Starting phenix.real_space_refine on Thu Nov 16 02:27:20 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jb6_6408/11_2023/3jb6_6408_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jb6_6408/11_2023/3jb6_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_6408/11_2023/3jb6_6408.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jb6_6408/11_2023/3jb6_6408.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jb6_6408/11_2023/3jb6_6408_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jb6_6408/11_2023/3jb6_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: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/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: 7.04, per 1000 atoms: 0.51 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: 5.73 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: 7.08 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: 5.15 Time building geometry restraints manager: 6.16 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: 0.160 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: 1.500 Check model and map are aligned: 0.230 Set scattering table: 0.160 Process input model: 40.000 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.370 ------------------------------------------------------------------------------- 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 *********************** 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 : 1.893 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 440 average time/residue: 0.3304 time to fit residues: 197.5349 Evaluate side-chains 279 residues out of total 1507 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 277 time to evaluate : 1.378 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1309 time to fit residues: 2.6396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9990 chunk 44 optimal weight: 0.0000 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: 4.9990 overall best weight: 1.8068 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 ASN A 161 GLN A 276 ASN A 413 HIS A 525 ASN A 653 GLN A 696 HIS A 725 GLN A 898 HIS A1020 HIS A1070 ASN A1108 ASN A1147 GLN B 63 HIS B 212 ASN B 369 GLN B 414 ASN C 127 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8776 moved from start: 0.2237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 14203 Z= 0.181 Angle : 0.555 7.850 19250 Z= 0.289 Chirality : 0.041 0.161 2147 Planarity : 0.004 0.059 2451 Dihedral : 7.134 135.822 1943 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 0.93 % Allowed : 7.70 % Favored : 91.37 % 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: -2.08 (0.18), residues: 1717 helix: -2.00 (0.15), residues: 823 sheet: -0.89 (0.36), residues: 137 loop : -0.47 (0.21), residues: 757 *********************** 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 334 residues out of total 1507 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 320 time to evaluate : 1.730 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 7 residues processed: 329 average time/residue: 0.3127 time to fit residues: 143.7790 Evaluate side-chains 273 residues out of total 1507 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 266 time to evaluate : 1.792 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1300 time to fit residues: 3.9702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 10.0000 chunk 129 optimal weight: 0.9990 chunk 105 optimal weight: 8.9990 chunk 42 optimal weight: 7.9990 chunk 155 optimal weight: 9.9990 chunk 168 optimal weight: 10.0000 chunk 138 optimal weight: 9.9990 chunk 154 optimal weight: 4.9990 chunk 53 optimal weight: 6.9990 chunk 124 optimal weight: 0.3980 overall best weight: 4.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 ASN A 46 ASN A 64 GLN A 276 ASN A 525 ASN A 705 ASN A1108 ASN B 63 HIS B 170 ASN B 369 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8839 moved from start: 0.2693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 14203 Z= 0.306 Angle : 0.566 9.143 19250 Z= 0.293 Chirality : 0.043 0.167 2147 Planarity : 0.004 0.060 2451 Dihedral : 7.044 136.964 1943 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 2.32 % Allowed : 8.76 % Favored : 88.91 % 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: -1.30 (0.19), residues: 1717 helix: -1.09 (0.17), residues: 830 sheet: -0.77 (0.40), residues: 134 loop : -0.36 (0.21), residues: 753 *********************** 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 309 residues out of total 1507 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 274 time to evaluate : 2.472 Fit side-chains revert: symmetry clash outliers start: 35 outliers final: 19 residues processed: 292 average time/residue: 0.2836 time to fit residues: 119.0413 Evaluate side-chains 274 residues out of total 1507 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 255 time to evaluate : 1.641 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.1451 time to fit residues: 7.0937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 153 optimal weight: 6.9990 chunk 116 optimal weight: 7.9990 chunk 80 optimal weight: 8.9990 chunk 17 optimal weight: 1.9990 chunk 74 optimal weight: 5.9990 chunk 104 optimal weight: 5.9990 chunk 156 optimal weight: 10.0000 chunk 165 optimal weight: 5.9990 chunk 81 optimal weight: 5.9990 chunk 147 optimal weight: 5.9990 chunk 44 optimal weight: 0.2980 overall best weight: 4.0588 ------------------------------------------------------------------------------- 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 258 GLN A 276 ASN A 525 ASN A 806 ASN ** A 807 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1082 ASN A1108 ASN B 63 HIS B 369 GLN C 131 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8840 moved from start: 0.2947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 14203 Z= 0.287 Angle : 0.535 8.174 19250 Z= 0.277 Chirality : 0.042 0.163 2147 Planarity : 0.004 0.059 2451 Dihedral : 7.014 139.343 1943 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 1.73 % Allowed : 9.50 % Favored : 88.78 % 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: -0.88 (0.19), residues: 1717 helix: -0.61 (0.17), residues: 829 sheet: -0.68 (0.40), residues: 139 loop : -0.31 (0.22), residues: 749 *********************** 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 292 residues out of total 1507 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 266 time to evaluate : 1.587 Fit side-chains revert: symmetry clash outliers start: 26 outliers final: 16 residues processed: 277 average time/residue: 0.2824 time to fit residues: 110.8896 Evaluate side-chains 267 residues out of total 1507 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 251 time to evaluate : 1.251 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.1396 time to fit residues: 5.4901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 137 optimal weight: 0.9990 chunk 93 optimal weight: 8.9990 chunk 2 optimal weight: 1.9990 chunk 123 optimal weight: 6.9990 chunk 68 optimal weight: 7.9990 chunk 141 optimal weight: 0.9980 chunk 114 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 84 optimal weight: 8.9990 chunk 148 optimal weight: 0.7980 chunk 41 optimal weight: 9.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- 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 369 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8816 moved from start: 0.3115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 14203 Z= 0.188 Angle : 0.490 8.360 19250 Z= 0.254 Chirality : 0.040 0.158 2147 Planarity : 0.003 0.054 2451 Dihedral : 6.832 140.005 1943 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 0.66 % Allowed : 11.29 % Favored : 88.05 % 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: -0.53 (0.19), residues: 1717 helix: -0.21 (0.18), residues: 826 sheet: -0.49 (0.40), residues: 149 loop : -0.27 (0.22), residues: 742 *********************** 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 270 residues out of total 1507 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 260 time to evaluate : 1.492 Fit side-chains revert: symmetry clash outliers start: 10 outliers final: 4 residues processed: 265 average time/residue: 0.2877 time to fit residues: 108.6513 Evaluate side-chains 255 residues out of total 1507 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 251 time to evaluate : 1.631 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.2052 time to fit residues: 3.5006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 55 optimal weight: 7.9990 chunk 148 optimal weight: 3.9990 chunk 32 optimal weight: 10.0000 chunk 97 optimal weight: 2.9990 chunk 40 optimal weight: 4.9990 chunk 165 optimal weight: 10.0000 chunk 137 optimal weight: 10.0000 chunk 76 optimal weight: 5.9990 chunk 13 optimal weight: 10.0000 chunk 54 optimal weight: 2.9990 chunk 86 optimal weight: 0.0000 overall best weight: 2.9992 ------------------------------------------------------------------------------- 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 ** A 807 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1108 ASN B 369 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8825 moved from start: 0.3234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 14203 Z= 0.225 Angle : 0.501 7.675 19250 Z= 0.259 Chirality : 0.040 0.159 2147 Planarity : 0.003 0.053 2451 Dihedral : 6.831 141.618 1943 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 1.06 % Allowed : 11.69 % Favored : 87.25 % 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: -0.35 (0.20), residues: 1717 helix: -0.03 (0.18), residues: 825 sheet: -0.44 (0.41), residues: 149 loop : -0.22 (0.22), residues: 743 *********************** 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 278 residues out of total 1507 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 262 time to evaluate : 1.669 Fit side-chains revert: symmetry clash outliers start: 16 outliers final: 10 residues processed: 267 average time/residue: 0.3015 time to fit residues: 114.9017 Evaluate side-chains 262 residues out of total 1507 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 252 time to evaluate : 1.850 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1377 time to fit residues: 4.7421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 159 optimal weight: 6.9990 chunk 18 optimal weight: 0.0980 chunk 94 optimal weight: 2.9990 chunk 120 optimal weight: 6.9990 chunk 93 optimal weight: 7.9990 chunk 139 optimal weight: 7.9990 chunk 92 optimal weight: 5.9990 chunk 164 optimal weight: 5.9990 chunk 103 optimal weight: 5.9990 chunk 100 optimal weight: 8.9990 chunk 76 optimal weight: 8.9990 overall best weight: 4.2188 ------------------------------------------------------------------------------- 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 364 HIS A 378 HIS A 514 ASN A 525 ASN A 705 ASN ** A 807 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1095 GLN A1108 ASN B 170 ASN B 369 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8844 moved from start: 0.3267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 14203 Z= 0.293 Angle : 0.539 8.880 19250 Z= 0.276 Chirality : 0.042 0.161 2147 Planarity : 0.004 0.051 2451 Dihedral : 6.949 143.049 1943 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 0.93 % Allowed : 12.42 % Favored : 86.65 % 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: -0.40 (0.20), residues: 1717 helix: -0.06 (0.18), residues: 826 sheet: -0.54 (0.40), residues: 149 loop : -0.25 (0.22), residues: 742 *********************** 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 263 residues out of total 1507 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 249 time to evaluate : 1.744 Fit side-chains revert: symmetry clash outliers start: 14 outliers final: 9 residues processed: 255 average time/residue: 0.2978 time to fit residues: 109.3205 Evaluate side-chains 251 residues out of total 1507 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 242 time to evaluate : 1.635 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1358 time to fit residues: 4.4604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 101 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 98 optimal weight: 0.0170 chunk 49 optimal weight: 5.9990 chunk 32 optimal weight: 8.9990 chunk 31 optimal weight: 6.9990 chunk 104 optimal weight: 4.9990 chunk 112 optimal weight: 2.9990 chunk 81 optimal weight: 20.0000 chunk 15 optimal weight: 4.9990 chunk 129 optimal weight: 7.9990 overall best weight: 2.8026 ------------------------------------------------------------------------------- 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 617 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 705 ASN A 806 ASN ** A 807 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1108 ASN B 369 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8825 moved from start: 0.3375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14203 Z= 0.213 Angle : 0.504 8.500 19250 Z= 0.259 Chirality : 0.040 0.158 2147 Planarity : 0.003 0.050 2451 Dihedral : 6.833 142.261 1943 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 0.53 % Allowed : 13.01 % Favored : 86.45 % 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: 0.09 (0.18), residues: 835 sheet: -0.51 (0.41), residues: 147 loop : -0.29 (0.22), residues: 735 *********************** 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 268 residues out of total 1507 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 260 time to evaluate : 1.727 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 5 residues processed: 262 average time/residue: 0.3059 time to fit residues: 114.8819 Evaluate side-chains 257 residues out of total 1507 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 252 time to evaluate : 1.692 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1376 time to fit residues: 3.6204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 149 optimal weight: 1.9990 chunk 157 optimal weight: 4.9990 chunk 144 optimal weight: 4.9990 chunk 153 optimal weight: 10.0000 chunk 92 optimal weight: 1.9990 chunk 66 optimal weight: 0.9990 chunk 120 optimal weight: 0.7980 chunk 47 optimal weight: 7.9990 chunk 138 optimal weight: 3.9990 chunk 145 optimal weight: 0.1980 chunk 100 optimal weight: 0.0060 overall best weight: 0.8000 ------------------------------------------------------------------------------- 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 364 HIS A 514 ASN A 525 ASN ** A 617 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 807 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1095 GLN A1108 ASN B 212 ASN B 369 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8771 moved from start: 0.3615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 14203 Z= 0.119 Angle : 0.468 10.019 19250 Z= 0.240 Chirality : 0.038 0.151 2147 Planarity : 0.003 0.046 2451 Dihedral : 6.540 139.609 1943 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 0.40 % Allowed : 13.55 % Favored : 86.06 % 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: 0.05 (0.20), residues: 1717 helix: 0.41 (0.19), residues: 835 sheet: -0.39 (0.42), residues: 147 loop : -0.13 (0.23), residues: 735 *********************** 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 285 residues out of total 1507 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 279 time to evaluate : 1.736 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 4 residues processed: 282 average time/residue: 0.2972 time to fit residues: 120.3524 Evaluate side-chains 259 residues out of total 1507 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 255 time to evaluate : 1.598 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1344 time to fit residues: 3.2201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 3.9990 chunk 77 optimal weight: 20.0000 chunk 112 optimal weight: 0.9980 chunk 170 optimal weight: 10.0000 chunk 156 optimal weight: 7.9990 chunk 135 optimal weight: 5.9990 chunk 14 optimal weight: 4.9990 chunk 104 optimal weight: 7.9990 chunk 83 optimal weight: 20.0000 chunk 107 optimal weight: 10.0000 overall best weight: 4.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 276 ASN A 705 ASN ** A 807 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1082 ASN A1108 ASN B 69 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8845 moved from start: 0.3480 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= 0.336 Angle : 0.572 10.047 19250 Z= 0.293 Chirality : 0.043 0.160 2147 Planarity : 0.004 0.049 2451 Dihedral : 6.833 141.472 1943 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 0.60 % Allowed : 14.34 % Favored : 85.06 % 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: -0.26 (0.20), residues: 1717 helix: 0.13 (0.18), residues: 831 sheet: -0.54 (0.41), residues: 142 loop : -0.27 (0.22), residues: 744 ********************** 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 260 residues out of total 1507 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 251 time to evaluate : 1.672 Fit side-chains revert: symmetry clash outliers start: 9 outliers final: 6 residues processed: 254 average time/residue: 0.3174 time to fit residues: 114.8736 Evaluate side-chains 255 residues out of total 1507 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 249 time to evaluate : 1.600 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1437 time to fit residues: 3.9813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 144 optimal weight: 3.9990 chunk 41 optimal weight: 9.9990 chunk 125 optimal weight: 0.7980 chunk 20 optimal weight: 3.9990 chunk 37 optimal weight: 6.9990 chunk 135 optimal weight: 0.9990 chunk 56 optimal weight: 0.5980 chunk 139 optimal weight: 0.8980 chunk 17 optimal weight: 0.9990 chunk 25 optimal weight: 2.9990 chunk 119 optimal weight: 0.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 276 ASN A 364 HIS ** A 807 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1108 ASN B 212 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.112284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.095380 restraints weight = 17845.454| |-----------------------------------------------------------------------------| r_work (start): 0.2886 rms_B_bonded: 1.44 r_work: 0.2787 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2666 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.2666 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 moved from start: 0.3722 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= 0.133 Angle : 0.488 10.641 19250 Z= 0.252 Chirality : 0.039 0.173 2147 Planarity : 0.003 0.046 2451 Dihedral : 6.522 137.928 1943 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 0.07 % Allowed : 15.34 % Favored : 84.59 % 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: 0.46 (0.19), residues: 830 sheet: -0.46 (0.40), residues: 147 loop : -0.17 (0.22), residues: 740 =============================================================================== Job complete usr+sys time: 3368.62 seconds wall clock time: 65 minutes 8.79 seconds (3908.79 seconds total)