: 0.8322 (m) cc_final: 0.8030 (p) REVERT: A 1023 GLU cc_start: 0.7408 (tt0) cc_final: 0.6930 (mm-30) REVERT: A 1065 LEU cc_start: 0.8649 (OUTLIER) cc_final: 0.8412 (pp) REVERT: A 1082 ASN cc_start: 0.8184 (t0) cc_final: 0.7431 (p0) REVERT: A 1138 GLU cc_start: 0.8865 (pm20) cc_final: 0.8180 (pt0) REVERT: A 1200 MET cc_start: 0.9477 (tpp) cc_final: 0.9255 (ttm) REVERT: B 160 ASP cc_start: 0.9149 (t0) cc_final: 0.8820 (t0) REVERT: B 235 GLU cc_start: 0.8583 (tt0) cc_final: 0.8118 (mp0) REVERT: B 242 LEU cc_start: 0.8872 (tp) cc_final: 0.8627 (mp) REVERT: B 510 ILE cc_start: 0.9369 (OUTLIER) cc_final: 0.9091 (pt) REVERT: B 558 LYS cc_start: 0.8764 (pttt) cc_final: 0.8365 (tttm) outliers start: 37 outliers final: 29 residues processed: 281 average time/residue: 0.2860 time to fit residues: 114.7273 Evaluate side-chains 285 residues out of total 1507 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 254 time to evaluate : 1.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 179 ASP Chi-restraints excluded: chain A residue 277 GLU Chi-restraints excluded: chain A residue 294 SER Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 354 ASP Chi-restraints excluded: chain A residue 514 ASN Chi-restraints excluded: chain A residue 680 ASP Chi-restraints excluded: chain A residue 681 ASP Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 794 LEU Chi-restraints excluded: chain A residue 796 VAL Chi-restraints excluded: chain A residue 826 THR Chi-restraints excluded: chain A residue 854 ASP Chi-restraints excluded: chain A residue 889 SER Chi-restraints excluded: chain A residue 940 LEU Chi-restraints excluded: chain A residue 1065 LEU Chi-restraints excluded: chain A residue 1119 LYS Chi-restraints excluded: chain A residue 1132 SER Chi-restraints excluded: chain A residue 1153 ASP Chi-restraints excluded: chain A residue 1190 ILE Chi-restraints excluded: chain A residue 1210 VAL Chi-restraints excluded: chain B residue 200 SER Chi-restraints excluded: chain B residue 317 SER Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain B residue 510 ILE Chi-restraints excluded: chain B residue 525 VAL Chi-restraints excluded: chain C residue 125 PHE Chi-restraints excluded: chain C residue 133 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 144 optimal weight: 6.9990 chunk 41 optimal weight: 0.9980 chunk 125 optimal weight: 0.0060 chunk 20 optimal weight: 2.9990 chunk 37 optimal weight: 8.9990 chunk 135 optimal weight: 0.9980 chunk 56 optimal weight: 5.9990 chunk 139 optimal weight: 2.9990 chunk 17 optimal weight: 8.9990 chunk 25 optimal weight: 4.9990 chunk 119 optimal weight: 10.0000 overall best weight: 1.6000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 276 ASN ** A 617 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 705 ASN A1095 GLN B 63 HIS B 212 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.110410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2850 r_free = 0.2850 target = 0.093189 restraints weight = 17950.036| |-----------------------------------------------------------------------------| r_work (start): 0.2852 rms_B_bonded: 1.50 r_work: 0.2747 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.2623 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.2623 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8617 moved from start: 0.3507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 14203 Z= 0.157 Angle : 0.492 9.473 19250 Z= 0.252 Chirality : 0.039 0.187 2147 Planarity : 0.003 0.047 2451 Dihedral : 6.653 139.033 1943 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 1.86 % Allowed : 13.15 % Favored : 84.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.30 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.20), residues: 1717 helix: 0.40 (0.19), residues: 821 sheet: -0.63 (0.39), residues: 140 loop : -0.19 (0.22), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 606 HIS 0.003 0.001 HIS B 466 PHE 0.007 0.001 PHE A1086 TYR 0.016 0.001 TYR A 805 ARG 0.006 0.000 ARG A 752 =============================================================================== Job complete usr+sys time: 3373.69 seconds wall clock time: 61 minutes 14.19 seconds (3674.19 seconds total)