Starting phenix.real_space_refine on Tue Jun 17 22:02:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8e5a_27908/06_2025/8e5a_27908.cif Found real_map, /net/cci-nas-00/data/ceres_data/8e5a_27908/06_2025/8e5a_27908.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/cci-nas-00/data/ceres_data/8e5a_27908/06_2025/8e5a_27908.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8e5a_27908/06_2025/8e5a_27908.map" model { file = "/net/cci-nas-00/data/ceres_data/8e5a_27908/06_2025/8e5a_27908.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8e5a_27908/06_2025/8e5a_27908.cif" } 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 Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 2 9.91 5 S 112 5.16 5 C 13059 2.51 5 N 3348 2.21 5 O 3736 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 82 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 20257 Number of models: 1 Model: "" Number of chains: 10 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: "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: "B" 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: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" 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: "G" 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: "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: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} 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: 11.37, per 1000 atoms: 0.56 Number of scatterers: 20257 At special positions: 0 Unit cell: (171.556, 170.442, 182.696, 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) Ca 2 19.99 S 112 16.00 O 3736 8.00 N 3348 7.00 C 13059 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=2.03 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=2.02 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 - 3.00 Amino acid : True - 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 B 2 " - " NAG B 3 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " NAG F 3 " " NAG F 3 " - " NAG F 4 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " NAG-ASN " NAG B 1 " - " ASN D 184 " " NAG D1201 " - " ASN D 92 " " NAG E 1 " - " ASN D 348 " " NAG F 1 " - " ASN D 468 " " NAG G 1 " - " ASN D 613 " " NAG H 1 " - " ASN D 895 " Time building additional restraints: 4.69 Conformation dependent library (CDL) restraints added in 2.5 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... Secondary structure from input PDB file: 107 helices and 16 sheets defined 53.6% alpha, 10.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.18 Creating SS restraints... Processing helix chain 'A' and resid 128 through 143 removed outlier: 3.808A pdb=" N LEU A 133 " --> pdb=" O ASP A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 153 removed outlier: 4.248A pdb=" N ASP A 152 " --> pdb=" O PHE A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 175 removed outlier: 3.704A pdb=" N LYS A 163 " --> pdb=" O HIS A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 217 removed outlier: 3.545A pdb=" N VAL A 205 " --> pdb=" O ASP A 201 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N GLY A 208 " --> pdb=" O ILE A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 244 removed outlier: 3.904A pdb=" N ARG A 240 " --> pdb=" O LYS A 237 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ALA A 241 " --> pdb=" O ALA A 238 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N PHE A 242 " --> pdb=" O LEU A 239 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ARG A 243 " --> pdb=" O ARG A 240 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N VAL A 244 " --> pdb=" O ALA A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 245 through 254 removed outlier: 3.753A pdb=" N LEU A 250 " --> pdb=" O ARG A 246 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N VAL A 251 " --> pdb=" O PRO A 247 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N SER A 252 " --> pdb=" O LEU A 248 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N GLY A 253 " --> pdb=" O ARG A 249 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N VAL A 254 " --> pdb=" O LEU A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 266 removed outlier: 4.184A pdb=" N VAL A 260 " --> pdb=" O SER A 256 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LEU A 261 " --> pdb=" O LEU A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 270 Proline residue: A 270 - end of helix No H-bonds generated for 'chain 'A' and resid 267 through 270' Processing helix chain 'A' and resid 271 through 293 Processing helix chain 'A' and resid 349 through 362 Processing helix chain 'A' and resid 365 through 377 removed outlier: 4.013A pdb=" N VAL A 369 " --> pdb=" O GLY A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 394 removed outlier: 3.922A pdb=" N TYR A 385 " --> pdb=" O LEU A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 418 removed outlier: 3.885A pdb=" N ALA A 418 " --> pdb=" O GLU A 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 420 through 441 removed outlier: 3.807A pdb=" N GLU A 432 " --> pdb=" O LYS A 428 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N GLU A 433 " --> pdb=" O GLN A 429 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N ASP A 434 " --> pdb=" O GLN A 430 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N LEU A 435 " --> pdb=" O LEU A 431 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ASP A 440 " --> pdb=" O LYS A 436 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N TRP A 441 " --> pdb=" O GLY A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 516 through 520 Processing helix chain 'A' and resid 522 through 541 removed outlier: 4.021A pdb=" N TYR A 526 " --> pdb=" O SER A 522 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LEU A 528 " --> pdb=" O THR A 524 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N VAL A 531 " --> pdb=" O TRP A 527 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ILE A 540 " --> pdb=" O ASN A 536 " (cutoff:3.500A) Processing helix chain 'A' and resid 548 through 573 removed outlier: 3.775A pdb=" N THR A 552 " --> pdb=" O PRO A 548 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N GLN A 553 " --> pdb=" O ASP A 549 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ILE A 554 " --> pdb=" O TRP A 550 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LYS A 560 " --> pdb=" O ASP A 556 " (cutoff:3.500A) Processing helix chain 'A' and resid 578 through 583 removed outlier: 3.908A pdb=" N PHE A 583 " --> pdb=" O LEU A 579 " (cutoff:3.500A) Processing helix chain 'A' and resid 585 through 607 removed outlier: 3.762A pdb=" N ARG A 589 " --> pdb=" O SER A 585 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N ILE A 603 " --> pdb=" O ILE A 599 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLU A 606 " --> pdb=" O THR A 602 " (cutoff:3.500A) Processing helix chain 'A' and resid 611 through 623 removed outlier: 4.209A pdb=" N SER A 616 " --> pdb=" O PRO A 612 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N PHE A 618 " --> pdb=" O GLY A 614 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ARG A 619 " --> pdb=" O ILE A 615 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N CYS A 620 " --> pdb=" O SER A 616 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N VAL A 621 " --> pdb=" O VAL A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 624 through 630 removed outlier: 3.815A pdb=" N LYS A 628 " --> pdb=" O ARG A 625 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL A 629 " --> pdb=" O ILE A 626 " (cutoff:3.500A) Processing helix chain 'A' and resid 636 through 646 removed outlier: 3.656A pdb=" N SER A 642 " --> pdb=" O ASN A 638 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ASN A 645 " --> pdb=" O ALA A 641 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N SER A 646 " --> pdb=" O SER A 642 " (cutoff:3.500A) Processing helix chain 'A' and resid 646 through 672 removed outlier: 3.827A pdb=" N SER A 652 " --> pdb=" O LYS A 648 " (cutoff:3.500A) Processing helix chain 'A' and resid 690 through 704 Processing helix chain 'A' and resid 706 through 717 Processing helix chain 'A' and resid 724 through 728 removed outlier: 3.742A pdb=" N ILE A 727 " --> pdb=" O SER A 724 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N VAL A 728 " --> pdb=" O GLY A 725 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 724 through 728' Processing helix chain 'A' and resid 729 through 747 removed outlier: 3.569A pdb=" N PHE A 736 " --> pdb=" O PHE A 732 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ILE A 742 " --> pdb=" O CYS A 738 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LEU A 744 " --> pdb=" O ASN A 740 " (cutoff:3.500A) Processing helix chain 'A' and resid 754 through 768 removed outlier: 3.674A pdb=" N ALA A 758 " --> pdb=" O ASN A 754 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLU A 759 " --> pdb=" O LEU A 755 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N SER A 760 " --> pdb=" O ALA A 756 " (cutoff:3.500A) Processing helix chain 'A' and resid 877 through 884 removed outlier: 3.563A pdb=" N LEU A 882 " --> pdb=" O GLY A 878 " (cutoff:3.500A) Processing helix chain 'A' and resid 887 through 904 removed outlier: 3.673A pdb=" N LEU A 893 " --> pdb=" O THR A 889 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N MET A 897 " --> pdb=" O LEU A 893 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ALA A 904 " --> pdb=" O SER A 900 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 940 removed outlier: 3.530A pdb=" N PHE A 922 " --> pdb=" O ILE A 918 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ASP A 923 " --> pdb=" O LEU A 919 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N TYR A 924 " --> pdb=" O GLY A 920 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N PHE A 930 " --> pdb=" O PHE A 926 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N MET A 938 " --> pdb=" O ILE A 934 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N THR A 940 " --> pdb=" O LEU A 936 " (cutoff:3.500A) Processing helix chain 'A' and resid 954 through 970 removed outlier: 3.810A pdb=" N LEU A 958 " --> pdb=" O TYR A 954 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ASP A 959 " --> pdb=" O PHE A 955 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N VAL A 963 " --> pdb=" O ASP A 959 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N SER A 966 " --> pdb=" O VAL A 962 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N PHE A 970 " --> pdb=" O SER A 966 " (cutoff:3.500A) Processing helix chain 'A' and resid 980 through 987 removed outlier: 3.635A pdb=" N ARG A 987 " --> pdb=" O LEU A 983 " (cutoff:3.500A) Processing helix chain 'A' and resid 988 through 995 Proline residue: A 991 - end of helix removed outlier: 3.725A pdb=" N ALA A 994 " --> pdb=" O PRO A 991 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ILE A 995 " --> pdb=" O LEU A 992 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 988 through 995' Processing helix chain 'A' and resid 998 through 1015 removed outlier: 3.563A pdb=" N THR A1014 " --> pdb=" O VAL A1010 " (cutoff:3.500A) Processing helix chain 'A' and resid 1016 through 1037 removed outlier: 3.522A pdb=" N ILE A1020 " --> pdb=" O GLY A1016 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N VAL A1021 " --> pdb=" O ASN A1017 " (cutoff:3.500A) Processing helix chain 'A' and resid 1064 through 1066 No H-bonds generated for 'chain 'A' and resid 1064 through 1066' Processing helix chain 'A' and resid 1086 through 1099 Processing helix chain 'A' and resid 1102 through 1112 removed outlier: 3.509A pdb=" N LEU A1106 " --> pdb=" O GLY A1102 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ASP A1112 " --> pdb=" O TYR A1108 " (cutoff:3.500A) Processing helix chain 'A' and resid 1125 through 1127 No H-bonds generated for 'chain 'A' and resid 1125 through 1127' Processing helix chain 'A' and resid 1128 through 1139 removed outlier: 4.222A pdb=" N PHE A1132 " --> pdb=" O ILE A1128 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1159 removed outlier: 3.503A pdb=" N ASN A1145 " --> pdb=" O PHE A1141 " (cutoff:3.500A) Processing helix chain 'A' and resid 1171 through 1176 removed outlier: 3.685A pdb=" N VAL A1176 " --> pdb=" O GLN A1172 " (cutoff:3.500A) Processing helix chain 'A' and resid 1176 through 1181 removed outlier: 3.748A pdb=" N LEU A1180 " --> pdb=" O VAL A1176 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LYS A1181 " --> pdb=" O GLU A1177 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1176 through 1181' Processing helix chain 'A' and resid 1192 through 1203 removed outlier: 3.531A pdb=" N TYR A1196 " --> pdb=" O ASN A1192 " (cutoff:3.500A) removed outlier: 5.179A pdb=" N PHE A1198 " --> pdb=" O TYR A1194 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ASN A1203 " --> pdb=" O TRP A1199 " (cutoff:3.500A) Processing helix chain 'A' and resid 1204 through 1223 removed outlier: 3.772A pdb=" N ILE A1215 " --> pdb=" O MET A1211 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N MET A1216 " --> pdb=" O PHE A1212 " (cutoff:3.500A) Processing helix chain 'A' and resid 1230 through 1257 removed outlier: 3.558A pdb=" N MET A1242 " --> pdb=" O ASP A1238 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ILE A1257 " --> pdb=" O VAL A1253 " (cutoff:3.500A) Processing helix chain 'A' and resid 1260 through 1265 Processing helix chain 'A' and resid 1267 through 1284 removed outlier: 3.613A pdb=" N THR A1271 " --> pdb=" O ASP A1267 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N LEU A1275 " --> pdb=" O THR A1271 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N ILE A1276 " --> pdb=" O PHE A1272 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N VAL A1284 " --> pdb=" O SER A1280 " (cutoff:3.500A) Processing helix chain 'A' and resid 1285 through 1287 No H-bonds generated for 'chain 'A' and resid 1285 through 1287' Processing helix chain 'A' and resid 1319 through 1323 removed outlier: 3.971A pdb=" N VAL A1323 " --> pdb=" O LEU A1320 " (cutoff:3.500A) Processing helix chain 'A' and resid 1336 through 1348 removed outlier: 3.733A pdb=" N PHE A1343 " --> pdb=" O LEU A1339 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N SER A1346 " --> pdb=" O THR A1342 " (cutoff:3.500A) Processing helix chain 'A' and resid 1350 through 1373 removed outlier: 4.493A pdb=" N ALA A1354 " --> pdb=" O LEU A1350 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU A1355 " --> pdb=" O PRO A1351 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU A1356 " --> pdb=" O TYR A1352 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ILE A1357 " --> pdb=" O VAL A1353 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLN A1370 " --> pdb=" O VAL A1366 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N MET A1371 " --> pdb=" O ILE A1367 " (cutoff:3.500A) Processing helix chain 'A' and resid 1391 through 1404 Processing helix chain 'A' and resid 1407 through 1415 Processing helix chain 'A' and resid 1439 through 1465 removed outlier: 3.640A pdb=" N ASP A1465 " --> pdb=" O ALA A1461 " (cutoff:3.500A) Processing helix chain 'A' and resid 1466 through 1471 Processing helix chain 'A' and resid 1478 through 1490 removed outlier: 3.614A pdb=" N LEU A1482 " --> pdb=" O GLY A1478 " (cutoff:3.500A) Processing helix chain 'A' and resid 1504 through 1511 removed outlier: 3.709A pdb=" N ARG A1511 " --> pdb=" O THR A1507 " (cutoff:3.500A) Processing helix chain 'A' and resid 1526 through 1534 removed outlier: 4.101A pdb=" N VAL A1532 " --> pdb=" O CYS A1528 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N MET A1534 " --> pdb=" O ARG A1530 " (cutoff:3.500A) Processing helix chain 'A' and resid 1546 through 1558 removed outlier: 3.745A pdb=" N PHE A1551 " --> pdb=" O ASN A1547 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LEU A1558 " --> pdb=" O VAL A1554 " (cutoff:3.500A) Processing helix chain 'A' and resid 1565 through 1576 removed outlier: 3.868A pdb=" N ALA A1569 " --> pdb=" O ASN A1565 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ASN A1570 " --> pdb=" O LEU A1566 " (cutoff:3.500A) Processing helix chain 'A' and resid 1584 through 1589 removed outlier: 4.331A pdb=" N LEU A1589 " --> pdb=" O SER A1585 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 52 removed outlier: 3.569A pdb=" N MET D 40 " --> pdb=" O TRP D 36 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASP D 43 " --> pdb=" O LYS D 39 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N LEU D 47 " --> pdb=" O ASP D 43 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N SER D 52 " --> pdb=" O ALA D 48 " (cutoff:3.500A) Processing helix chain 'D' and resid 53 through 63 Processing helix chain 'D' and resid 74 through 110 removed outlier: 3.563A pdb=" N ARG D 84 " --> pdb=" O GLU D 80 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLU D 103 " --> pdb=" O ARG D 99 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ALA D 110 " --> pdb=" O LYS D 106 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 186 removed outlier: 3.856A pdb=" N TRP D 185 " --> pdb=" O ASN D 181 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N THR D 186 " --> pdb=" O GLU D 182 " (cutoff:3.500A) Processing helix chain 'D' and resid 188 through 200 removed outlier: 4.279A pdb=" N VAL D 192 " --> pdb=" O ALA D 188 " (cutoff:3.500A) Processing helix chain 'D' and resid 237 through 240 Processing helix chain 'D' and resid 241 through 249 removed outlier: 3.811A pdb=" N GLY D 247 " --> pdb=" O TRP D 243 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ALA D 249 " --> pdb=" O ILE D 245 " (cutoff:3.500A) Processing helix chain 'D' and resid 261 through 265 removed outlier: 3.514A pdb=" N VAL D 264 " --> pdb=" O SER D 261 " (cutoff:3.500A) Processing helix chain 'D' and resid 266 through 281 removed outlier: 3.632A pdb=" N LYS D 270 " --> pdb=" O GLY D 266 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ILE D 272 " --> pdb=" O THR D 268 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLU D 281 " --> pdb=" O SER D 277 " (cutoff:3.500A) Processing helix chain 'D' and resid 311 through 323 removed outlier: 3.522A pdb=" N VAL D 317 " --> pdb=" O ARG D 313 " (cutoff:3.500A) Processing helix chain 'D' and resid 332 through 344 Processing helix chain 'D' and resid 369 through 377 Processing helix chain 'D' and resid 396 through 406 removed outlier: 3.779A pdb=" N CYS D 404 " --> pdb=" O GLN D 400 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ASN D 406 " --> pdb=" O MET D 402 " (cutoff:3.500A) Processing helix chain 'D' and resid 415 through 417 No H-bonds generated for 'chain 'D' and resid 415 through 417' Processing helix chain 'D' and resid 418 through 423 Processing helix chain 'D' and resid 425 through 431 removed outlier: 4.293A pdb=" N VAL D 429 " --> pdb=" O GLU D 425 " (cutoff:3.500A) Processing helix chain 'D' and resid 431 through 438 removed outlier: 3.924A pdb=" N GLY D 438 " --> pdb=" O MET D 434 " (cutoff:3.500A) Processing helix chain 'D' and resid 439 through 442 removed outlier: 3.572A pdb=" N LYS D 442 " --> pdb=" O ASP D 439 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 439 through 442' Processing helix chain 'D' and resid 494 through 500 removed outlier: 3.803A pdb=" N LEU D 500 " --> pdb=" O ASP D 496 " (cutoff:3.500A) Processing helix chain 'D' and resid 560 through 565 removed outlier: 3.738A pdb=" N GLU D 565 " --> pdb=" O PHE D 561 " (cutoff:3.500A) Processing helix chain 'D' and resid 568 through 580 removed outlier: 4.220A pdb=" N GLU D 573 " --> pdb=" O ASP D 569 " (cutoff:3.500A) Processing helix chain 'D' and resid 638 through 646 removed outlier: 3.787A pdb=" N ARG D 643 " --> pdb=" O ILE D 639 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N TYR D 644 " --> pdb=" O THR D 640 " (cutoff:3.500A) Processing helix chain 'D' and resid 647 through 651 Proline residue: D 650 - end of helix No H-bonds generated for 'chain 'D' and resid 647 through 651' Processing helix chain 'D' and resid 652 through 657 Processing helix chain 'D' and resid 677 through 689 removed outlier: 4.119A pdb=" N LEU D 681 " --> pdb=" O THR D 677 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ASP D 688 " --> pdb=" O ASN D 684 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ARG D 689 " --> pdb=" O GLU D 685 " (cutoff:3.500A) Processing helix chain 'D' and resid 699 through 719 removed outlier: 3.942A pdb=" N VAL D 705 " --> pdb=" O LEU D 701 " (cutoff:3.500A) Processing helix chain 'D' and resid 745 through 752 removed outlier: 4.105A pdb=" N GLU D 750 " --> pdb=" O GLU D 747 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N TRP D 752 " --> pdb=" O GLY D 749 " (cutoff:3.500A) Processing helix chain 'D' and resid 757 through 760 Processing helix chain 'D' and resid 761 through 770 removed outlier: 3.673A pdb=" N ASP D 769 " --> pdb=" O LYS D 765 " (cutoff:3.500A) Processing helix chain 'D' and resid 817 through 827 removed outlier: 3.799A pdb=" N GLU D 823 " --> pdb=" O ASN D 819 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ASN D 824 " --> pdb=" O SER D 820 " (cutoff:3.500A) Processing helix chain 'D' and resid 865 through 870 removed outlier: 3.575A pdb=" N GLN D 870 " --> pdb=" O ASP D 866 " (cutoff:3.500A) Processing helix chain 'D' and resid 874 through 878 Processing helix chain 'D' and resid 879 through 889 Processing helix chain 'C' and resid 39 through 56 Processing helix chain 'C' and resid 120 through 132 Processing helix chain 'C' and resid 155 through 159 removed outlier: 3.505A pdb=" N LYS C 159 " --> pdb=" O SER C 156 " (cutoff:3.500A) Processing helix chain 'C' and resid 190 through 208 removed outlier: 4.196A pdb=" N LEU C 200 " --> pdb=" O MET C 196 " (cutoff:3.500A) Processing helix chain 'C' and resid 246 through 263 Processing helix chain 'C' and resid 276 through 281 removed outlier: 4.007A pdb=" N ALA C 281 " --> pdb=" O ALA C 278 " (cutoff:3.500A) Processing helix chain 'C' and resid 296 through 306 Processing helix chain 'C' and resid 308 through 314 removed outlier: 3.972A pdb=" N HIS C 314 " --> pdb=" O SER C 310 " (cutoff:3.500A) Processing helix chain 'C' and resid 314 through 328 Processing helix chain 'C' and resid 329 through 333 Processing helix chain 'C' and resid 341 through 360 Processing sheet with id=AA1, first strand: chain 'A' and resid 301 through 303 removed outlier: 3.566A pdb=" N GLU A 332 " --> pdb=" O PHE A 302 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 1058 through 1062 Processing sheet with id=AA3, first strand: chain 'A' and resid 1499 through 1500 Processing sheet with id=AA4, first strand: chain 'D' and resid 68 through 72 Processing sheet with id=AA5, first strand: chain 'D' and resid 122 through 123 removed outlier: 6.618A pdb=" N VAL D 122 " --> pdb=" O GLN D 143 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'D' and resid 125 through 126 removed outlier: 6.647A pdb=" N TYR D 125 " --> pdb=" O VAL D 166 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N VAL D 490 " --> pdb=" O GLY D 462 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 125 through 126 removed outlier: 6.647A pdb=" N TYR D 125 " --> pdb=" O VAL D 166 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N VAL D 490 " --> pdb=" O GLY D 462 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 150 through 151 Processing sheet with id=AA9, first strand: chain 'D' and resid 298 through 300 removed outlier: 8.440A pdb=" N ALA D 292 " --> pdb=" O MET D 254 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N ILE D 256 " --> pdb=" O ALA D 292 " (cutoff:3.500A) removed outlier: 7.685A pdb=" N PHE D 294 " --> pdb=" O ILE D 256 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N VAL D 258 " --> pdb=" O PHE D 294 " (cutoff:3.500A) removed outlier: 8.593A pdb=" N TYR D 411 " --> pdb=" O VAL D 384 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N THR D 386 " --> pdb=" O TYR D 411 " (cutoff:3.500A) removed outlier: 7.838A pdb=" N ILE D 413 " --> pdb=" O THR D 386 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N SER D 388 " --> pdb=" O ILE D 413 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 521 through 523 removed outlier: 6.096A pdb=" N ALA D 514 " --> pdb=" O LEU D 522 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 658 through 659 removed outlier: 3.857A pdb=" N ALA D 731 " --> pdb=" O LYS D 815 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N MET D 793 " --> pdb=" O THR D 776 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 800 through 801 Processing sheet with id=AB4, first strand: chain 'D' and resid 859 through 861 removed outlier: 6.872A pdb=" N ILE D 852 " --> pdb=" O LEU D 860 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N GLU D1019 " --> pdb=" O ILE D1002 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N ILE D1002 " --> pdb=" O GLU D1019 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 892 through 904 removed outlier: 3.574A pdb=" N ASN D 895 " --> pdb=" O GLN D 980 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLN D 980 " --> pdb=" O ASN D 895 " (cutoff:3.500A) removed outlier: 4.950A pdb=" N GLN D 901 " --> pdb=" O CYS D 974 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N CYS D 974 " --> pdb=" O GLN D 901 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N VAL D 903 " --> pdb=" O GLN D 972 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N GLN D 972 " --> pdb=" O VAL D 903 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N ILE D 975 " --> pdb=" O SER D1038 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 62 through 65 removed outlier: 3.611A pdb=" N LYS C 96 " --> pdb=" O ILE C 105 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N ILE C 105 " --> pdb=" O LYS C 96 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N LYS C 98 " --> pdb=" O TRP C 103 " (cutoff:3.500A) removed outlier: 8.563A pdb=" N TRP C 103 " --> pdb=" O LYS C 98 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 212 through 215 removed outlier: 3.508A pdb=" N VAL C 268 " --> pdb=" O SER C 213 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N THR C 215 " --> pdb=" O VAL C 268 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N VAL C 180 " --> pdb=" O LEU C 269 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N VAL C 181 " --> pdb=" O VAL C 290 " (cutoff:3.500A) removed outlier: 7.445A pdb=" N VAL C 292 " --> pdb=" O VAL C 181 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N VAL C 183 " --> pdb=" O VAL C 292 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N ILE C 289 " --> pdb=" O VAL C 335 " (cutoff:3.500A) removed outlier: 7.786A pdb=" N LEU C 337 " --> pdb=" O ILE C 289 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N PHE C 291 " --> pdb=" O LEU C 337 " (cutoff:3.500A) 923 hydrogen bonds defined for protein. 2643 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: 7.26 Time building geometry restraints manager: 5.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6459 1.34 - 1.46: 4741 1.46 - 1.58: 9311 1.58 - 1.70: 2 1.70 - 1.82: 176 Bond restraints: 20689 Sorted by residual: bond pdb=" C1 NAG F 3 " pdb=" O5 NAG F 3 " ideal model delta sigma weight residual 1.406 1.484 -0.078 2.00e-02 2.50e+03 1.54e+01 bond pdb=" CA LYS D 634 " pdb=" CB LYS D 634 " ideal model delta sigma weight residual 1.528 1.576 -0.048 1.51e-02 4.39e+03 9.93e+00 bond pdb=" C1 NAG H 1 " pdb=" O5 NAG H 1 " ideal model delta sigma weight residual 1.406 1.467 -0.061 2.00e-02 2.50e+03 9.27e+00 bond pdb=" CB PRO C 121 " pdb=" CG PRO C 121 " ideal model delta sigma weight residual 1.492 1.600 -0.108 5.00e-02 4.00e+02 4.68e+00 bond pdb=" C1 NAG F 4 " pdb=" O5 NAG F 4 " ideal model delta sigma weight residual 1.406 1.440 -0.034 2.00e-02 2.50e+03 2.91e+00 ... (remaining 20684 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.84: 27284 1.84 - 3.68: 634 3.68 - 5.53: 80 5.53 - 7.37: 20 7.37 - 9.21: 4 Bond angle restraints: 28022 Sorted by residual: angle pdb=" N VAL A 752 " pdb=" CA VAL A 752 " pdb=" C VAL A 752 " ideal model delta sigma weight residual 113.10 107.40 5.70 9.70e-01 1.06e+00 3.46e+01 angle pdb=" N VAL A 193 " pdb=" CA VAL A 193 " pdb=" C VAL A 193 " ideal model delta sigma weight residual 113.71 108.32 5.39 9.50e-01 1.11e+00 3.22e+01 angle pdb=" N VAL D 891 " pdb=" CA VAL D 891 " pdb=" C VAL D 891 " ideal model delta sigma weight residual 112.96 108.32 4.64 1.00e+00 1.00e+00 2.16e+01 angle pdb=" N SER A 635 " pdb=" CA SER A 635 " pdb=" C SER A 635 " ideal model delta sigma weight residual 114.56 109.02 5.54 1.27e+00 6.20e-01 1.90e+01 angle pdb=" CA PRO C 121 " pdb=" N PRO C 121 " pdb=" CD PRO C 121 " ideal model delta sigma weight residual 112.00 105.97 6.03 1.40e+00 5.10e-01 1.86e+01 ... (remaining 28017 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.01: 11653 23.01 - 46.03: 770 46.03 - 69.04: 105 69.04 - 92.05: 33 92.05 - 115.06: 32 Dihedral angle restraints: 12593 sinusoidal: 5276 harmonic: 7317 Sorted by residual: dihedral pdb=" CB CYS D 904 " pdb=" SG CYS D 904 " pdb=" SG CYS D 974 " pdb=" CB CYS D 974 " ideal model delta sinusoidal sigma weight residual 93.00 167.10 -74.10 1 1.00e+01 1.00e-02 6.97e+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 45.10 47.90 1 1.00e+01 1.00e-02 3.16e+01 dihedral pdb=" CB CYS A 301 " pdb=" SG CYS A 301 " pdb=" SG CYS A 326 " pdb=" CB CYS A 326 " ideal model delta sinusoidal sigma weight residual 93.00 48.18 44.82 1 1.00e+01 1.00e-02 2.79e+01 ... (remaining 12590 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.138: 3182 0.138 - 0.275: 15 0.275 - 0.413: 0 0.413 - 0.551: 0 0.551 - 0.688: 2 Chirality restraints: 3199 Sorted by residual: chirality pdb=" C1 NAG H 1 " pdb=" ND2 ASN D 895 " pdb=" C2 NAG H 1 " pdb=" O5 NAG H 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.71 -0.69 2.00e-01 2.50e+01 1.19e+01 chirality pdb=" C1 NAG B 1 " pdb=" ND2 ASN D 184 " pdb=" C2 NAG B 1 " pdb=" O5 NAG B 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.83 -0.57 2.00e-01 2.50e+01 8.03e+00 chirality pdb=" CA ASN C 140 " pdb=" N ASN C 140 " pdb=" C ASN C 140 " pdb=" CB ASN C 140 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.83e-01 ... (remaining 3196 not shown) Planarity restraints: 3556 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER C 120 " -0.070 5.00e-02 4.00e+02 1.03e-01 1.71e+01 pdb=" N PRO C 121 " 0.179 5.00e-02 4.00e+02 pdb=" CA PRO C 121 " -0.052 5.00e-02 4.00e+02 pdb=" CD PRO C 121 " -0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 953 " 0.015 2.00e-02 2.50e+03 2.98e-02 8.87e+00 pdb=" C ASN A 953 " -0.052 2.00e-02 2.50e+03 pdb=" O ASN A 953 " 0.019 2.00e-02 2.50e+03 pdb=" N TYR A 954 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN D 184 " 0.027 2.00e-02 2.50e+03 2.55e-02 8.13e+00 pdb=" CG ASN D 184 " -0.036 2.00e-02 2.50e+03 pdb=" OD1 ASN D 184 " 0.007 2.00e-02 2.50e+03 pdb=" ND2 ASN D 184 " -0.024 2.00e-02 2.50e+03 pdb=" C1 NAG B 1 " 0.025 2.00e-02 2.50e+03 ... (remaining 3553 not shown) Histogram of nonbonded interaction distances: 1.74 - 2.37: 33 2.37 - 3.00: 10605 3.00 - 3.63: 29694 3.63 - 4.27: 44557 4.27 - 4.90: 74340 Nonbonded interactions: 159229 Sorted by model distance: nonbonded pdb=" OD1 ASP A 434 " pdb=" ND2 ASN C 340 " model vdw 1.735 3.120 nonbonded pdb=" OD1 ASN D 895 " pdb=" O3 NAG H 1 " model vdw 2.072 3.040 nonbonded pdb=" N GLU A1431 " pdb=" OE1 GLU A1431 " model vdw 2.172 3.120 nonbonded pdb=" O4 NAG E 2 " pdb=" O7 NAG E 2 " model vdw 2.210 3.040 nonbonded pdb=" ND1 HIS A 912 " pdb=" OD2 ASP A1426 " model vdw 2.222 3.120 ... (remaining 159224 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'H' } 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: 1.900 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.890 Check model and map are aligned: 0.140 Set scattering table: 0.170 Process input model: 44.230 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.080 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:2.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 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 : 0.003 0.108 20713 Z= 0.163 Angle : 0.693 10.765 28084 Z= 0.407 Chirality : 0.045 0.688 3199 Planarity : 0.004 0.103 3550 Dihedral : 16.357 115.064 7827 Min Nonbonded Distance : 1.735 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.98 % Favored : 94.82 % Rotamer: Outliers : 1.86 % Allowed : 1.09 % Favored : 97.06 % 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: -1.24 (0.17), residues: 2472 helix: -0.20 (0.15), residues: 1171 sheet: -0.20 (0.35), residues: 233 loop : -1.62 (0.18), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP D 185 HIS 0.003 0.000 HIS A 912 PHE 0.022 0.001 PHE A1147 TYR 0.020 0.001 TYR D1068 ARG 0.010 0.000 ARG C 302 Details of bonding type rmsd link_NAG-ASN : bond 0.01336 ( 6) link_NAG-ASN : angle 5.29750 ( 18) link_BETA1-4 : bond 0.00976 ( 8) link_BETA1-4 : angle 3.00951 ( 24) hydrogen bonds : bond 0.22469 ( 904) hydrogen bonds : angle 7.14481 ( 2643) SS BOND : bond 0.00351 ( 10) SS BOND : angle 1.22123 ( 20) covalent geometry : bond 0.00310 (20689) covalent geometry : angle 0.67437 (28022) *********************** 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 402 residues out of total 2210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 361 time to evaluate : 2.085 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 124 GLU cc_start: 0.7917 (OUTLIER) cc_final: 0.7467 (mp0) REVERT: A 587 PHE cc_start: 0.6348 (m-10) cc_final: 0.6098 (m-10) REVERT: A 647 MET cc_start: 0.7880 (ttp) cc_final: 0.7515 (ttm) REVERT: A 1019 MET cc_start: 0.8043 (OUTLIER) cc_final: 0.7756 (mtp) REVERT: A 1020 ILE cc_start: 0.9184 (OUTLIER) cc_final: 0.8712 (mt) REVERT: A 1464 MET cc_start: 0.6534 (ttt) cc_final: 0.6109 (ttp) REVERT: D 865 ASP cc_start: 0.6952 (t0) cc_final: 0.6528 (t0) REVERT: D 990 PHE cc_start: 0.7828 (m-80) cc_final: 0.7578 (m-80) REVERT: C 128 ARG cc_start: 0.1660 (ttp-170) cc_final: 0.1207 (mmt180) REVERT: C 254 ILE cc_start: 0.6119 (mm) cc_final: 0.5865 (mt) REVERT: C 288 ILE cc_start: 0.4437 (mt) cc_final: 0.3986 (tt) REVERT: C 301 GLN cc_start: 0.4858 (pp30) cc_final: 0.4573 (tm-30) REVERT: C 323 ASP cc_start: 0.6150 (p0) cc_final: 0.5800 (p0) REVERT: C 342 LEU cc_start: 0.2231 (OUTLIER) cc_final: 0.1928 (pp) outliers start: 41 outliers final: 22 residues processed: 394 average time/residue: 0.3338 time to fit residues: 205.1847 Evaluate side-chains 286 residues out of total 2210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 260 time to evaluate : 2.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 GLU Chi-restraints excluded: chain A residue 128 PHE Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 179 LYS Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 619 ARG Chi-restraints excluded: chain A residue 622 ARG Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 625 ARG Chi-restraints excluded: chain A residue 759 GLU Chi-restraints excluded: chain A residue 760 SER Chi-restraints excluded: chain A residue 761 LEU Chi-restraints excluded: chain A residue 763 THR Chi-restraints excluded: chain A residue 955 PHE Chi-restraints excluded: chain A residue 957 LEU Chi-restraints excluded: chain A residue 962 VAL Chi-restraints excluded: chain A residue 967 LEU Chi-restraints excluded: chain A residue 1019 MET Chi-restraints excluded: chain A residue 1020 ILE Chi-restraints excluded: chain A residue 1037 PHE Chi-restraints excluded: chain A residue 1212 PHE Chi-restraints excluded: chain A residue 1214 LEU Chi-restraints excluded: chain D residue 667 CYS Chi-restraints excluded: chain D residue 668 ASN Chi-restraints excluded: chain C residue 342 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 210 optimal weight: 5.9990 chunk 188 optimal weight: 0.9990 chunk 104 optimal weight: 3.9990 chunk 64 optimal weight: 10.0000 chunk 127 optimal weight: 10.0000 chunk 100 optimal weight: 0.9980 chunk 195 optimal weight: 1.9990 chunk 75 optimal weight: 0.8980 chunk 118 optimal weight: 7.9990 chunk 145 optimal weight: 0.9990 chunk 226 optimal weight: 9.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 754 ASN A1003 HIS ** A1114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1171 ASN A1172 GLN ** D 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 698 ASN D 713 ASN ** C 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 311 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.177109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.120617 restraints weight = 29223.909| |-----------------------------------------------------------------------------| r_work (start): 0.3339 rms_B_bonded: 2.84 r_work: 0.3080 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.1421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 20713 Z= 0.149 Angle : 0.660 16.425 28084 Z= 0.322 Chirality : 0.045 0.493 3199 Planarity : 0.004 0.057 3550 Dihedral : 11.573 103.527 3070 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.14 % Favored : 94.82 % Rotamer: Outliers : 1.63 % Allowed : 8.37 % Favored : 90.00 % 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: -0.86 (0.17), residues: 2472 helix: 0.31 (0.15), residues: 1219 sheet: -0.54 (0.33), residues: 255 loop : -1.65 (0.19), residues: 998 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 441 HIS 0.004 0.001 HIS D1004 PHE 0.016 0.001 PHE A 128 TYR 0.013 0.001 TYR D1068 ARG 0.005 0.000 ARG A 685 Details of bonding type rmsd link_NAG-ASN : bond 0.01161 ( 6) link_NAG-ASN : angle 4.60575 ( 18) link_BETA1-4 : bond 0.00790 ( 8) link_BETA1-4 : angle 2.63254 ( 24) hydrogen bonds : bond 0.05281 ( 904) hydrogen bonds : angle 4.74471 ( 2643) SS BOND : bond 0.00498 ( 10) SS BOND : angle 1.47131 ( 20) covalent geometry : bond 0.00334 (20689) covalent geometry : angle 0.64434 (28022) *********************** 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 324 residues out of total 2210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 288 time to evaluate : 2.265 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 124 GLU cc_start: 0.8278 (OUTLIER) cc_final: 0.7951 (pm20) REVERT: A 126 LYS cc_start: 0.5988 (OUTLIER) cc_final: 0.5440 (tmmt) REVERT: A 152 ASP cc_start: 0.8630 (t0) cc_final: 0.8294 (t0) REVERT: A 587 PHE cc_start: 0.5909 (m-10) cc_final: 0.5657 (m-10) REVERT: A 759 GLU cc_start: 0.8265 (OUTLIER) cc_final: 0.7567 (mp0) REVERT: A 1020 ILE cc_start: 0.8992 (OUTLIER) cc_final: 0.8754 (mt) REVERT: A 1209 TYR cc_start: 0.5174 (m-80) cc_final: 0.4825 (m-80) REVERT: A 1278 ILE cc_start: 0.8289 (mm) cc_final: 0.7998 (pt) REVERT: A 1464 MET cc_start: 0.7092 (ttt) cc_final: 0.6641 (ttp) REVERT: D 532 ILE cc_start: 0.9109 (pt) cc_final: 0.8754 (mt) REVERT: D 668 ASN cc_start: 0.7082 (OUTLIER) cc_final: 0.6486 (p0) REVERT: D 690 LYS cc_start: 0.6461 (tptt) cc_final: 0.5349 (tptp) REVERT: D 990 PHE cc_start: 0.7921 (m-80) cc_final: 0.7694 (m-80) REVERT: C 302 ARG cc_start: 0.5195 (mmm-85) cc_final: 0.4822 (ptp-110) outliers start: 36 outliers final: 19 residues processed: 312 average time/residue: 0.3028 time to fit residues: 150.2745 Evaluate side-chains 273 residues out of total 2210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 249 time to evaluate : 2.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 GLU Chi-restraints excluded: chain A residue 126 LYS Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 380 GLU Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 759 GLU Chi-restraints excluded: chain A residue 957 LEU Chi-restraints excluded: chain A residue 967 LEU Chi-restraints excluded: chain A residue 1020 ILE Chi-restraints excluded: chain A residue 1214 LEU Chi-restraints excluded: chain D residue 668 ASN Chi-restraints excluded: chain D residue 740 ILE Chi-restraints excluded: chain D residue 741 THR Chi-restraints excluded: chain D residue 818 VAL Chi-restraints excluded: chain D residue 1016 ILE Chi-restraints excluded: chain D residue 1065 LEU Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 342 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 36 optimal weight: 8.9990 chunk 229 optimal weight: 0.0010 chunk 101 optimal weight: 0.5980 chunk 84 optimal weight: 9.9990 chunk 49 optimal weight: 0.6980 chunk 35 optimal weight: 6.9990 chunk 125 optimal weight: 10.0000 chunk 149 optimal weight: 0.1980 chunk 2 optimal weight: 0.9980 chunk 93 optimal weight: 2.9990 chunk 54 optimal weight: 3.9990 overall best weight: 0.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 51 GLN C 276 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.179161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.122886 restraints weight = 29297.155| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 2.86 r_work: 0.3112 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.1801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.064 20713 Z= 0.110 Angle : 0.608 16.780 28084 Z= 0.288 Chirality : 0.043 0.310 3199 Planarity : 0.004 0.059 3550 Dihedral : 9.524 100.388 3035 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 1.95 % Allowed : 10.54 % Favored : 87.51 % 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: -0.48 (0.17), residues: 2472 helix: 0.73 (0.15), residues: 1219 sheet: -0.47 (0.31), residues: 277 loop : -1.60 (0.20), residues: 976 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 441 HIS 0.002 0.000 HIS D 864 PHE 0.016 0.001 PHE A 202 TYR 0.016 0.001 TYR D1068 ARG 0.006 0.000 ARG A 997 Details of bonding type rmsd link_NAG-ASN : bond 0.01028 ( 6) link_NAG-ASN : angle 4.42894 ( 18) link_BETA1-4 : bond 0.00902 ( 8) link_BETA1-4 : angle 2.78366 ( 24) hydrogen bonds : bond 0.04040 ( 904) hydrogen bonds : angle 4.31091 ( 2643) SS BOND : bond 0.00319 ( 10) SS BOND : angle 1.21428 ( 20) covalent geometry : bond 0.00233 (20689) covalent geometry : angle 0.59188 (28022) *********************** 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 317 residues out of total 2210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 274 time to evaluate : 2.059 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 124 GLU cc_start: 0.8204 (OUTLIER) cc_final: 0.7854 (pm20) REVERT: A 126 LYS cc_start: 0.5934 (OUTLIER) cc_final: 0.5601 (tmmt) REVERT: A 152 ASP cc_start: 0.8743 (t0) cc_final: 0.8298 (t0) REVERT: A 680 GLU cc_start: 0.8347 (tt0) cc_final: 0.8122 (tt0) REVERT: A 759 GLU cc_start: 0.8238 (OUTLIER) cc_final: 0.7490 (mp0) REVERT: A 1209 TYR cc_start: 0.5208 (m-80) cc_final: 0.4872 (m-80) REVERT: A 1278 ILE cc_start: 0.8237 (mm) cc_final: 0.7900 (pt) REVERT: A 1464 MET cc_start: 0.7188 (ttt) cc_final: 0.6777 (ttp) REVERT: D 532 ILE cc_start: 0.9044 (OUTLIER) cc_final: 0.8823 (mt) REVERT: D 554 GLN cc_start: 0.6395 (mp10) cc_final: 0.6178 (pm20) REVERT: D 668 ASN cc_start: 0.7020 (OUTLIER) cc_final: 0.6553 (p0) REVERT: D 690 LYS cc_start: 0.6452 (tptt) cc_final: 0.5309 (tptp) REVERT: D 1009 MET cc_start: 0.8486 (mmm) cc_final: 0.7799 (mtp) REVERT: C 302 ARG cc_start: 0.4997 (mmm-85) cc_final: 0.4608 (ptp-110) outliers start: 43 outliers final: 23 residues processed: 301 average time/residue: 0.2874 time to fit residues: 139.8169 Evaluate side-chains 271 residues out of total 2210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 243 time to evaluate : 2.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 GLU Chi-restraints excluded: chain A residue 126 LYS Chi-restraints excluded: chain A residue 140 CYS Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 636 LEU Chi-restraints excluded: chain A residue 759 GLU Chi-restraints excluded: chain A residue 900 SER Chi-restraints excluded: chain A residue 957 LEU Chi-restraints excluded: chain A residue 967 LEU Chi-restraints excluded: chain A residue 1008 VAL Chi-restraints excluded: chain D residue 284 SER Chi-restraints excluded: chain D residue 532 ILE Chi-restraints excluded: chain D residue 667 CYS Chi-restraints excluded: chain D residue 668 ASN Chi-restraints excluded: chain D residue 740 ILE Chi-restraints excluded: chain D residue 869 ASN Chi-restraints excluded: chain D residue 1010 ASN Chi-restraints excluded: chain D residue 1065 LEU Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 254 ILE Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 288 ILE Chi-restraints excluded: chain C residue 342 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 176 optimal weight: 2.9990 chunk 230 optimal weight: 0.0770 chunk 11 optimal weight: 0.8980 chunk 30 optimal weight: 0.0970 chunk 108 optimal weight: 3.9990 chunk 73 optimal weight: 3.9990 chunk 171 optimal weight: 1.9990 chunk 85 optimal weight: 0.0970 chunk 84 optimal weight: 10.0000 chunk 199 optimal weight: 4.9990 chunk 198 optimal weight: 5.9990 overall best weight: 0.6336 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 677 ASN ** D 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.179095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.123169 restraints weight = 29520.650| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 2.57 r_work: 0.3131 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3010 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.2080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.074 20713 Z= 0.110 Angle : 0.581 16.451 28084 Z= 0.278 Chirality : 0.042 0.280 3199 Planarity : 0.004 0.059 3550 Dihedral : 8.282 98.895 3030 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 1.58 % Allowed : 12.58 % Favored : 85.84 % 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: -0.37 (0.17), residues: 2472 helix: 0.85 (0.15), residues: 1233 sheet: -0.43 (0.32), residues: 262 loop : -1.61 (0.19), residues: 977 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 441 HIS 0.003 0.000 HIS D 864 PHE 0.012 0.001 PHE A 970 TYR 0.015 0.001 TYR D1068 ARG 0.005 0.000 ARG C 211 Details of bonding type rmsd link_NAG-ASN : bond 0.00865 ( 6) link_NAG-ASN : angle 4.73625 ( 18) link_BETA1-4 : bond 0.00969 ( 8) link_BETA1-4 : angle 2.87226 ( 24) hydrogen bonds : bond 0.03587 ( 904) hydrogen bonds : angle 4.12067 ( 2643) SS BOND : bond 0.00388 ( 10) SS BOND : angle 1.33210 ( 20) covalent geometry : bond 0.00244 (20689) covalent geometry : angle 0.56199 (28022) *********************** 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 308 residues out of total 2210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 273 time to evaluate : 2.089 Fit side-chains revert: symmetry clash REVERT: A 124 GLU cc_start: 0.8254 (OUTLIER) cc_final: 0.7597 (mp0) REVERT: A 126 LYS cc_start: 0.6063 (OUTLIER) cc_final: 0.5850 (tmmt) REVERT: A 152 ASP cc_start: 0.8988 (t0) cc_final: 0.8562 (t0) REVERT: A 680 GLU cc_start: 0.8557 (tt0) cc_final: 0.8282 (tt0) REVERT: A 759 GLU cc_start: 0.8164 (OUTLIER) cc_final: 0.7433 (mp0) REVERT: A 1019 MET cc_start: 0.8733 (mtp) cc_final: 0.8443 (mtt) REVERT: A 1209 TYR cc_start: 0.5131 (m-80) cc_final: 0.4775 (m-80) REVERT: A 1278 ILE cc_start: 0.8282 (mm) cc_final: 0.7861 (pt) REVERT: A 1464 MET cc_start: 0.6972 (ttt) cc_final: 0.6597 (ttp) REVERT: A 1465 ASP cc_start: 0.8441 (t0) cc_final: 0.8241 (t0) REVERT: D 554 GLN cc_start: 0.6465 (mp10) cc_final: 0.6191 (pm20) REVERT: D 668 ASN cc_start: 0.7654 (OUTLIER) cc_final: 0.7279 (p0) REVERT: D 690 LYS cc_start: 0.6395 (tptt) cc_final: 0.5231 (tptp) REVERT: D 1009 MET cc_start: 0.8602 (mmm) cc_final: 0.7795 (mtp) REVERT: C 211 ARG cc_start: 0.4118 (mtm-85) cc_final: 0.3814 (ptt-90) REVERT: C 302 ARG cc_start: 0.4898 (mmm-85) cc_final: 0.4508 (ptp-110) REVERT: C 312 MET cc_start: 0.5538 (mmp) cc_final: 0.5267 (mmp) REVERT: C 313 LYS cc_start: 0.6291 (mmmt) cc_final: 0.6036 (pttt) REVERT: C 342 LEU cc_start: 0.1975 (OUTLIER) cc_final: 0.1719 (tp) outliers start: 35 outliers final: 21 residues processed: 297 average time/residue: 0.3036 time to fit residues: 145.1261 Evaluate side-chains 265 residues out of total 2210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 239 time to evaluate : 2.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 GLU Chi-restraints excluded: chain A residue 126 LYS Chi-restraints excluded: chain A residue 140 CYS Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 380 GLU Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 636 LEU Chi-restraints excluded: chain A residue 702 LEU Chi-restraints excluded: chain A residue 759 GLU Chi-restraints excluded: chain A residue 900 SER Chi-restraints excluded: chain D residue 284 SER Chi-restraints excluded: chain D residue 667 CYS Chi-restraints excluded: chain D residue 668 ASN Chi-restraints excluded: chain D residue 740 ILE Chi-restraints excluded: chain D residue 818 VAL Chi-restraints excluded: chain D residue 869 ASN Chi-restraints excluded: chain D residue 1010 ASN Chi-restraints excluded: chain D residue 1065 LEU Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 254 ILE Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain C residue 342 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 213 optimal weight: 6.9990 chunk 16 optimal weight: 4.9990 chunk 63 optimal weight: 5.9990 chunk 208 optimal weight: 2.9990 chunk 166 optimal weight: 6.9990 chunk 210 optimal weight: 6.9990 chunk 215 optimal weight: 7.9990 chunk 146 optimal weight: 2.9990 chunk 232 optimal weight: 6.9990 chunk 43 optimal weight: 0.9980 chunk 202 optimal weight: 0.0170 overall best weight: 2.4024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 668 ASN ** D 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 684 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 713 ASN D 869 ASN D1062 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.174596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.112039 restraints weight = 29260.982| |-----------------------------------------------------------------------------| r_work (start): 0.3136 rms_B_bonded: 2.00 r_work: 0.3012 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2893 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.2316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.092 20713 Z= 0.203 Angle : 0.643 14.881 28084 Z= 0.318 Chirality : 0.045 0.251 3199 Planarity : 0.004 0.059 3550 Dihedral : 8.087 100.656 3024 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 1.99 % Allowed : 13.80 % Favored : 84.21 % 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: 0.84 (0.15), residues: 1213 sheet: -0.66 (0.32), residues: 251 loop : -1.63 (0.19), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 441 HIS 0.007 0.001 HIS A 912 PHE 0.019 0.002 PHE A 293 TYR 0.019 0.002 TYR D 376 ARG 0.005 0.000 ARG A 685 Details of bonding type rmsd link_NAG-ASN : bond 0.00812 ( 6) link_NAG-ASN : angle 4.05501 ( 18) link_BETA1-4 : bond 0.00852 ( 8) link_BETA1-4 : angle 2.94330 ( 24) hydrogen bonds : bond 0.04186 ( 904) hydrogen bonds : angle 4.24036 ( 2643) SS BOND : bond 0.00432 ( 10) SS BOND : angle 1.87284 ( 20) covalent geometry : bond 0.00492 (20689) covalent geometry : angle 0.62793 (28022) *********************** 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 287 residues out of total 2210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 243 time to evaluate : 2.183 Fit side-chains revert: symmetry clash REVERT: A 124 GLU cc_start: 0.8094 (OUTLIER) cc_final: 0.7560 (mp0) REVERT: A 126 LYS cc_start: 0.5852 (OUTLIER) cc_final: 0.5623 (ttpp) REVERT: A 152 ASP cc_start: 0.9015 (t0) cc_final: 0.8583 (t0) REVERT: A 262 ASN cc_start: 0.8273 (p0) cc_final: 0.8068 (p0) REVERT: A 293 PHE cc_start: 0.8773 (OUTLIER) cc_final: 0.6465 (p90) REVERT: A 759 GLU cc_start: 0.8126 (OUTLIER) cc_final: 0.7435 (mp0) REVERT: A 1009 PHE cc_start: 0.8131 (m-80) cc_final: 0.7791 (m-80) REVERT: A 1209 TYR cc_start: 0.5044 (m-80) cc_final: 0.4698 (m-80) REVERT: A 1278 ILE cc_start: 0.8250 (mm) cc_final: 0.7697 (pt) REVERT: A 1370 GLN cc_start: 0.8462 (OUTLIER) cc_final: 0.7382 (mp10) REVERT: A 1464 MET cc_start: 0.6853 (ttt) cc_final: 0.6425 (ttp) REVERT: D 40 MET cc_start: 0.8105 (ttp) cc_final: 0.7471 (ptm) REVERT: D 554 GLN cc_start: 0.6473 (mp10) cc_final: 0.6189 (pm20) REVERT: D 690 LYS cc_start: 0.6179 (tptt) cc_final: 0.5011 (tptp) REVERT: D 1009 MET cc_start: 0.8378 (mmm) cc_final: 0.7617 (mtp) REVERT: C 302 ARG cc_start: 0.4794 (mmm-85) cc_final: 0.4440 (ptp-110) REVERT: C 312 MET cc_start: 0.5615 (mmp) cc_final: 0.5377 (mmp) REVERT: C 313 LYS cc_start: 0.6357 (mmmt) cc_final: 0.6094 (pttt) REVERT: C 342 LEU cc_start: 0.2154 (OUTLIER) cc_final: 0.1796 (tp) outliers start: 44 outliers final: 23 residues processed: 276 average time/residue: 0.2942 time to fit residues: 131.4708 Evaluate side-chains 261 residues out of total 2210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 232 time to evaluate : 2.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 GLU Chi-restraints excluded: chain A residue 126 LYS Chi-restraints excluded: chain A residue 140 CYS Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 293 PHE Chi-restraints excluded: chain A residue 380 GLU Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 636 LEU Chi-restraints excluded: chain A residue 702 LEU Chi-restraints excluded: chain A residue 759 GLU Chi-restraints excluded: chain A residue 900 SER Chi-restraints excluded: chain A residue 1008 VAL Chi-restraints excluded: chain A residue 1370 GLN Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 591 LEU Chi-restraints excluded: chain D residue 667 CYS Chi-restraints excluded: chain D residue 740 ILE Chi-restraints excluded: chain D residue 741 THR Chi-restraints excluded: chain D residue 818 VAL Chi-restraints excluded: chain D residue 1065 LEU Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 254 ILE Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 299 VAL Chi-restraints excluded: chain C residue 342 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 110 optimal weight: 0.9980 chunk 137 optimal weight: 0.7980 chunk 156 optimal weight: 1.9990 chunk 4 optimal weight: 0.7980 chunk 90 optimal weight: 10.0000 chunk 64 optimal weight: 3.9990 chunk 49 optimal weight: 0.5980 chunk 83 optimal weight: 1.9990 chunk 173 optimal weight: 3.9990 chunk 229 optimal weight: 3.9990 chunk 15 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 668 ASN ** D 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 869 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.176064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.114877 restraints weight = 28966.621| |-----------------------------------------------------------------------------| r_work (start): 0.3219 rms_B_bonded: 2.31 r_work: 0.3083 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2961 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.2421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 20713 Z= 0.113 Angle : 0.576 15.689 28084 Z= 0.280 Chirality : 0.042 0.258 3199 Planarity : 0.004 0.059 3550 Dihedral : 7.619 100.747 3022 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 1.81 % Allowed : 14.71 % Favored : 83.48 % 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: -0.27 (0.17), residues: 2472 helix: 1.00 (0.15), residues: 1225 sheet: -0.42 (0.32), residues: 264 loop : -1.63 (0.19), residues: 983 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 441 HIS 0.005 0.001 HIS A 912 PHE 0.021 0.001 PHE D 686 TYR 0.017 0.001 TYR D1068 ARG 0.005 0.000 ARG A1378 Details of bonding type rmsd link_NAG-ASN : bond 0.00808 ( 6) link_NAG-ASN : angle 4.04196 ( 18) link_BETA1-4 : bond 0.00871 ( 8) link_BETA1-4 : angle 2.92657 ( 24) hydrogen bonds : bond 0.03496 ( 904) hydrogen bonds : angle 4.06454 ( 2643) SS BOND : bond 0.00311 ( 10) SS BOND : angle 1.31897 ( 20) covalent geometry : bond 0.00254 (20689) covalent geometry : angle 0.55987 (28022) *********************** 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 297 residues out of total 2210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 257 time to evaluate : 2.143 Fit side-chains revert: symmetry clash REVERT: A 124 GLU cc_start: 0.8193 (OUTLIER) cc_final: 0.7818 (mp0) REVERT: A 152 ASP cc_start: 0.9016 (t0) cc_final: 0.8605 (t0) REVERT: A 680 GLU cc_start: 0.8550 (tt0) cc_final: 0.8275 (tt0) REVERT: A 759 GLU cc_start: 0.8134 (OUTLIER) cc_final: 0.7461 (mp0) REVERT: A 1209 TYR cc_start: 0.5082 (m-80) cc_final: 0.4728 (m-80) REVERT: A 1278 ILE cc_start: 0.8246 (mm) cc_final: 0.7700 (pt) REVERT: A 1370 GLN cc_start: 0.8367 (OUTLIER) cc_final: 0.7391 (mp10) REVERT: A 1464 MET cc_start: 0.6933 (ttt) cc_final: 0.6544 (ttp) REVERT: D 40 MET cc_start: 0.8172 (ttp) cc_final: 0.7561 (ptm) REVERT: D 554 GLN cc_start: 0.6524 (mp10) cc_final: 0.6270 (pm20) REVERT: D 690 LYS cc_start: 0.6272 (tptt) cc_final: 0.5052 (tptp) REVERT: D 1009 MET cc_start: 0.8353 (mmm) cc_final: 0.7683 (mtp) REVERT: C 211 ARG cc_start: 0.3978 (mtm-85) cc_final: 0.3632 (ptt-90) REVERT: C 302 ARG cc_start: 0.4912 (mmm-85) cc_final: 0.4610 (ptp-110) REVERT: C 313 LYS cc_start: 0.6264 (mmmt) cc_final: 0.6056 (pttt) REVERT: C 342 LEU cc_start: 0.2308 (OUTLIER) cc_final: 0.1862 (tp) outliers start: 40 outliers final: 22 residues processed: 288 average time/residue: 0.2903 time to fit residues: 133.3551 Evaluate side-chains 264 residues out of total 2210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 238 time to evaluate : 2.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 GLU Chi-restraints excluded: chain A residue 140 CYS Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 380 GLU Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 636 LEU Chi-restraints excluded: chain A residue 702 LEU Chi-restraints excluded: chain A residue 759 GLU Chi-restraints excluded: chain A residue 900 SER Chi-restraints excluded: chain A residue 1008 VAL Chi-restraints excluded: chain A residue 1370 GLN Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 532 ILE Chi-restraints excluded: chain D residue 591 LEU Chi-restraints excluded: chain D residue 667 CYS Chi-restraints excluded: chain D residue 818 VAL Chi-restraints excluded: chain D residue 1028 THR Chi-restraints excluded: chain D residue 1065 LEU Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 254 ILE Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 342 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 224 optimal weight: 4.9990 chunk 232 optimal weight: 7.9990 chunk 32 optimal weight: 0.9990 chunk 79 optimal weight: 1.9990 chunk 186 optimal weight: 1.9990 chunk 135 optimal weight: 2.9990 chunk 247 optimal weight: 4.9990 chunk 194 optimal weight: 3.9990 chunk 117 optimal weight: 0.0070 chunk 146 optimal weight: 1.9990 chunk 203 optimal weight: 3.9990 overall best weight: 1.4006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.175394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.118402 restraints weight = 28981.160| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 2.66 r_work: 0.2963 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2836 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.2567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.116 20713 Z= 0.142 Angle : 0.594 15.302 28084 Z= 0.291 Chirality : 0.043 0.247 3199 Planarity : 0.004 0.059 3550 Dihedral : 7.430 101.871 3022 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 1.86 % Allowed : 15.02 % Favored : 83.12 % 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: -0.25 (0.17), residues: 2472 helix: 1.05 (0.15), residues: 1216 sheet: -0.44 (0.32), residues: 264 loop : -1.64 (0.19), residues: 992 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 441 HIS 0.003 0.001 HIS A 544 PHE 0.025 0.001 PHE D 686 TYR 0.017 0.001 TYR D1068 ARG 0.007 0.000 ARG A 997 Details of bonding type rmsd link_NAG-ASN : bond 0.00768 ( 6) link_NAG-ASN : angle 3.98233 ( 18) link_BETA1-4 : bond 0.00838 ( 8) link_BETA1-4 : angle 2.99626 ( 24) hydrogen bonds : bond 0.03590 ( 904) hydrogen bonds : angle 4.03916 ( 2643) SS BOND : bond 0.00331 ( 10) SS BOND : angle 1.44075 ( 20) covalent geometry : bond 0.00339 (20689) covalent geometry : angle 0.57810 (28022) *********************** 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 288 residues out of total 2210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 247 time to evaluate : 2.080 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 152 ASP cc_start: 0.9101 (t0) cc_final: 0.8714 (t0) REVERT: A 293 PHE cc_start: 0.8756 (OUTLIER) cc_final: 0.6867 (p90) REVERT: A 759 GLU cc_start: 0.8155 (OUTLIER) cc_final: 0.7515 (mp0) REVERT: A 1009 PHE cc_start: 0.8105 (m-80) cc_final: 0.7760 (m-80) REVERT: A 1209 TYR cc_start: 0.5063 (m-80) cc_final: 0.4711 (m-80) REVERT: A 1237 MET cc_start: 0.8066 (OUTLIER) cc_final: 0.7860 (mmm) REVERT: A 1278 ILE cc_start: 0.8268 (mm) cc_final: 0.7741 (pt) REVERT: A 1370 GLN cc_start: 0.8513 (OUTLIER) cc_final: 0.7506 (mp10) REVERT: A 1410 GLU cc_start: 0.8976 (mm-30) cc_final: 0.8769 (mm-30) REVERT: A 1464 MET cc_start: 0.7074 (ttt) cc_final: 0.6668 (ttp) REVERT: D 40 MET cc_start: 0.8216 (ttp) cc_final: 0.7603 (ptm) REVERT: D 554 GLN cc_start: 0.6581 (mp10) cc_final: 0.6285 (pm20) REVERT: D 671 LYS cc_start: 0.7815 (pttt) cc_final: 0.7561 (pttp) REVERT: D 690 LYS cc_start: 0.6319 (tptt) cc_final: 0.5036 (tptp) REVERT: D 1009 MET cc_start: 0.8404 (mmm) cc_final: 0.7658 (mtp) REVERT: C 211 ARG cc_start: 0.3801 (mtm-85) cc_final: 0.3420 (ptt-90) REVERT: C 302 ARG cc_start: 0.4957 (mmm-85) cc_final: 0.4614 (ptp-110) REVERT: C 312 MET cc_start: 0.5697 (mmp) cc_final: 0.5440 (mmp) REVERT: C 313 LYS cc_start: 0.6150 (mmmt) cc_final: 0.5848 (pttt) REVERT: C 342 LEU cc_start: 0.2325 (OUTLIER) cc_final: 0.1837 (tp) outliers start: 41 outliers final: 33 residues processed: 278 average time/residue: 0.3051 time to fit residues: 135.3263 Evaluate side-chains 275 residues out of total 2210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 237 time to evaluate : 2.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 140 CYS Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 293 PHE Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 379 PHE Chi-restraints excluded: chain A residue 380 GLU Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 620 CYS Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 636 LEU Chi-restraints excluded: chain A residue 702 LEU Chi-restraints excluded: chain A residue 759 GLU Chi-restraints excluded: chain A residue 900 SER Chi-restraints excluded: chain A residue 1008 VAL Chi-restraints excluded: chain A residue 1237 MET Chi-restraints excluded: chain A residue 1276 ILE Chi-restraints excluded: chain A residue 1370 GLN Chi-restraints excluded: chain D residue 192 VAL Chi-restraints excluded: chain D residue 246 GLN Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 284 SER Chi-restraints excluded: chain D residue 328 LYS Chi-restraints excluded: chain D residue 532 ILE Chi-restraints excluded: chain D residue 591 LEU Chi-restraints excluded: chain D residue 667 CYS Chi-restraints excluded: chain D residue 740 ILE Chi-restraints excluded: chain D residue 818 VAL Chi-restraints excluded: chain D residue 869 ASN Chi-restraints excluded: chain D residue 1028 THR Chi-restraints excluded: chain D residue 1065 LEU Chi-restraints excluded: chain D residue 1071 CYS Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 254 ILE Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 299 VAL Chi-restraints excluded: chain C residue 342 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 30 optimal weight: 0.8980 chunk 12 optimal weight: 3.9990 chunk 9 optimal weight: 0.6980 chunk 75 optimal weight: 2.9990 chunk 170 optimal weight: 2.9990 chunk 62 optimal weight: 6.9990 chunk 177 optimal weight: 5.9990 chunk 116 optimal weight: 0.2980 chunk 93 optimal weight: 9.9990 chunk 202 optimal weight: 2.9990 chunk 101 optimal weight: 5.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 869 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.174506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.114431 restraints weight = 29184.357| |-----------------------------------------------------------------------------| r_work (start): 0.3156 rms_B_bonded: 2.32 r_work: 0.2984 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2864 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.2709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.097 20713 Z= 0.149 Angle : 0.607 15.167 28084 Z= 0.294 Chirality : 0.043 0.243 3199 Planarity : 0.004 0.059 3550 Dihedral : 7.084 101.582 3019 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 1.63 % Allowed : 15.61 % Favored : 82.76 % 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: -0.22 (0.17), residues: 2472 helix: 1.07 (0.15), residues: 1210 sheet: -0.43 (0.32), residues: 264 loop : -1.60 (0.19), residues: 998 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A1269 HIS 0.003 0.001 HIS A 544 PHE 0.026 0.001 PHE D 686 TYR 0.017 0.001 TYR D1068 ARG 0.007 0.000 ARG A 997 Details of bonding type rmsd link_NAG-ASN : bond 0.00738 ( 6) link_NAG-ASN : angle 3.97448 ( 18) link_BETA1-4 : bond 0.00852 ( 8) link_BETA1-4 : angle 3.06858 ( 24) hydrogen bonds : bond 0.03599 ( 904) hydrogen bonds : angle 4.05150 ( 2643) SS BOND : bond 0.00338 ( 10) SS BOND : angle 1.48690 ( 20) covalent geometry : bond 0.00357 (20689) covalent geometry : angle 0.59160 (28022) *********************** REFINEMENT MACRO_CYCLE 8 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 282 residues out of total 2210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 246 time to evaluate : 2.091 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 152 ASP cc_start: 0.9033 (t0) cc_final: 0.8662 (t0) REVERT: A 570 MET cc_start: 0.6980 (tpp) cc_final: 0.6600 (tpp) REVERT: A 1009 PHE cc_start: 0.8053 (m-80) cc_final: 0.7713 (m-80) REVERT: A 1209 TYR cc_start: 0.4980 (m-80) cc_final: 0.4651 (m-80) REVERT: A 1269 TRP cc_start: 0.7671 (m100) cc_final: 0.7275 (m100) REVERT: A 1278 ILE cc_start: 0.8236 (mm) cc_final: 0.7723 (pt) REVERT: A 1370 GLN cc_start: 0.8434 (OUTLIER) cc_final: 0.7375 (mp10) REVERT: D 40 MET cc_start: 0.8142 (ttp) cc_final: 0.7581 (ptm) REVERT: D 554 GLN cc_start: 0.6571 (mp10) cc_final: 0.6307 (pm20) REVERT: D 671 LYS cc_start: 0.7850 (pttt) cc_final: 0.7616 (pttp) REVERT: D 690 LYS cc_start: 0.6251 (tptt) cc_final: 0.5017 (tptp) REVERT: D 750 GLU cc_start: 0.7434 (mp0) cc_final: 0.7176 (mp0) REVERT: D 1009 MET cc_start: 0.8358 (mmm) cc_final: 0.7645 (mtp) REVERT: C 302 ARG cc_start: 0.5027 (mmm-85) cc_final: 0.4712 (ptp-110) REVERT: C 312 MET cc_start: 0.5813 (mmp) cc_final: 0.5504 (mmp) REVERT: C 313 LYS cc_start: 0.6055 (mmmt) cc_final: 0.5835 (pttt) REVERT: C 342 LEU cc_start: 0.2156 (OUTLIER) cc_final: 0.1729 (tp) outliers start: 36 outliers final: 29 residues processed: 271 average time/residue: 0.2933 time to fit residues: 127.9498 Evaluate side-chains 265 residues out of total 2210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 234 time to evaluate : 2.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 CYS Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 380 GLU Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 620 CYS Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 636 LEU Chi-restraints excluded: chain A residue 702 LEU Chi-restraints excluded: chain A residue 900 SER Chi-restraints excluded: chain A residue 1008 VAL Chi-restraints excluded: chain A residue 1276 ILE Chi-restraints excluded: chain A residue 1370 GLN Chi-restraints excluded: chain A residue 1455 ILE Chi-restraints excluded: chain D residue 192 VAL Chi-restraints excluded: chain D residue 246 GLN Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 284 SER Chi-restraints excluded: chain D residue 532 ILE Chi-restraints excluded: chain D residue 591 LEU Chi-restraints excluded: chain D residue 667 CYS Chi-restraints excluded: chain D residue 740 ILE Chi-restraints excluded: chain D residue 818 VAL Chi-restraints excluded: chain D residue 1028 THR Chi-restraints excluded: chain D residue 1065 LEU Chi-restraints excluded: chain D residue 1071 CYS Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 299 VAL Chi-restraints excluded: chain C residue 342 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 6 optimal weight: 0.8980 chunk 103 optimal weight: 0.9990 chunk 204 optimal weight: 2.9990 chunk 55 optimal weight: 8.9990 chunk 212 optimal weight: 0.5980 chunk 123 optimal weight: 3.9990 chunk 25 optimal weight: 0.8980 chunk 138 optimal weight: 4.9990 chunk 232 optimal weight: 5.9990 chunk 141 optimal weight: 0.3980 chunk 245 optimal weight: 1.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 886 HIS ** D 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 703 ASN D 869 ASN ** C 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.175943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.121649 restraints weight = 29080.918| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 2.68 r_work: 0.3005 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2881 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.2777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.140 20713 Z= 0.114 Angle : 0.578 15.739 28084 Z= 0.281 Chirality : 0.042 0.254 3199 Planarity : 0.004 0.059 3550 Dihedral : 6.773 101.775 3016 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 1.54 % Allowed : 15.88 % Favored : 82.58 % 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: -0.07 (0.17), residues: 2472 helix: 1.18 (0.15), residues: 1216 sheet: -0.37 (0.32), residues: 262 loop : -1.52 (0.20), residues: 994 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 441 HIS 0.002 0.000 HIS A 544 PHE 0.026 0.001 PHE D 686 TYR 0.016 0.001 TYR D1068 ARG 0.006 0.000 ARG A 997 Details of bonding type rmsd link_NAG-ASN : bond 0.00781 ( 6) link_NAG-ASN : angle 3.93914 ( 18) link_BETA1-4 : bond 0.00832 ( 8) link_BETA1-4 : angle 3.04963 ( 24) hydrogen bonds : bond 0.03338 ( 904) hydrogen bonds : angle 3.98256 ( 2643) SS BOND : bond 0.00280 ( 10) SS BOND : angle 1.22142 ( 20) covalent geometry : bond 0.00272 (20689) covalent geometry : angle 0.56219 (28022) *********************** REFINEMENT MACRO_CYCLE 9 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 277 residues out of total 2210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 243 time to evaluate : 2.813 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 152 ASP cc_start: 0.9058 (t0) cc_final: 0.8726 (t0) REVERT: A 293 PHE cc_start: 0.8691 (OUTLIER) cc_final: 0.7001 (p90) REVERT: A 570 MET cc_start: 0.6958 (tpp) cc_final: 0.6531 (tpp) REVERT: A 1009 PHE cc_start: 0.8101 (m-80) cc_final: 0.7786 (m-80) REVERT: A 1209 TYR cc_start: 0.5085 (m-80) cc_final: 0.4734 (m-80) REVERT: A 1237 MET cc_start: 0.7588 (mmm) cc_final: 0.7386 (mmt) REVERT: A 1278 ILE cc_start: 0.8245 (mm) cc_final: 0.7784 (pt) REVERT: A 1370 GLN cc_start: 0.8415 (OUTLIER) cc_final: 0.7415 (mp10) REVERT: A 1586 MET cc_start: 0.3579 (tpt) cc_final: 0.2171 (mpp) REVERT: D 40 MET cc_start: 0.8164 (ttp) cc_final: 0.7648 (ptm) REVERT: D 554 GLN cc_start: 0.6585 (mp10) cc_final: 0.6328 (pm20) REVERT: D 601 ASP cc_start: 0.8147 (t0) cc_final: 0.7844 (p0) REVERT: D 667 CYS cc_start: 0.7209 (OUTLIER) cc_final: 0.6542 (p) REVERT: D 671 LYS cc_start: 0.7884 (pttt) cc_final: 0.7653 (pttp) REVERT: D 690 LYS cc_start: 0.6301 (tptt) cc_final: 0.5075 (tptp) REVERT: D 750 GLU cc_start: 0.7459 (mp0) cc_final: 0.7194 (mp0) REVERT: D 1009 MET cc_start: 0.8363 (mmm) cc_final: 0.7665 (mtp) REVERT: C 342 LEU cc_start: 0.2516 (OUTLIER) cc_final: 0.2078 (tp) outliers start: 34 outliers final: 27 residues processed: 269 average time/residue: 0.4258 time to fit residues: 189.1838 Evaluate side-chains 259 residues out of total 2210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 228 time to evaluate : 2.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 140 CYS Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 293 PHE Chi-restraints excluded: chain A residue 379 PHE Chi-restraints excluded: chain A residue 380 GLU Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 620 CYS Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 636 LEU Chi-restraints excluded: chain A residue 702 LEU Chi-restraints excluded: chain A residue 900 SER Chi-restraints excluded: chain A residue 1008 VAL Chi-restraints excluded: chain A residue 1276 ILE Chi-restraints excluded: chain A residue 1370 GLN Chi-restraints excluded: chain D residue 192 VAL Chi-restraints excluded: chain D residue 246 GLN Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 284 SER Chi-restraints excluded: chain D residue 532 ILE Chi-restraints excluded: chain D residue 591 LEU Chi-restraints excluded: chain D residue 667 CYS Chi-restraints excluded: chain D residue 818 VAL Chi-restraints excluded: chain D residue 1028 THR Chi-restraints excluded: chain D residue 1065 LEU Chi-restraints excluded: chain D residue 1071 CYS Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 299 VAL Chi-restraints excluded: chain C residue 342 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 187 optimal weight: 2.9990 chunk 153 optimal weight: 0.0980 chunk 53 optimal weight: 6.9990 chunk 200 optimal weight: 10.0000 chunk 102 optimal weight: 7.9990 chunk 195 optimal weight: 5.9990 chunk 109 optimal weight: 0.8980 chunk 119 optimal weight: 6.9990 chunk 227 optimal weight: 30.0000 chunk 13 optimal weight: 0.9990 chunk 123 optimal weight: 0.0040 overall best weight: 0.9996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 869 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.176297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.117450 restraints weight = 29378.102| |-----------------------------------------------------------------------------| r_work (start): 0.3251 rms_B_bonded: 2.70 r_work: 0.3056 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2933 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.2841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.134 20713 Z= 0.123 Angle : 0.591 15.788 28084 Z= 0.288 Chirality : 0.043 0.253 3199 Planarity : 0.004 0.059 3550 Dihedral : 6.693 101.241 3016 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 1.63 % Allowed : 16.02 % 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: -0.06 (0.17), residues: 2472 helix: 1.17 (0.15), residues: 1211 sheet: -0.35 (0.32), residues: 262 loop : -1.49 (0.20), residues: 999 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A1269 HIS 0.002 0.001 HIS A 544 PHE 0.025 0.001 PHE D 686 TYR 0.017 0.001 TYR D1068 ARG 0.006 0.000 ARG A 997 Details of bonding type rmsd link_NAG-ASN : bond 0.00778 ( 6) link_NAG-ASN : angle 3.92804 ( 18) link_BETA1-4 : bond 0.00821 ( 8) link_BETA1-4 : angle 3.02907 ( 24) hydrogen bonds : bond 0.03420 ( 904) hydrogen bonds : angle 3.99154 ( 2643) SS BOND : bond 0.00299 ( 10) SS BOND : angle 1.24714 ( 20) covalent geometry : bond 0.00299 (20689) covalent geometry : angle 0.57503 (28022) ********************** REFINEMENT MACRO_CYCLE 10 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 276 residues out of total 2210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 240 time to evaluate : 3.859 Fit side-chains revert: symmetry clash REVERT: A 152 ASP cc_start: 0.9037 (t0) cc_final: 0.8717 (t0) REVERT: A 293 PHE cc_start: 0.8793 (OUTLIER) cc_final: 0.7077 (p90) REVERT: A 570 MET cc_start: 0.7054 (tpp) cc_final: 0.6594 (tpp) REVERT: A 1009 PHE cc_start: 0.8220 (m-80) cc_final: 0.7902 (m-80) REVERT: A 1146 ILE cc_start: 0.8640 (OUTLIER) cc_final: 0.8026 (tt) REVERT: A 1209 TYR cc_start: 0.5145 (m-80) cc_final: 0.4798 (m-80) REVERT: A 1278 ILE cc_start: 0.8289 (mm) cc_final: 0.7826 (pt) REVERT: A 1370 GLN cc_start: 0.8409 (OUTLIER) cc_final: 0.7427 (mp10) REVERT: A 1464 MET cc_start: 0.7018 (ttt) cc_final: 0.6671 (ttp) REVERT: A 1586 MET cc_start: 0.3920 (tpt) cc_final: 0.2449 (mpp) REVERT: D 40 MET cc_start: 0.8157 (ttp) cc_final: 0.7667 (ptm) REVERT: D 554 GLN cc_start: 0.6621 (mp10) cc_final: 0.6368 (pm20) REVERT: D 601 ASP cc_start: 0.8110 (t0) cc_final: 0.7889 (p0) REVERT: D 667 CYS cc_start: 0.7071 (OUTLIER) cc_final: 0.6619 (p) REVERT: D 671 LYS cc_start: 0.7899 (pttt) cc_final: 0.7655 (pttp) REVERT: D 690 LYS cc_start: 0.6403 (tptt) cc_final: 0.5133 (tptp) REVERT: D 750 GLU cc_start: 0.7427 (mp0) cc_final: 0.7190 (mp0) REVERT: D 1009 MET cc_start: 0.8349 (mmm) cc_final: 0.7700 (mtp) REVERT: C 342 LEU cc_start: 0.2442 (OUTLIER) cc_final: 0.1961 (tp) outliers start: 36 outliers final: 28 residues processed: 269 average time/residue: 0.3968 time to fit residues: 176.9224 Evaluate side-chains 263 residues out of total 2210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 230 time to evaluate : 2.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 140 CYS Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 293 PHE Chi-restraints excluded: chain A residue 379 PHE Chi-restraints excluded: chain A residue 380 GLU Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 620 CYS Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 636 LEU Chi-restraints excluded: chain A residue 702 LEU Chi-restraints excluded: chain A residue 900 SER Chi-restraints excluded: chain A residue 1008 VAL Chi-restraints excluded: chain A residue 1146 ILE Chi-restraints excluded: chain A residue 1276 ILE Chi-restraints excluded: chain A residue 1370 GLN Chi-restraints excluded: chain D residue 192 VAL Chi-restraints excluded: chain D residue 246 GLN Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 284 SER Chi-restraints excluded: chain D residue 532 ILE Chi-restraints excluded: chain D residue 591 LEU Chi-restraints excluded: chain D residue 667 CYS Chi-restraints excluded: chain D residue 818 VAL Chi-restraints excluded: chain D residue 1028 THR Chi-restraints excluded: chain D residue 1065 LEU Chi-restraints excluded: chain D residue 1071 CYS Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 299 VAL Chi-restraints excluded: chain C residue 318 GLN Chi-restraints excluded: chain C residue 342 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 159 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 chunk 108 optimal weight: 0.6980 chunk 242 optimal weight: 3.9990 chunk 228 optimal weight: 8.9990 chunk 23 optimal weight: 0.9980 chunk 118 optimal weight: 8.9990 chunk 33 optimal weight: 0.8980 chunk 140 optimal weight: 0.0370 chunk 244 optimal weight: 3.9990 chunk 246 optimal weight: 0.9990 overall best weight: 0.7058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1466 ASN D 377 ASN ** D 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 869 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.177176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.118606 restraints weight = 29437.258| |-----------------------------------------------------------------------------| r_work (start): 0.3263 rms_B_bonded: 2.62 r_work: 0.3068 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2947 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.2902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.170 20713 Z= 0.111 Angle : 0.584 18.061 28084 Z= 0.283 Chirality : 0.042 0.257 3199 Planarity : 0.004 0.059 3550 Dihedral : 6.552 100.474 3016 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 1.63 % Allowed : 16.43 % Favored : 81.95 % Cbeta Deviations : 0.04 % 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: -0.00 (0.17), residues: 2472 helix: 1.22 (0.16), residues: 1212 sheet: -0.35 (0.32), residues: 262 loop : -1.45 (0.20), residues: 998 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A1269 HIS 0.012 0.001 HIS C 314 PHE 0.026 0.001 PHE D 686 TYR 0.017 0.001 TYR D1068 ARG 0.006 0.000 ARG A 997 Details of bonding type rmsd link_NAG-ASN : bond 0.00805 ( 6) link_NAG-ASN : angle 3.90688 ( 18) link_BETA1-4 : bond 0.00830 ( 8) link_BETA1-4 : angle 2.99109 ( 24) hydrogen bonds : bond 0.03263 ( 904) hydrogen bonds : angle 3.94029 ( 2643) SS BOND : bond 0.00276 ( 10) SS BOND : angle 1.14637 ( 20) covalent geometry : bond 0.00273 (20689) covalent geometry : angle 0.56920 (28022) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 22274.98 seconds wall clock time: 395 minutes 29.28 seconds (23729.28 seconds total)