Starting phenix.real_space_refine on Mon Mar 18 09:03:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uhg_26514/03_2024/7uhg_26514_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uhg_26514/03_2024/7uhg_26514.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uhg_26514/03_2024/7uhg_26514.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uhg_26514/03_2024/7uhg_26514.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uhg_26514/03_2024/7uhg_26514_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uhg_26514/03_2024/7uhg_26514_updated.pdb" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.005 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: 6 Type Number sf(0) Gaussians Ca 2 9.91 5 P 1 5.49 5 S 112 5.16 5 C 13191 2.51 5 N 3351 2.21 5 O 3757 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C GLU 343": "OE1" <-> "OE2" Residue "A TYR 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 162": "OE1" <-> "OE2" Residue "A GLU 291": "OE1" <-> "OE2" Residue "A PHE 293": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 412": "OE1" <-> "OE2" Residue "A GLU 543": "OE1" <-> "OE2" Residue "A PHE 627": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 895": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 914": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 941": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 959": "OD1" <-> "OD2" Residue "A PHE 1150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 129": "OD1" <-> "OD2" Residue "D GLU 191": "OE1" <-> "OE2" Residue "D GLU 278": "OE1" <-> "OE2" Residue "D ASP 300": "OD1" <-> "OD2" Residue "D ASP 320": "OD1" <-> "OD2" Residue "D GLU 342": "OE1" <-> "OE2" Residue "D ASP 439": "OD1" <-> "OD2" Residue "D TYR 512": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 555": "OE1" <-> "OE2" Residue "D ASP 569": "OD1" <-> "OD2" Residue "D ASP 616": "OD1" <-> "OD2" Residue "D TYR 719": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 1003": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 20414 Number of models: 1 Model: "" Number of chains: 11 Chain: "C" Number of atoms: 2575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 324, 2575 Classifications: {'peptide': 324} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 304} Chain: "A" Number of atoms: 9900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1230, 9900 Classifications: {'peptide': 1230} Link IDs: {'PTRANS': 36, 'TRANS': 1193} Chain breaks: 7 Chain: "D" Number of atoms: 7570 Number of conformers: 1 Conformer: "" Number of residues, atoms: 948, 7570 Classifications: {'peptide': 948} Link IDs: {'PCIS': 2, 'PTRANS': 38, 'TRANS': 907} Chain breaks: 5 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 130 Unusual residues: {' CA': 1, '3PE': 1, 'CLR': 3} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 6 Chain: "D" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' CA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 11.31, per 1000 atoms: 0.55 Number of scatterers: 20414 At special positions: 0 Unit cell: (172.67, 170.442, 182.696, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 2 19.99 S 112 16.00 P 1 15.00 O 3757 8.00 N 3351 7.00 C 13191 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS A 301 " - pdb=" SG CYS A 326 " distance=2.04 Simple disulfide: pdb=" SG CYS A 317 " - pdb=" SG CYS A 333 " distance=2.03 Simple disulfide: pdb=" SG CYS A1044 " - pdb=" SG CYS A1055 " distance=2.03 Simple disulfide: pdb=" SG CYS A1421 " - pdb=" SG CYS A1435 " distance=2.03 Simple disulfide: pdb=" SG CYS D 303 " - pdb=" SG CYS D1044 " distance=2.03 Simple disulfide: pdb=" SG CYS D 404 " - pdb=" SG CYS D1071 " distance=2.03 Simple disulfide: pdb=" SG CYS D 667 " - pdb=" SG CYS D 697 " distance=2.03 Simple disulfide: pdb=" SG CYS D 904 " - pdb=" SG CYS D 974 " distance=2.03 Simple disulfide: pdb=" SG CYS D 996 " - pdb=" SG CYS D1026 " distance=2.03 Simple disulfide: pdb=" SG CYS D 999 " - pdb=" SG CYS D1024 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " NAG E 3 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " NAG G 3 " " NAG G 3 " - " NAG G 4 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " NAG-ASN " NAG B 1 " - " ASN A 329 " " NAG D1201 " - " ASN D 92 " " NAG E 1 " - " ASN D 184 " " NAG F 1 " - " ASN D 348 " " NAG G 1 " - " ASN D 468 " " NAG H 1 " - " ASN D 613 " " NAG I 1 " - " ASN D 895 " Time building additional restraints: 8.38 Conformation dependent library (CDL) restraints added in 3.5 seconds 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4736 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 100 helices and 14 sheets defined 49.2% alpha, 8.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.87 Creating SS restraints... Processing helix chain 'C' and resid 39 through 55 Processing helix chain 'C' and resid 121 through 132 removed outlier: 3.760A pdb=" N GLU C 132 " --> pdb=" O ARG C 128 " (cutoff:3.500A) Processing helix chain 'C' and resid 156 through 158 No H-bonds generated for 'chain 'C' and resid 156 through 158' Processing helix chain 'C' and resid 191 through 207 removed outlier: 4.415A pdb=" N LEU C 200 " --> pdb=" O MET C 196 " (cutoff:3.500A) Processing helix chain 'C' and resid 247 through 263 Processing helix chain 'C' and resid 297 through 307 Processing helix chain 'C' and resid 309 through 313 Processing helix chain 'C' and resid 315 through 327 Processing helix chain 'C' and resid 330 through 332 No H-bonds generated for 'chain 'C' and resid 330 through 332' Processing helix chain 'C' and resid 342 through 360 Processing helix chain 'A' and resid 129 through 144 Processing helix chain 'A' and resid 150 through 152 No H-bonds generated for 'chain 'A' and resid 150 through 152' Processing helix chain 'A' and resid 156 through 179 removed outlier: 3.817A pdb=" N LYS A 163 " --> pdb=" O HIS A 159 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N THR A 176 " --> pdb=" O PHE A 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 216 removed outlier: 3.530A pdb=" N VAL A 205 " --> pdb=" O ASP A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 236 through 245 removed outlier: 3.535A pdb=" N ARG A 240 " --> pdb=" O LYS A 237 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N PHE A 242 " --> pdb=" O LEU A 239 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 252 Processing helix chain 'A' and resid 255 through 267 removed outlier: 3.649A pdb=" N VAL A 259 " --> pdb=" O PRO A 255 " (cutoff:3.500A) removed outlier: 4.998A pdb=" N VAL A 260 " --> pdb=" O SER A 256 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LEU A 261 " --> pdb=" O LEU A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 292 removed outlier: 4.342A pdb=" N HIS A 273 " --> pdb=" O VAL A 269 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N ILE A 274 " --> pdb=" O PRO A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 361 Processing helix chain 'A' and resid 366 through 376 removed outlier: 3.564A pdb=" N ASP A 375 " --> pdb=" O TYR A 371 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 393 Processing helix chain 'A' and resid 395 through 419 removed outlier: 3.545A pdb=" N GLU A 412 " --> pdb=" O GLU A 408 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ARG A 413 " --> pdb=" O PHE A 409 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLU A 414 " --> pdb=" O SER A 410 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N ALA A 418 " --> pdb=" O GLU A 414 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N ARG A 419 " --> pdb=" O LYS A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 430 Processing helix chain 'A' and resid 432 through 439 removed outlier: 4.293A pdb=" N LYS A 436 " --> pdb=" O GLU A 432 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLY A 437 " --> pdb=" O GLU A 433 " (cutoff:3.500A) Processing helix chain 'A' and resid 518 through 521 No H-bonds generated for 'chain 'A' and resid 518 through 521' Processing helix chain 'A' and resid 523 through 541 removed outlier: 3.582A pdb=" N ILE A 540 " --> pdb=" O ASN A 536 " (cutoff:3.500A) Processing helix chain 'A' and resid 549 through 577 removed outlier: 3.670A pdb=" N SER A 576 " --> pdb=" O VAL A 572 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N LEU A 577 " --> pdb=" O LYS A 573 " (cutoff:3.500A) Processing helix chain 'A' and resid 579 through 584 removed outlier: 3.549A pdb=" N VAL A 584 " --> pdb=" O GLN A 580 " (cutoff:3.500A) Processing helix chain 'A' and resid 586 through 606 removed outlier: 3.640A pdb=" N THR A 602 " --> pdb=" O GLY A 598 " (cutoff:3.500A) Processing helix chain 'A' and resid 614 through 619 Processing helix chain 'A' and resid 622 through 628 removed outlier: 3.907A pdb=" N ARG A 625 " --> pdb=" O ARG A 622 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ILE A 626 " --> pdb=" O LEU A 623 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N PHE A 627 " --> pdb=" O LEU A 624 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 632 No H-bonds generated for 'chain 'A' and resid 630 through 632' Processing helix chain 'A' and resid 637 through 644 Processing helix chain 'A' and resid 647 through 672 removed outlier: 3.612A pdb=" N SER A 652 " --> pdb=" O LYS A 648 " (cutoff:3.500A) Processing helix chain 'A' and resid 691 through 703 Processing helix chain 'A' and resid 707 through 718 removed outlier: 3.727A pdb=" N TYR A 718 " --> pdb=" O GLY A 714 " (cutoff:3.500A) Processing helix chain 'A' and resid 727 through 746 removed outlier: 3.601A pdb=" N ILE A 734 " --> pdb=" O TYR A 731 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU A 735 " --> pdb=" O PHE A 732 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N CYS A 738 " --> pdb=" O LEU A 735 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ASN A 740 " --> pdb=" O ILE A 737 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N TYR A 741 " --> pdb=" O CYS A 738 " (cutoff:3.500A) Processing helix chain 'A' and resid 748 through 753 removed outlier: 3.551A pdb=" N VAL A 752 " --> pdb=" O LEU A 748 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ASP A 753 " --> pdb=" O ALA A 749 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 748 through 753' Processing helix chain 'A' and resid 755 through 771 removed outlier: 3.620A pdb=" N GLU A 767 " --> pdb=" O THR A 763 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLU A 771 " --> pdb=" O GLU A 767 " (cutoff:3.500A) Processing helix chain 'A' and resid 877 through 883 removed outlier: 3.673A pdb=" N LEU A 882 " --> pdb=" O GLY A 878 " (cutoff:3.500A) Processing helix chain 'A' and resid 888 through 904 removed outlier: 4.035A pdb=" N ALA A 901 " --> pdb=" O MET A 897 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ALA A 902 " --> pdb=" O LEU A 898 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU A 903 " --> pdb=" O SER A 899 " (cutoff:3.500A) Processing helix chain 'A' and resid 914 through 940 removed outlier: 3.579A pdb=" N LEU A 935 " --> pdb=" O THR A 931 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LEU A 936 " --> pdb=" O VAL A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 954 through 969 removed outlier: 3.508A pdb=" N ASP A 959 " --> pdb=" O PHE A 955 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N MET A 960 " --> pdb=" O ASN A 956 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N SER A 966 " --> pdb=" O VAL A 962 " (cutoff:3.500A) Processing helix chain 'A' and resid 980 through 997 removed outlier: 4.769A pdb=" N VAL A 988 " --> pdb=" O ARG A 984 " (cutoff:3.500A) removed outlier: 5.296A pdb=" N LEU A 989 " --> pdb=" O VAL A 985 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N ARG A 990 " --> pdb=" O LEU A 986 " (cutoff:3.500A) Proline residue: A 991 - end of helix removed outlier: 4.391A pdb=" N ALA A 994 " --> pdb=" O ARG A 990 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N ILE A 995 " --> pdb=" O PRO A 991 " (cutoff:3.500A) removed outlier: 5.594A pdb=" N ASN A 996 " --> pdb=" O LEU A 992 " (cutoff:3.500A) removed outlier: 4.870A pdb=" N ARG A 997 " --> pdb=" O ARG A 993 " (cutoff:3.500A) Processing helix chain 'A' and resid 999 through 1016 removed outlier: 3.648A pdb=" N HIS A1003 " --> pdb=" O LYS A 999 " (cutoff:3.500A) Processing helix chain 'A' and resid 1018 through 1037 removed outlier: 3.515A pdb=" N THR A1023 " --> pdb=" O MET A1019 " (cutoff:3.500A) Processing helix chain 'A' and resid 1063 through 1065 No H-bonds generated for 'chain 'A' and resid 1063 through 1065' Processing helix chain 'A' and resid 1087 through 1098 Processing helix chain 'A' and resid 1103 through 1111 Processing helix chain 'A' and resid 1126 through 1138 removed outlier: 3.738A pdb=" N ILE A1134 " --> pdb=" O PHE A1131 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N TYR A1135 " --> pdb=" O PHE A1132 " (cutoff:3.500A) Processing helix chain 'A' and resid 1142 through 1161 removed outlier: 3.607A pdb=" N VAL A1148 " --> pdb=" O MET A1144 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N LYS A1161 " --> pdb=" O GLU A1157 " (cutoff:3.500A) Processing helix chain 'A' and resid 1170 through 1180 removed outlier: 3.840A pdb=" N GLN A1174 " --> pdb=" O LYS A1170 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N CYS A1175 " --> pdb=" O ASN A1171 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N GLU A1177 " --> pdb=" O ARG A1173 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N TYR A1178 " --> pdb=" O GLN A1174 " (cutoff:3.500A) Processing helix chain 'A' and resid 1193 through 1202 removed outlier: 4.514A pdb=" N PHE A1198 " --> pdb=" O TYR A1194 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N TRP A1199 " --> pdb=" O GLN A1195 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N TYR A1200 " --> pdb=" O TYR A1196 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N VAL A1201 " --> pdb=" O LYS A1197 " (cutoff:3.500A) Processing helix chain 'A' and resid 1205 through 1223 Processing helix chain 'A' and resid 1231 through 1259 removed outlier: 4.164A pdb=" N ALA A1258 " --> pdb=" O LEU A1254 " (cutoff:3.500A) Processing helix chain 'A' and resid 1261 through 1264 No H-bonds generated for 'chain 'A' and resid 1261 through 1264' Processing helix chain 'A' and resid 1268 through 1287 removed outlier: 3.819A pdb=" N PHE A1272 " --> pdb=" O ALA A1268 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N LEU A1275 " --> pdb=" O THR A1271 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ILE A1276 " --> pdb=" O PHE A1272 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N VAL A1277 " --> pdb=" O ASP A1273 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ASP A1283 " --> pdb=" O GLY A1279 " (cutoff:3.500A) Processing helix chain 'A' and resid 1316 through 1330 removed outlier: 3.509A pdb=" N LEU A1320 " --> pdb=" O THR A1316 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N PHE A1321 " --> pdb=" O PHE A1317 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ARG A1322 " --> pdb=" O PHE A1318 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N VAL A1323 " --> pdb=" O ARG A1319 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N MET A1324 " --> pdb=" O LEU A1320 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ARG A1325 " --> pdb=" O PHE A1321 " (cutoff:3.500A) removed outlier: 5.024A pdb=" N LEU A1326 " --> pdb=" O ARG A1322 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N VAL A1327 " --> pdb=" O VAL A1323 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N LYS A1328 " --> pdb=" O MET A1324 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N LEU A1329 " --> pdb=" O ARG A1325 " (cutoff:3.500A) Processing helix chain 'A' and resid 1337 through 1349 Processing helix chain 'A' and resid 1353 through 1372 removed outlier: 3.944A pdb=" N ILE A1357 " --> pdb=" O VAL A1353 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLN A1370 " --> pdb=" O VAL A1366 " (cutoff:3.500A) Processing helix chain 'A' and resid 1392 through 1403 Processing helix chain 'A' and resid 1408 through 1415 Processing helix chain 'A' and resid 1438 through 1470 removed outlier: 3.681A pdb=" N ILE A1441 " --> pdb=" O ASN A1438 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N PHE A1444 " --> pdb=" O ILE A1441 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N ILE A1445 " --> pdb=" O VAL A1442 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N SER A1446 " --> pdb=" O TYR A1443 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N MET A1449 " --> pdb=" O SER A1446 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N CYS A1451 " --> pdb=" O TYR A1448 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALA A1452 " --> pdb=" O MET A1449 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LEU A1454 " --> pdb=" O CYS A1451 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ILE A1455 " --> pdb=" O ALA A1452 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ILE A1456 " --> pdb=" O PHE A1453 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N VAL A1460 " --> pdb=" O ASN A1457 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N PHE A1467 " --> pdb=" O MET A1464 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N ASP A1468 " --> pdb=" O ASP A1465 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LEU A1470 " --> pdb=" O PHE A1467 " (cutoff:3.500A) Processing helix chain 'A' and resid 1479 through 1491 Processing helix chain 'A' and resid 1502 through 1510 removed outlier: 4.441A pdb=" N VAL A1506 " --> pdb=" O LEU A1503 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ARG A1510 " --> pdb=" O THR A1507 " (cutoff:3.500A) Processing helix chain 'A' and resid 1527 through 1533 removed outlier: 4.255A pdb=" N VAL A1532 " --> pdb=" O CYS A1528 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ALA A1533 " --> pdb=" O LYS A1529 " (cutoff:3.500A) Processing helix chain 'A' and resid 1546 through 1557 removed outlier: 4.423A pdb=" N LEU A1550 " --> pdb=" O ASN A1547 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N PHE A1551 " --> pdb=" O ALA A1548 " (cutoff:3.500A) Processing helix chain 'A' and resid 1566 through 1575 removed outlier: 3.937A pdb=" N ASN A1570 " --> pdb=" O LEU A1566 " (cutoff:3.500A) Processing helix chain 'A' and resid 1585 through 1588 No H-bonds generated for 'chain 'A' and resid 1585 through 1588' Processing helix chain 'D' and resid 30 through 51 removed outlier: 3.855A pdb=" N GLU D 42 " --> pdb=" O ASP D 38 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N LEU D 47 " --> pdb=" O ASP D 43 " (cutoff:3.500A) Processing helix chain 'D' and resid 54 through 64 removed outlier: 3.509A pdb=" N VAL D 58 " --> pdb=" O VAL D 54 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N TYR D 64 " --> pdb=" O ILE D 60 " (cutoff:3.500A) Processing helix chain 'D' and resid 75 through 110 removed outlier: 3.905A pdb=" N VAL D 79 " --> pdb=" O ALA D 75 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ARG D 93 " --> pdb=" O LEU D 89 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLU D 103 " --> pdb=" O ARG D 99 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ALA D 110 " --> pdb=" O LYS D 106 " (cutoff:3.500A) Processing helix chain 'D' and resid 177 through 185 removed outlier: 3.670A pdb=" N ASN D 184 " --> pdb=" O LEU D 180 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N TRP D 185 " --> pdb=" O ASN D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 187 through 199 removed outlier: 3.620A pdb=" N ASP D 190 " --> pdb=" O SER D 187 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLU D 191 " --> pdb=" O ALA D 188 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ASN D 196 " --> pdb=" O PHE D 193 " (cutoff:3.500A) Processing helix chain 'D' and resid 238 through 240 No H-bonds generated for 'chain 'D' and resid 238 through 240' Processing helix chain 'D' and resid 242 through 248 removed outlier: 3.867A pdb=" N GLY D 247 " --> pdb=" O TRP D 243 " (cutoff:3.500A) Processing helix chain 'D' and resid 262 through 264 No H-bonds generated for 'chain 'D' and resid 262 through 264' Processing helix chain 'D' and resid 267 through 282 removed outlier: 3.645A pdb=" N GLU D 281 " --> pdb=" O SER D 277 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N THR D 282 " --> pdb=" O GLU D 278 " (cutoff:3.500A) Processing helix chain 'D' and resid 312 through 324 removed outlier: 3.557A pdb=" N LYS D 316 " --> pdb=" O VAL D 312 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ASN D 324 " --> pdb=" O ASP D 320 " (cutoff:3.500A) Processing helix chain 'D' and resid 333 through 345 removed outlier: 3.715A pdb=" N LEU D 345 " --> pdb=" O PHE D 341 " (cutoff:3.500A) Processing helix chain 'D' and resid 370 through 376 Processing helix chain 'D' and resid 397 through 405 removed outlier: 3.552A pdb=" N ALA D 403 " --> pdb=" O ILE D 399 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N CYS D 404 " --> pdb=" O GLN D 400 " (cutoff:3.500A) Processing helix chain 'D' and resid 416 through 422 removed outlier: 4.340A pdb=" N ARG D 420 " --> pdb=" O GLY D 417 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ILE D 421 " --> pdb=" O ALA D 418 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ASN D 422 " --> pdb=" O ILE D 419 " (cutoff:3.500A) Processing helix chain 'D' and resid 425 through 430 removed outlier: 3.617A pdb=" N LEU D 430 " --> pdb=" O LEU D 427 " (cutoff:3.500A) Processing helix chain 'D' and resid 432 through 437 Processing helix chain 'D' and resid 439 through 441 No H-bonds generated for 'chain 'D' and resid 439 through 441' Processing helix chain 'D' and resid 494 through 500 removed outlier: 3.787A pdb=" N LEU D 500 " --> pdb=" O ASP D 496 " (cutoff:3.500A) Processing helix chain 'D' and resid 561 through 564 No H-bonds generated for 'chain 'D' and resid 561 through 564' Processing helix chain 'D' and resid 569 through 579 removed outlier: 4.111A pdb=" N GLU D 573 " --> pdb=" O ASP D 569 " (cutoff:3.500A) Processing helix chain 'D' and resid 639 through 648 removed outlier: 4.325A pdb=" N TYR D 644 " --> pdb=" O THR D 640 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N THR D 647 " --> pdb=" O ARG D 643 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N LEU D 648 " --> pdb=" O TYR D 644 " (cutoff:3.500A) Processing helix chain 'D' and resid 650 through 656 removed outlier: 4.618A pdb=" N GLU D 654 " --> pdb=" O ASP D 651 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLU D 655 " --> pdb=" O ASN D 652 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N SER D 656 " --> pdb=" O PHE D 653 " (cutoff:3.500A) Processing helix chain 'D' and resid 679 through 687 Processing helix chain 'D' and resid 700 through 718 removed outlier: 3.844A pdb=" N VAL D 705 " --> pdb=" O LEU D 701 " (cutoff:3.500A) Processing helix chain 'D' and resid 746 through 751 removed outlier: 3.632A pdb=" N GLU D 750 " --> pdb=" O GLU D 747 " (cutoff:3.500A) Processing helix chain 'D' and resid 758 through 760 No H-bonds generated for 'chain 'D' and resid 758 through 760' Processing helix chain 'D' and resid 762 through 769 removed outlier: 3.641A pdb=" N ASP D 769 " --> pdb=" O LYS D 765 " (cutoff:3.500A) Processing helix chain 'D' and resid 818 through 826 removed outlier: 3.588A pdb=" N GLU D 823 " --> pdb=" O ASN D 819 " (cutoff:3.500A) Processing helix chain 'D' and resid 875 through 877 No H-bonds generated for 'chain 'D' and resid 875 through 877' Processing helix chain 'D' and resid 880 through 888 Processing helix chain 'D' and resid 1047 through 1049 No H-bonds generated for 'chain 'D' and resid 1047 through 1049' Processing sheet with id= A, first strand: chain 'C' and resid 171 through 173 removed outlier: 3.877A pdb=" N ASP C 172 " --> pdb=" O ARG C 65 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ARG C 65 " --> pdb=" O ASP C 172 " (cutoff:3.500A) removed outlier: 7.819A pdb=" N ILE C 105 " --> pdb=" O LYS C 96 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N LYS C 98 " --> pdb=" O TRP C 103 " (cutoff:3.500A) removed outlier: 8.779A pdb=" N TRP C 103 " --> pdb=" O LYS C 98 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'C' and resid 180 through 183 removed outlier: 6.103A pdb=" N ILE C 288 " --> pdb=" O VAL C 181 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N VAL C 183 " --> pdb=" O ILE C 288 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N VAL C 290 " --> pdb=" O VAL C 183 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N VAL C 335 " --> pdb=" O PHE C 291 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'C' and resid 212 through 215 removed outlier: 6.610A pdb=" N LEU C 266 " --> pdb=" O SER C 213 " (cutoff:3.500A) removed outlier: 7.890A pdb=" N THR C 215 " --> pdb=" O LEU C 266 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N VAL C 268 " --> pdb=" O THR C 215 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'A' and resid 299 through 303 removed outlier: 3.869A pdb=" N THR A 300 " --> pdb=" O ARG A 334 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ARG A 334 " --> pdb=" O THR A 300 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 1058 through 1062 Processing sheet with id= F, first strand: chain 'D' and resid 68 through 72 Processing sheet with id= G, first strand: chain 'D' and resid 122 through 124 Processing sheet with id= H, first strand: chain 'D' and resid 165 through 167 removed outlier: 6.652A pdb=" N VAL D 466 " --> pdb=" O LEU D 485 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N VAL D 487 " --> pdb=" O LEU D 464 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N LEU D 464 " --> pdb=" O VAL D 487 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N GLY D 489 " --> pdb=" O GLY D 462 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N GLY D 462 " --> pdb=" O GLY D 489 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N ASP D 491 " --> pdb=" O ILE D 460 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N ILE D 460 " --> pdb=" O ASP D 491 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'D' and resid 298 through 300 removed outlier: 6.851A pdb=" N ASN D 355 " --> pdb=" O ASP D 253 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N LEU D 255 " --> pdb=" O ASN D 355 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N ILE D 357 " --> pdb=" O LEU D 255 " (cutoff:3.500A) removed outlier: 7.589A pdb=" N LEU D 257 " --> pdb=" O ILE D 357 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N MET D 359 " --> pdb=" O LEU D 257 " (cutoff:3.500A) removed outlier: 7.318A pdb=" N ASP D 259 " --> pdb=" O MET D 359 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N PHE D 361 " --> pdb=" O ASP D 259 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N ARG D 383 " --> pdb=" O ILE D 358 " (cutoff:3.500A) removed outlier: 7.716A pdb=" N LEU D 360 " --> pdb=" O ARG D 383 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N PHE D 385 " --> pdb=" O LEU D 360 " (cutoff:3.500A) removed outlier: 7.768A pdb=" N THR D 362 " --> pdb=" O PHE D 385 " (cutoff:3.500A) removed outlier: 5.707A pdb=" N PHE D 387 " --> pdb=" O THR D 362 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'D' and resid 511 through 515 Processing sheet with id= K, first strand: chain 'D' and resid 741 through 743 removed outlier: 6.297A pdb=" N LYS D 815 " --> pdb=" O LYS D 730 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N ARG D 732 " --> pdb=" O GLY D 813 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N GLY D 813 " --> pdb=" O ARG D 732 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N VAL D 734 " --> pdb=" O VAL D 811 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N VAL D 811 " --> pdb=" O VAL D 734 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N MET D 793 " --> pdb=" O THR D 776 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'D' and resid 848 through 854 removed outlier: 4.249A pdb=" N GLU D1019 " --> pdb=" O ILE D1002 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N ILE D1002 " --> pdb=" O GLU D1019 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'D' and resid 892 through 899 removed outlier: 4.000A pdb=" N ILE D 975 " --> pdb=" O SER D1038 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'D' and resid 150 through 152 removed outlier: 4.151A pdb=" N ASP D 152 " --> pdb=" O ARG D 157 " (cutoff:3.500A) removed outlier: 5.380A pdb=" N ARG D 157 " --> pdb=" O ASP D 152 " (cutoff:3.500A) 819 hydrogen bonds defined for protein. 2208 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: 7.06 Time building geometry restraints manager: 9.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 3596 1.33 - 1.45: 5346 1.45 - 1.57: 11719 1.57 - 1.69: 17 1.69 - 1.82: 176 Bond restraints: 20854 Sorted by residual: bond pdb=" C1 NAG B 1 " pdb=" O5 NAG B 1 " ideal model delta sigma weight residual 1.406 1.492 -0.086 2.00e-02 2.50e+03 1.84e+01 bond pdb=" C1 NAG G 3 " pdb=" O5 NAG G 3 " ideal model delta sigma weight residual 1.406 1.489 -0.083 2.00e-02 2.50e+03 1.72e+01 bond pdb=" C1 NAG I 1 " pdb=" O5 NAG I 1 " ideal model delta sigma weight residual 1.406 1.465 -0.059 2.00e-02 2.50e+03 8.78e+00 bond pdb=" C6 CLR A2203 " pdb=" C7 CLR A2203 " ideal model delta sigma weight residual 1.492 1.540 -0.048 2.00e-02 2.50e+03 5.67e+00 bond pdb=" C6 CLR A2205 " pdb=" C7 CLR A2205 " ideal model delta sigma weight residual 1.492 1.539 -0.047 2.00e-02 2.50e+03 5.50e+00 ... (remaining 20849 not shown) Histogram of bond angle deviations from ideal: 97.69 - 104.96: 334 104.96 - 112.23: 10369 112.23 - 119.51: 7087 119.51 - 126.78: 10213 126.78 - 134.05: 250 Bond angle restraints: 28253 Sorted by residual: angle pdb=" N GLU C 351 " pdb=" CA GLU C 351 " pdb=" CB GLU C 351 " ideal model delta sigma weight residual 110.28 117.24 -6.96 1.55e+00 4.16e-01 2.02e+01 angle pdb=" N CYS A 333 " pdb=" CA CYS A 333 " pdb=" C CYS A 333 " ideal model delta sigma weight residual 109.40 116.35 -6.95 1.63e+00 3.76e-01 1.82e+01 angle pdb=" N THR A 331 " pdb=" CA THR A 331 " pdb=" C THR A 331 " ideal model delta sigma weight residual 109.50 115.57 -6.07 1.58e+00 4.01e-01 1.47e+01 angle pdb=" C ALA C 350 " pdb=" N GLU C 351 " pdb=" CA GLU C 351 " ideal model delta sigma weight residual 120.31 115.10 5.21 1.52e+00 4.33e-01 1.18e+01 angle pdb=" CA GLU C 351 " pdb=" CB GLU C 351 " pdb=" CG GLU C 351 " ideal model delta sigma weight residual 114.10 120.38 -6.28 2.00e+00 2.50e-01 9.85e+00 ... (remaining 28248 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.76: 11900 22.76 - 45.53: 784 45.53 - 68.29: 123 68.29 - 91.05: 31 91.05 - 113.81: 35 Dihedral angle restraints: 12873 sinusoidal: 5556 harmonic: 7317 Sorted by residual: dihedral pdb=" CB CYS D 667 " pdb=" SG CYS D 667 " pdb=" SG CYS D 697 " pdb=" CB CYS D 697 " ideal model delta sinusoidal sigma weight residual -86.00 -21.20 -64.80 1 1.00e+01 1.00e-02 5.51e+01 dihedral pdb=" CB CYS D 404 " pdb=" SG CYS D 404 " pdb=" SG CYS D1071 " pdb=" CB CYS D1071 " ideal model delta sinusoidal sigma weight residual 93.00 49.80 43.20 1 1.00e+01 1.00e-02 2.60e+01 dihedral pdb=" CB CYS A 317 " pdb=" SG CYS A 317 " pdb=" SG CYS A 333 " pdb=" CB CYS A 333 " ideal model delta sinusoidal sigma weight residual -86.00 -125.52 39.52 1 1.00e+01 1.00e-02 2.19e+01 ... (remaining 12870 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.128: 3198 0.128 - 0.257: 21 0.257 - 0.385: 12 0.385 - 0.514: 2 0.514 - 0.642: 1 Chirality restraints: 3234 Sorted by residual: chirality pdb=" C1 NAG F 1 " pdb=" ND2 ASN D 348 " pdb=" C2 NAG F 1 " pdb=" O5 NAG F 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.76 -0.64 2.00e-01 2.50e+01 1.03e+01 chirality pdb=" C1 NAG I 1 " pdb=" ND2 ASN D 895 " pdb=" C2 NAG I 1 " pdb=" O5 NAG I 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.92 -0.48 2.00e-01 2.50e+01 5.66e+00 chirality pdb=" C17 CLR A2203 " pdb=" C13 CLR A2203 " pdb=" C16 CLR A2203 " pdb=" C20 CLR A2203 " both_signs ideal model delta sigma weight residual False 2.55 2.94 -0.39 2.00e-01 2.50e+01 3.75e+00 ... (remaining 3231 not shown) Planarity restraints: 3561 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C CYS C 328 " -0.075 5.00e-02 4.00e+02 1.12e-01 2.02e+01 pdb=" N PRO C 329 " 0.194 5.00e-02 4.00e+02 pdb=" CA PRO C 329 " -0.060 5.00e-02 4.00e+02 pdb=" CD PRO C 329 " -0.059 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 254 " -0.070 5.00e-02 4.00e+02 1.05e-01 1.78e+01 pdb=" N PRO A 255 " 0.182 5.00e-02 4.00e+02 pdb=" CA PRO A 255 " -0.055 5.00e-02 4.00e+02 pdb=" CD PRO A 255 " -0.057 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASN D 613 " -0.024 2.00e-02 2.50e+03 2.24e-02 6.29e+00 pdb=" CG ASN D 613 " 0.021 2.00e-02 2.50e+03 pdb=" OD1 ASN D 613 " 0.001 2.00e-02 2.50e+03 pdb=" ND2 ASN D 613 " 0.028 2.00e-02 2.50e+03 pdb=" C1 NAG H 1 " -0.027 2.00e-02 2.50e+03 ... (remaining 3558 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 571 2.71 - 3.26: 20798 3.26 - 3.81: 31205 3.81 - 4.35: 41142 4.35 - 4.90: 67468 Nonbonded interactions: 161184 Sorted by model distance: nonbonded pdb=" O4 NAG F 2 " pdb=" O7 NAG F 2 " model vdw 2.167 2.440 nonbonded pdb=" O VAL A 390 " pdb=" OG SER A 394 " model vdw 2.169 2.440 nonbonded pdb=" OG SER C 186 " pdb=" OG1 THR C 193 " model vdw 2.208 2.440 nonbonded pdb=" O TYR A1364 " pdb=" OH TYR A1443 " model vdw 2.242 2.440 nonbonded pdb=" OG SER C 69 " pdb=" OE1 GLU C 88 " model vdw 2.256 2.440 ... (remaining 161179 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'F' selection = chain 'H' selection = chain 'I' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.050 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: 5.860 Check model and map are aligned: 0.260 Set scattering table: 0.160 Process input model: 55.390 Find NCS groups from input model: 0.560 Set up NCS constraints: 0.110 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:14.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 77.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 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 : 0.004 0.086 20854 Z= 0.231 Angle : 0.579 8.743 28253 Z= 0.282 Chirality : 0.049 0.642 3234 Planarity : 0.004 0.112 3554 Dihedral : 16.292 113.814 8107 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.41 % Favored : 95.51 % Rotamer: Outliers : 0.09 % Allowed : 0.36 % Favored : 99.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (0.16), residues: 2472 helix: -0.30 (0.15), residues: 1198 sheet: -0.55 (0.32), residues: 258 loop : -1.14 (0.19), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1103 HIS 0.003 0.001 HIS A 632 PHE 0.028 0.001 PHE A 293 TYR 0.012 0.001 TYR D 512 ARG 0.003 0.000 ARG A1319 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 2210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 317 time to evaluate : 2.136 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 107 ARG cc_start: 0.1531 (mtt-85) cc_final: 0.0788 (mtp180) REVERT: C 196 MET cc_start: 0.4327 (ttt) cc_final: 0.4009 (pp-130) REVERT: A 332 GLU cc_start: 0.7733 (OUTLIER) cc_final: 0.7252 (pt0) REVERT: A 1210 MET cc_start: 0.5928 (tpt) cc_final: 0.4454 (tmt) REVERT: A 1449 MET cc_start: 0.8405 (mtm) cc_final: 0.8170 (mtm) REVERT: A 1545 MET cc_start: 0.3788 (mmt) cc_final: 0.3301 (ppp) outliers start: 2 outliers final: 1 residues processed: 319 average time/residue: 1.1163 time to fit residues: 409.5958 Evaluate side-chains 241 residues out of total 2210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 239 time to evaluate : 2.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 332 GLU Chi-restraints excluded: chain A residue 334 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 210 optimal weight: 0.9980 chunk 188 optimal weight: 1.9990 chunk 104 optimal weight: 3.9990 chunk 64 optimal weight: 5.9990 chunk 127 optimal weight: 5.9990 chunk 100 optimal weight: 0.4980 chunk 195 optimal weight: 0.0070 chunk 75 optimal weight: 4.9990 chunk 118 optimal weight: 7.9990 chunk 145 optimal weight: 20.0000 chunk 226 optimal weight: 0.9990 overall best weight: 0.9002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1035 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1172 GLN ** A1466 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 41 GLN ** D 675 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 824 ASN D 972 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.1094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 20854 Z= 0.176 Angle : 0.588 10.863 28253 Z= 0.288 Chirality : 0.044 0.405 3234 Planarity : 0.004 0.078 3554 Dihedral : 12.403 105.083 3299 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.37 % Favored : 95.55 % Rotamer: Outliers : 1.86 % Allowed : 10.81 % Favored : 87.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.17), residues: 2472 helix: 0.32 (0.15), residues: 1206 sheet: -0.34 (0.31), residues: 271 loop : -1.18 (0.20), residues: 995 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 357 HIS 0.004 0.001 HIS D1004 PHE 0.016 0.001 PHE D 686 TYR 0.010 0.001 TYR D 409 ARG 0.006 0.000 ARG D 157 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 2210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 258 time to evaluate : 2.110 Fit side-chains revert: symmetry clash REVERT: C 107 ARG cc_start: 0.1479 (mtt-85) cc_final: 0.0763 (mtm110) REVERT: C 196 MET cc_start: 0.4027 (ttt) cc_final: 0.3752 (pp-130) REVERT: C 307 ARG cc_start: 0.4082 (mmm160) cc_final: 0.3248 (mmt90) REVERT: A 242 PHE cc_start: 0.8830 (m-80) cc_final: 0.8607 (m-80) REVERT: A 1053 GLU cc_start: 0.7413 (OUTLIER) cc_final: 0.7151 (mt-10) REVERT: A 1208 GLU cc_start: 0.7197 (pp20) cc_final: 0.6938 (pp20) REVERT: A 1210 MET cc_start: 0.5795 (tpt) cc_final: 0.4652 (tmt) REVERT: A 1269 TRP cc_start: 0.7698 (OUTLIER) cc_final: 0.5714 (m-90) REVERT: A 1370 GLN cc_start: 0.7656 (OUTLIER) cc_final: 0.6430 (mt0) REVERT: D 803 GLN cc_start: 0.7555 (mp-120) cc_final: 0.7273 (mm-40) REVERT: D 883 MET cc_start: 0.8220 (tpt) cc_final: 0.8009 (tpt) REVERT: D 985 ASN cc_start: 0.7156 (OUTLIER) cc_final: 0.6617 (m-40) outliers start: 41 outliers final: 14 residues processed: 282 average time/residue: 1.1076 time to fit residues: 360.7553 Evaluate side-chains 253 residues out of total 2210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 235 time to evaluate : 2.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 882 LEU Chi-restraints excluded: chain A residue 892 ILE Chi-restraints excluded: chain A residue 1028 MET Chi-restraints excluded: chain A residue 1053 GLU Chi-restraints excluded: chain A residue 1219 THR Chi-restraints excluded: chain A residue 1269 TRP Chi-restraints excluded: chain A residue 1370 GLN Chi-restraints excluded: chain A residue 1456 ILE Chi-restraints excluded: chain D residue 536 ILE Chi-restraints excluded: chain D residue 673 SER Chi-restraints excluded: chain D residue 741 THR Chi-restraints excluded: chain D residue 771 ASP Chi-restraints excluded: chain D residue 798 VAL Chi-restraints excluded: chain D residue 851 VAL Chi-restraints excluded: chain D residue 881 SER Chi-restraints excluded: chain D residue 985 ASN Chi-restraints excluded: chain D residue 1009 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 125 optimal weight: 7.9990 chunk 70 optimal weight: 0.9990 chunk 188 optimal weight: 4.9990 chunk 153 optimal weight: 0.8980 chunk 62 optimal weight: 20.0000 chunk 226 optimal weight: 0.7980 chunk 244 optimal weight: 0.9980 chunk 201 optimal weight: 4.9990 chunk 224 optimal weight: 0.3980 chunk 77 optimal weight: 0.8980 chunk 181 optimal weight: 0.0670 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 953 ASN A1035 GLN A1466 ASN ** D 675 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.1439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 20854 Z= 0.141 Angle : 0.541 12.882 28253 Z= 0.259 Chirality : 0.042 0.267 3234 Planarity : 0.004 0.065 3554 Dihedral : 10.767 105.627 3292 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.29 % Favored : 95.63 % Rotamer: Outliers : 1.86 % Allowed : 14.07 % Favored : 84.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.17), residues: 2472 helix: 0.59 (0.15), residues: 1202 sheet: -0.23 (0.31), residues: 277 loop : -1.13 (0.20), residues: 993 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 205 HIS 0.004 0.000 HIS D1004 PHE 0.023 0.001 PHE A1147 TYR 0.010 0.001 TYR D 719 ARG 0.005 0.000 ARG D1029 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 2210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 257 time to evaluate : 2.187 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 107 ARG cc_start: 0.1543 (mtt-85) cc_final: 0.0910 (mtm110) REVERT: C 343 GLU cc_start: 0.5963 (OUTLIER) cc_final: 0.5709 (mm-30) REVERT: A 293 PHE cc_start: 0.8278 (OUTLIER) cc_final: 0.6192 (p90) REVERT: A 373 MET cc_start: 0.7903 (mmt) cc_final: 0.7365 (mmp) REVERT: A 402 LEU cc_start: 0.8335 (tp) cc_final: 0.8115 (mm) REVERT: A 562 LEU cc_start: 0.8288 (mm) cc_final: 0.8041 (mm) REVERT: A 953 ASN cc_start: 0.5881 (OUTLIER) cc_final: 0.5394 (p0) REVERT: A 1143 MET cc_start: 0.7858 (tpp) cc_final: 0.7645 (mpp) REVERT: A 1208 GLU cc_start: 0.7185 (pp20) cc_final: 0.6942 (pp20) REVERT: A 1269 TRP cc_start: 0.7649 (OUTLIER) cc_final: 0.5584 (m-90) REVERT: A 1534 MET cc_start: 0.5252 (mpp) cc_final: 0.4076 (pmt) REVERT: D 279 MET cc_start: 0.8407 (OUTLIER) cc_final: 0.8067 (tpp) REVERT: D 803 GLN cc_start: 0.7590 (mp-120) cc_final: 0.7286 (mm-40) REVERT: D 883 MET cc_start: 0.8245 (tpt) cc_final: 0.7990 (tpt) REVERT: D 985 ASN cc_start: 0.7097 (OUTLIER) cc_final: 0.6564 (m-40) REVERT: D 1017 MET cc_start: 0.7155 (ttm) cc_final: 0.6951 (ttm) outliers start: 41 outliers final: 12 residues processed: 281 average time/residue: 1.1207 time to fit residues: 365.8756 Evaluate side-chains 262 residues out of total 2210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 244 time to evaluate : 2.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 343 GLU Chi-restraints excluded: chain A residue 293 PHE Chi-restraints excluded: chain A residue 882 LEU Chi-restraints excluded: chain A residue 892 ILE Chi-restraints excluded: chain A residue 953 ASN Chi-restraints excluded: chain A residue 1269 TRP Chi-restraints excluded: chain A residue 1454 LEU Chi-restraints excluded: chain A residue 1456 ILE Chi-restraints excluded: chain D residue 42 GLU Chi-restraints excluded: chain D residue 232 LYS Chi-restraints excluded: chain D residue 279 MET Chi-restraints excluded: chain D residue 536 ILE Chi-restraints excluded: chain D residue 673 SER Chi-restraints excluded: chain D residue 741 THR Chi-restraints excluded: chain D residue 851 VAL Chi-restraints excluded: chain D residue 985 ASN Chi-restraints excluded: chain D residue 1009 MET Chi-restraints excluded: chain D residue 1011 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 223 optimal weight: 0.5980 chunk 170 optimal weight: 0.7980 chunk 117 optimal weight: 8.9990 chunk 25 optimal weight: 0.9980 chunk 108 optimal weight: 0.6980 chunk 152 optimal weight: 6.9990 chunk 227 optimal weight: 5.9990 chunk 240 optimal weight: 4.9990 chunk 118 optimal weight: 2.9990 chunk 215 optimal weight: 0.8980 chunk 64 optimal weight: 5.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 140 ASN A 953 ASN ** D 675 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.1570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 20854 Z= 0.152 Angle : 0.530 12.805 28253 Z= 0.256 Chirality : 0.042 0.265 3234 Planarity : 0.004 0.059 3554 Dihedral : 10.068 105.356 3292 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.37 % Favored : 95.55 % Rotamer: Outliers : 2.26 % Allowed : 15.38 % Favored : 82.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.17), residues: 2472 helix: 0.70 (0.15), residues: 1204 sheet: -0.24 (0.31), residues: 278 loop : -1.13 (0.20), residues: 990 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1103 HIS 0.002 0.000 HIS A 632 PHE 0.029 0.001 PHE A1212 TYR 0.009 0.001 TYR A 954 ARG 0.006 0.000 ARG A 984 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 2210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 245 time to evaluate : 2.243 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 107 ARG cc_start: 0.1533 (mtt-85) cc_final: 0.0931 (mtm110) REVERT: C 254 ILE cc_start: 0.3840 (mt) cc_final: 0.3591 (mm) REVERT: C 255 GLU cc_start: 0.2851 (OUTLIER) cc_final: 0.2027 (tt0) REVERT: C 343 GLU cc_start: 0.6013 (OUTLIER) cc_final: 0.5475 (pt0) REVERT: A 293 PHE cc_start: 0.8341 (OUTLIER) cc_final: 0.6361 (p90) REVERT: A 312 GLU cc_start: 0.6509 (pm20) cc_final: 0.6296 (pt0) REVERT: A 373 MET cc_start: 0.7969 (mmt) cc_final: 0.7508 (mmm) REVERT: A 417 LYS cc_start: 0.5321 (OUTLIER) cc_final: 0.4623 (mptp) REVERT: A 562 LEU cc_start: 0.8352 (mm) cc_final: 0.8119 (mm) REVERT: A 1208 GLU cc_start: 0.7183 (pp20) cc_final: 0.6934 (pp20) REVERT: A 1262 LYS cc_start: 0.6932 (pptt) cc_final: 0.6172 (mmtt) REVERT: A 1269 TRP cc_start: 0.7644 (OUTLIER) cc_final: 0.5480 (m-90) REVERT: A 1534 MET cc_start: 0.5243 (mpp) cc_final: 0.4073 (pmt) REVERT: D 279 MET cc_start: 0.8458 (OUTLIER) cc_final: 0.8183 (tpp) REVERT: D 667 CYS cc_start: 0.2116 (OUTLIER) cc_final: 0.1910 (t) REVERT: D 803 GLN cc_start: 0.7614 (mp-120) cc_final: 0.7269 (mm-40) REVERT: D 1017 MET cc_start: 0.7326 (ttm) cc_final: 0.7056 (ttm) outliers start: 50 outliers final: 22 residues processed: 281 average time/residue: 1.1346 time to fit residues: 368.4070 Evaluate side-chains 264 residues out of total 2210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 235 time to evaluate : 2.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 255 GLU Chi-restraints excluded: chain C residue 343 GLU Chi-restraints excluded: chain A residue 293 PHE Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 417 LYS Chi-restraints excluded: chain A residue 882 LEU Chi-restraints excluded: chain A residue 892 ILE Chi-restraints excluded: chain A residue 953 ASN Chi-restraints excluded: chain A residue 1028 MET Chi-restraints excluded: chain A residue 1156 GLN Chi-restraints excluded: chain A residue 1224 MET Chi-restraints excluded: chain A residue 1256 VAL Chi-restraints excluded: chain A residue 1269 TRP Chi-restraints excluded: chain A residue 1360 LEU Chi-restraints excluded: chain A residue 1370 GLN Chi-restraints excluded: chain A residue 1454 LEU Chi-restraints excluded: chain A residue 1456 ILE Chi-restraints excluded: chain D residue 42 GLU Chi-restraints excluded: chain D residue 232 LYS Chi-restraints excluded: chain D residue 279 MET Chi-restraints excluded: chain D residue 284 SER Chi-restraints excluded: chain D residue 297 ASN Chi-restraints excluded: chain D residue 667 CYS Chi-restraints excluded: chain D residue 673 SER Chi-restraints excluded: chain D residue 741 THR Chi-restraints excluded: chain D residue 851 VAL Chi-restraints excluded: chain D residue 1009 MET Chi-restraints excluded: chain D residue 1011 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 200 optimal weight: 0.8980 chunk 136 optimal weight: 2.9990 chunk 3 optimal weight: 10.0000 chunk 179 optimal weight: 3.9990 chunk 99 optimal weight: 3.9990 chunk 205 optimal weight: 3.9990 chunk 166 optimal weight: 3.9990 chunk 0 optimal weight: 40.0000 chunk 122 optimal weight: 7.9990 chunk 216 optimal weight: 0.7980 chunk 60 optimal weight: 9.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 444 GLN A 953 ASN A1145 ASN D 41 GLN ** D 675 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.1690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 20854 Z= 0.322 Angle : 0.609 10.734 28253 Z= 0.299 Chirality : 0.046 0.281 3234 Planarity : 0.004 0.055 3554 Dihedral : 10.019 105.059 3292 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.85 % Favored : 95.06 % Rotamer: Outliers : 3.21 % Allowed : 15.79 % Favored : 81.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.17), residues: 2472 helix: 0.51 (0.15), residues: 1211 sheet: -0.35 (0.31), residues: 278 loop : -1.25 (0.20), residues: 983 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 113 HIS 0.003 0.001 HIS D 306 PHE 0.027 0.002 PHE A1212 TYR 0.018 0.002 TYR D1068 ARG 0.009 0.001 ARG A 984 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 2210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 255 time to evaluate : 2.089 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 177 MET cc_start: 0.0134 (pp-130) cc_final: -0.0090 (ppp) REVERT: C 254 ILE cc_start: 0.3818 (mt) cc_final: 0.3616 (mm) REVERT: C 255 GLU cc_start: 0.2801 (OUTLIER) cc_final: 0.2030 (tt0) REVERT: C 304 ILE cc_start: 0.5461 (mm) cc_final: 0.5149 (tt) REVERT: C 343 GLU cc_start: 0.5901 (OUTLIER) cc_final: 0.5468 (pt0) REVERT: A 291 GLU cc_start: 0.7620 (OUTLIER) cc_final: 0.7090 (mp0) REVERT: A 293 PHE cc_start: 0.8804 (OUTLIER) cc_final: 0.6746 (p90) REVERT: A 308 ILE cc_start: 0.8420 (OUTLIER) cc_final: 0.8209 (mt) REVERT: A 373 MET cc_start: 0.8025 (mmt) cc_final: 0.7600 (mmp) REVERT: A 1199 TRP cc_start: 0.6752 (OUTLIER) cc_final: 0.5592 (t60) REVERT: A 1269 TRP cc_start: 0.7717 (OUTLIER) cc_final: 0.5532 (m-90) REVERT: D 199 GLU cc_start: 0.7127 (OUTLIER) cc_final: 0.6858 (mt-10) REVERT: D 279 MET cc_start: 0.8492 (OUTLIER) cc_final: 0.8178 (tpp) REVERT: D 803 GLN cc_start: 0.7631 (mp-120) cc_final: 0.7253 (mm-40) REVERT: D 985 ASN cc_start: 0.7252 (OUTLIER) cc_final: 0.6797 (m-40) outliers start: 71 outliers final: 33 residues processed: 294 average time/residue: 1.1730 time to fit residues: 397.8295 Evaluate side-chains 276 residues out of total 2210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 233 time to evaluate : 2.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 255 GLU Chi-restraints excluded: chain C residue 343 GLU Chi-restraints excluded: chain A residue 170 ILE Chi-restraints excluded: chain A residue 291 GLU Chi-restraints excluded: chain A residue 293 PHE Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 394 SER Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 882 LEU Chi-restraints excluded: chain A residue 892 ILE Chi-restraints excluded: chain A residue 929 ILE Chi-restraints excluded: chain A residue 953 ASN Chi-restraints excluded: chain A residue 1028 MET Chi-restraints excluded: chain A residue 1053 GLU Chi-restraints excluded: chain A residue 1156 GLN Chi-restraints excluded: chain A residue 1199 TRP Chi-restraints excluded: chain A residue 1256 VAL Chi-restraints excluded: chain A residue 1269 TRP Chi-restraints excluded: chain A residue 1324 MET Chi-restraints excluded: chain A residue 1370 GLN Chi-restraints excluded: chain A residue 1416 LEU Chi-restraints excluded: chain A residue 1454 LEU Chi-restraints excluded: chain A residue 1456 ILE Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 42 GLU Chi-restraints excluded: chain D residue 199 GLU Chi-restraints excluded: chain D residue 232 LYS Chi-restraints excluded: chain D residue 255 LEU Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 279 MET Chi-restraints excluded: chain D residue 284 SER Chi-restraints excluded: chain D residue 536 ILE Chi-restraints excluded: chain D residue 591 LEU Chi-restraints excluded: chain D residue 673 SER Chi-restraints excluded: chain D residue 741 THR Chi-restraints excluded: chain D residue 798 VAL Chi-restraints excluded: chain D residue 826 THR Chi-restraints excluded: chain D residue 851 VAL Chi-restraints excluded: chain D residue 881 SER Chi-restraints excluded: chain D residue 985 ASN Chi-restraints excluded: chain D residue 1011 THR Chi-restraints excluded: chain D residue 1057 ASP Chi-restraints excluded: chain D residue 1064 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 80 optimal weight: 0.8980 chunk 216 optimal weight: 0.0970 chunk 47 optimal weight: 0.8980 chunk 141 optimal weight: 0.7980 chunk 59 optimal weight: 10.0000 chunk 240 optimal weight: 5.9990 chunk 199 optimal weight: 0.4980 chunk 111 optimal weight: 0.7980 chunk 20 optimal weight: 30.0000 chunk 79 optimal weight: 2.9990 chunk 126 optimal weight: 5.9990 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 547 GLN A 690 ASN A 953 ASN A 996 ASN D 41 GLN ** D 675 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.1802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.059 20854 Z= 0.143 Angle : 0.540 10.893 28253 Z= 0.263 Chirality : 0.042 0.264 3234 Planarity : 0.004 0.053 3554 Dihedral : 9.491 105.559 3292 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.29 % Favored : 95.63 % Rotamer: Outliers : 2.31 % Allowed : 17.60 % Favored : 80.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.17), residues: 2472 helix: 0.79 (0.15), residues: 1194 sheet: -0.29 (0.31), residues: 275 loop : -1.12 (0.20), residues: 1003 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1103 HIS 0.002 0.000 HIS C 348 PHE 0.025 0.001 PHE A1212 TYR 0.010 0.001 TYR D 512 ARG 0.006 0.000 ARG D1029 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 2210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 242 time to evaluate : 2.185 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 107 ARG cc_start: 0.1297 (mtt-85) cc_final: 0.0772 (mtp180) REVERT: C 115 ILE cc_start: 0.2718 (tt) cc_final: 0.2389 (tp) REVERT: C 255 GLU cc_start: 0.2994 (OUTLIER) cc_final: 0.2174 (tt0) REVERT: C 304 ILE cc_start: 0.5589 (mm) cc_final: 0.5232 (tt) REVERT: C 343 GLU cc_start: 0.5946 (OUTLIER) cc_final: 0.5465 (pt0) REVERT: A 291 GLU cc_start: 0.7666 (OUTLIER) cc_final: 0.7126 (mp0) REVERT: A 293 PHE cc_start: 0.8700 (OUTLIER) cc_final: 0.6801 (p90) REVERT: A 373 MET cc_start: 0.8038 (mmt) cc_final: 0.7678 (mmt) REVERT: A 1199 TRP cc_start: 0.6677 (OUTLIER) cc_final: 0.5200 (t60) REVERT: A 1269 TRP cc_start: 0.7676 (OUTLIER) cc_final: 0.5521 (m-90) REVERT: A 1324 MET cc_start: 0.7604 (OUTLIER) cc_final: 0.7296 (tpp) REVERT: A 1534 MET cc_start: 0.5227 (mpp) cc_final: 0.3992 (pmt) REVERT: D 199 GLU cc_start: 0.7148 (OUTLIER) cc_final: 0.6840 (mt-10) REVERT: D 803 GLN cc_start: 0.7588 (mp-120) cc_final: 0.7270 (mm-40) REVERT: D 843 ARG cc_start: 0.6570 (tpp80) cc_final: 0.5040 (tpp80) REVERT: D 883 MET cc_start: 0.8337 (tpt) cc_final: 0.8107 (tpt) REVERT: D 985 ASN cc_start: 0.7281 (OUTLIER) cc_final: 0.6780 (m-40) outliers start: 51 outliers final: 21 residues processed: 277 average time/residue: 1.1227 time to fit residues: 359.8995 Evaluate side-chains 260 residues out of total 2210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 230 time to evaluate : 2.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 255 GLU Chi-restraints excluded: chain C residue 343 GLU Chi-restraints excluded: chain A residue 170 ILE Chi-restraints excluded: chain A residue 291 GLU Chi-restraints excluded: chain A residue 293 PHE Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 690 ASN Chi-restraints excluded: chain A residue 882 LEU Chi-restraints excluded: chain A residue 892 ILE Chi-restraints excluded: chain A residue 1028 MET Chi-restraints excluded: chain A residue 1199 TRP Chi-restraints excluded: chain A residue 1269 TRP Chi-restraints excluded: chain A residue 1324 MET Chi-restraints excluded: chain A residue 1360 LEU Chi-restraints excluded: chain A residue 1370 GLN Chi-restraints excluded: chain A residue 1456 ILE Chi-restraints excluded: chain D residue 42 GLU Chi-restraints excluded: chain D residue 199 GLU Chi-restraints excluded: chain D residue 255 LEU Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 297 ASN Chi-restraints excluded: chain D residue 591 LEU Chi-restraints excluded: chain D residue 673 SER Chi-restraints excluded: chain D residue 741 THR Chi-restraints excluded: chain D residue 851 VAL Chi-restraints excluded: chain D residue 881 SER Chi-restraints excluded: chain D residue 985 ASN Chi-restraints excluded: chain D residue 1009 MET Chi-restraints excluded: chain D residue 1011 THR Chi-restraints excluded: chain D residue 1064 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 232 optimal weight: 8.9990 chunk 27 optimal weight: 9.9990 chunk 137 optimal weight: 0.0980 chunk 175 optimal weight: 0.9990 chunk 136 optimal weight: 0.5980 chunk 202 optimal weight: 2.9990 chunk 134 optimal weight: 0.7980 chunk 239 optimal weight: 9.9990 chunk 150 optimal weight: 6.9990 chunk 146 optimal weight: 2.9990 chunk 110 optimal weight: 2.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 745 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 754 ASN A 953 ASN ** D 675 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.1853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 20854 Z= 0.181 Angle : 0.555 11.244 28253 Z= 0.270 Chirality : 0.043 0.268 3234 Planarity : 0.004 0.052 3554 Dihedral : 9.311 105.284 3292 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.41 % Favored : 95.51 % Rotamer: Outliers : 2.17 % Allowed : 18.37 % Favored : 79.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.17), residues: 2472 helix: 0.80 (0.15), residues: 1200 sheet: -0.31 (0.31), residues: 280 loop : -1.11 (0.20), residues: 992 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1103 HIS 0.002 0.000 HIS A 159 PHE 0.021 0.001 PHE D 686 TYR 0.011 0.001 TYR D1068 ARG 0.006 0.000 ARG D1029 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 2210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 235 time to evaluate : 2.338 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 107 ARG cc_start: 0.1292 (mtt-85) cc_final: 0.0779 (mtp-110) REVERT: C 115 ILE cc_start: 0.2708 (tt) cc_final: 0.2422 (tp) REVERT: C 255 GLU cc_start: 0.2985 (OUTLIER) cc_final: 0.2124 (tt0) REVERT: C 304 ILE cc_start: 0.5518 (mm) cc_final: 0.5130 (tt) REVERT: C 343 GLU cc_start: 0.6007 (OUTLIER) cc_final: 0.5496 (pt0) REVERT: A 291 GLU cc_start: 0.7593 (OUTLIER) cc_final: 0.7063 (mp0) REVERT: A 293 PHE cc_start: 0.8720 (OUTLIER) cc_final: 0.6732 (p90) REVERT: A 373 MET cc_start: 0.8050 (mmt) cc_final: 0.7625 (mmm) REVERT: A 1199 TRP cc_start: 0.6681 (OUTLIER) cc_final: 0.5196 (t60) REVERT: A 1269 TRP cc_start: 0.7674 (OUTLIER) cc_final: 0.5592 (m-90) REVERT: A 1534 MET cc_start: 0.5220 (mpp) cc_final: 0.4005 (pmt) REVERT: D 199 GLU cc_start: 0.7165 (OUTLIER) cc_final: 0.6846 (mt-10) REVERT: D 803 GLN cc_start: 0.7554 (mp-120) cc_final: 0.7224 (mm-40) REVERT: D 843 ARG cc_start: 0.6558 (tpp80) cc_final: 0.5110 (tpp80) REVERT: D 985 ASN cc_start: 0.7282 (OUTLIER) cc_final: 0.6773 (m-40) outliers start: 48 outliers final: 25 residues processed: 264 average time/residue: 1.1197 time to fit residues: 343.3066 Evaluate side-chains 262 residues out of total 2210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 229 time to evaluate : 2.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 255 GLU Chi-restraints excluded: chain C residue 343 GLU Chi-restraints excluded: chain A residue 291 GLU Chi-restraints excluded: chain A residue 293 PHE Chi-restraints excluded: chain A residue 394 SER Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 882 LEU Chi-restraints excluded: chain A residue 892 ILE Chi-restraints excluded: chain A residue 1028 MET Chi-restraints excluded: chain A residue 1199 TRP Chi-restraints excluded: chain A residue 1220 LEU Chi-restraints excluded: chain A residue 1269 TRP Chi-restraints excluded: chain A residue 1324 MET Chi-restraints excluded: chain A residue 1360 LEU Chi-restraints excluded: chain A residue 1370 GLN Chi-restraints excluded: chain A residue 1456 ILE Chi-restraints excluded: chain A residue 1544 VAL Chi-restraints excluded: chain D residue 42 GLU Chi-restraints excluded: chain D residue 199 GLU Chi-restraints excluded: chain D residue 232 LYS Chi-restraints excluded: chain D residue 255 LEU Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 284 SER Chi-restraints excluded: chain D residue 591 LEU Chi-restraints excluded: chain D residue 673 SER Chi-restraints excluded: chain D residue 741 THR Chi-restraints excluded: chain D residue 771 ASP Chi-restraints excluded: chain D residue 798 VAL Chi-restraints excluded: chain D residue 851 VAL Chi-restraints excluded: chain D residue 985 ASN Chi-restraints excluded: chain D residue 1011 THR Chi-restraints excluded: chain D residue 1064 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 50.9307 > 50: distance: 56 - 77: 4.864 distance: 79 - 80: 5.556 distance: 79 - 89: 3.796 distance: 82 - 83: 4.008 distance: 82 - 84: 3.184 distance: 83 - 85: 8.343 distance: 84 - 86: 4.472 distance: 85 - 87: 10.598 distance: 86 - 87: 11.354 distance: 87 - 88: 11.557 distance: 89 - 90: 4.634 distance: 90 - 91: 5.697 distance: 90 - 93: 3.250 distance: 91 - 92: 5.113 distance: 91 - 97: 5.981 distance: 93 - 94: 10.502 distance: 94 - 95: 7.638 distance: 94 - 96: 13.630 distance: 97 - 98: 12.708 distance: 98 - 99: 4.225 distance: 98 - 101: 3.093 distance: 99 - 100: 5.456 distance: 99 - 104: 6.350 distance: 101 - 102: 8.540 distance: 101 - 103: 27.756 distance: 104 - 105: 8.948 distance: 105 - 106: 8.861 distance: 105 - 108: 12.524 distance: 106 - 115: 5.916 distance: 108 - 109: 6.323 distance: 109 - 110: 4.370 distance: 110 - 111: 7.631 distance: 111 - 112: 8.910 distance: 112 - 113: 8.389 distance: 112 - 114: 12.707 distance: 115 - 116: 12.892 distance: 116 - 117: 11.069 distance: 116 - 119: 10.304 distance: 117 - 118: 22.607 distance: 117 - 123: 16.019 distance: 120 - 121: 4.762 distance: 120 - 122: 10.655 distance: 123 - 124: 20.008 distance: 124 - 125: 15.156 distance: 124 - 127: 10.091 distance: 125 - 126: 28.398 distance: 125 - 137: 25.246 distance: 127 - 128: 6.304 distance: 128 - 129: 17.171 distance: 128 - 130: 9.756 distance: 129 - 131: 9.284 distance: 130 - 132: 13.225 distance: 130 - 133: 16.632 distance: 131 - 132: 16.728 distance: 132 - 134: 18.920 distance: 133 - 135: 7.961 distance: 134 - 136: 12.582 distance: 135 - 136: 17.205 distance: 137 - 138: 3.169 distance: 138 - 139: 21.036 distance: 138 - 141: 12.628 distance: 139 - 140: 24.830 distance: 139 - 143: 16.310 distance: 141 - 142: 7.804 distance: 143 - 144: 5.610 distance: 144 - 145: 16.132 distance: 144 - 147: 6.307 distance: 145 - 146: 7.775 distance: 145 - 151: 4.886 distance: 147 - 148: 10.662 distance: 147 - 149: 13.265 distance: 148 - 150: 21.175 distance: 151 - 152: 8.202 distance: 152 - 153: 7.759 distance: 152 - 155: 12.555 distance: 153 - 154: 13.269 distance: 153 - 159: 7.388 distance: 155 - 156: 12.406 distance: 156 - 157: 10.408 distance: 156 - 158: 15.577 distance: 159 - 160: 3.975 distance: 160 - 161: 3.589 distance: 161 - 162: 4.856 distance: 161 - 163: 5.542