Starting phenix.real_space_refine on Sat Sep 28 21:24:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e5a_27908/09_2024/8e5a_27908.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e5a_27908/09_2024/8e5a_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e5a_27908/09_2024/8e5a_27908.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e5a_27908/09_2024/8e5a_27908.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e5a_27908/09_2024/8e5a_27908.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e5a_27908/09_2024/8e5a_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-5461/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: 11.31, 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: 5.65 Conformation dependent library (CDL) restraints added in 2.6 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: 2.72 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: 7.30 Time building geometry restraints manager: 6.28 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: 1.200 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.860 Check model and map are aligned: 0.150 Set scattering table: 0.190 Process input model: 46.130 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.090 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: 51.640 ------------------------------------------------------------------------------- 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 20689 Z= 0.197 Angle : 0.674 9.211 28022 Z= 0.404 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 *********************** 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 fitting. rotamer outliers: 41 poor density : 361 time to evaluate : 2.291 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: 0.3159 time to fit residues: 191.7356 Evaluate side-chains 286 residues out of total 2210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 260 time to evaluate : 2.200 ------------------------------------------------------------------------------- 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: 4.9990 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 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 20689 Z= 0.214 Angle : 0.644 16.425 28022 Z= 0.318 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 *********************** 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 fitting. rotamer outliers: 36 poor density : 288 time to evaluate : 2.267 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 124 GLU cc_start: 0.7999 (OUTLIER) cc_final: 0.7652 (pm20) REVERT: A 126 LYS cc_start: 0.5983 (OUTLIER) cc_final: 0.5484 (tmmt) REVERT: A 152 ASP cc_start: 0.7600 (t0) cc_final: 0.7298 (t0) REVERT: A 587 PHE cc_start: 0.6084 (m-10) cc_final: 0.5842 (m-10) REVERT: A 759 GLU cc_start: 0.8275 (OUTLIER) cc_final: 0.7616 (mp0) REVERT: A 1020 ILE cc_start: 0.9030 (OUTLIER) cc_final: 0.8764 (mt) REVERT: A 1209 TYR cc_start: 0.5158 (m-80) cc_final: 0.4818 (m-80) REVERT: A 1278 ILE cc_start: 0.8433 (mm) cc_final: 0.8202 (pt) REVERT: A 1464 MET cc_start: 0.6600 (ttt) cc_final: 0.6237 (ttp) REVERT: D 532 ILE cc_start: 0.8975 (pt) cc_final: 0.8680 (mt) REVERT: D 668 ASN cc_start: 0.6996 (OUTLIER) cc_final: 0.6326 (p0) REVERT: D 690 LYS cc_start: 0.6751 (tptt) cc_final: 0.5567 (tptp) outliers start: 36 outliers final: 19 residues processed: 312 average time/residue: 0.2957 time to fit residues: 145.9829 Evaluate side-chains 271 residues out of total 2210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 247 time to evaluate : 2.422 ------------------------------------------------------------------------------- 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 125 optimal weight: 10.0000 chunk 70 optimal weight: 3.9990 chunk 188 optimal weight: 3.9990 chunk 153 optimal weight: 2.9990 chunk 62 optimal weight: 0.6980 chunk 226 optimal weight: 9.9990 chunk 244 optimal weight: 6.9990 chunk 201 optimal weight: 5.9990 chunk 224 optimal weight: 0.3980 chunk 77 optimal weight: 3.9990 chunk 181 optimal weight: 0.8980 overall best weight: 1.7984 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.1946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 20689 Z= 0.255 Angle : 0.632 15.590 28022 Z= 0.308 Chirality : 0.044 0.303 3199 Planarity : 0.004 0.059 3550 Dihedral : 9.606 101.233 3035 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 2.17 % Allowed : 11.09 % Favored : 86.74 % 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: -0.64 (0.17), residues: 2472 helix: 0.61 (0.15), residues: 1215 sheet: -0.61 (0.30), residues: 282 loop : -1.67 (0.20), residues: 975 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 441 HIS 0.005 0.001 HIS A 544 PHE 0.017 0.002 PHE A 293 TYR 0.018 0.001 TYR D1068 ARG 0.006 0.000 ARG A 997 *********************** 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 303 residues out of total 2210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 255 time to evaluate : 2.299 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 124 GLU cc_start: 0.7932 (OUTLIER) cc_final: 0.7526 (mp0) REVERT: A 126 LYS cc_start: 0.5968 (OUTLIER) cc_final: 0.5676 (tmmt) REVERT: A 152 ASP cc_start: 0.7755 (t0) cc_final: 0.7386 (t0) REVERT: A 587 PHE cc_start: 0.6103 (m-10) cc_final: 0.5786 (m-10) REVERT: A 759 GLU cc_start: 0.8245 (OUTLIER) cc_final: 0.7549 (mp0) REVERT: A 1209 TYR cc_start: 0.5112 (m-80) cc_final: 0.4839 (m-80) REVERT: A 1278 ILE cc_start: 0.8404 (mm) cc_final: 0.8049 (pt) REVERT: A 1464 MET cc_start: 0.6620 (ttt) cc_final: 0.6204 (ttp) REVERT: D 668 ASN cc_start: 0.6917 (OUTLIER) cc_final: 0.6682 (p0) REVERT: D 690 LYS cc_start: 0.6703 (tptt) cc_final: 0.5519 (tptp) outliers start: 48 outliers final: 28 residues processed: 288 average time/residue: 0.2926 time to fit residues: 135.3178 Evaluate side-chains 258 residues out of total 2210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 226 time to evaluate : 2.465 ------------------------------------------------------------------------------- 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 140 CYS Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 204 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 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 957 LEU Chi-restraints excluded: chain A residue 1008 VAL Chi-restraints excluded: chain A residue 1271 THR 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 741 THR Chi-restraints excluded: chain D residue 816 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 221 LEU Chi-restraints excluded: chain C residue 254 ILE Chi-restraints excluded: chain C residue 260 LEU 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 223 optimal weight: 20.0000 chunk 170 optimal weight: 3.9990 chunk 117 optimal weight: 40.0000 chunk 25 optimal weight: 4.9990 chunk 108 optimal weight: 0.6980 chunk 152 optimal weight: 0.9980 chunk 227 optimal weight: 0.7980 chunk 240 optimal weight: 0.0970 chunk 118 optimal weight: 10.0000 chunk 215 optimal weight: 4.9990 chunk 64 optimal weight: 10.0000 overall best weight: 1.3180 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.2182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 20689 Z= 0.210 Angle : 0.581 16.203 28022 Z= 0.287 Chirality : 0.043 0.286 3199 Planarity : 0.004 0.058 3550 Dihedral : 8.568 101.404 3028 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 2.13 % Allowed : 12.90 % Favored : 84.98 % 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: -0.52 (0.17), residues: 2472 helix: 0.76 (0.15), residues: 1215 sheet: -0.52 (0.30), residues: 285 loop : -1.71 (0.19), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 441 HIS 0.003 0.001 HIS A 544 PHE 0.013 0.001 PHE D 588 TYR 0.016 0.001 TYR D1068 ARG 0.004 0.000 ARG A 685 *********************** 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 305 residues out of total 2210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 258 time to evaluate : 2.127 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 124 GLU cc_start: 0.7864 (OUTLIER) cc_final: 0.7385 (mp0) REVERT: A 126 LYS cc_start: 0.5908 (OUTLIER) cc_final: 0.5665 (tmmt) REVERT: A 152 ASP cc_start: 0.7765 (t0) cc_final: 0.7409 (t0) REVERT: A 759 GLU cc_start: 0.8173 (OUTLIER) cc_final: 0.7516 (mp0) REVERT: A 983 LEU cc_start: 0.8867 (OUTLIER) cc_final: 0.8635 (mp) REVERT: A 1209 TYR cc_start: 0.5095 (m-80) cc_final: 0.4769 (m-80) REVERT: A 1278 ILE cc_start: 0.8473 (mm) cc_final: 0.8027 (pt) REVERT: A 1370 GLN cc_start: 0.7884 (OUTLIER) cc_final: 0.6819 (mp10) REVERT: A 1464 MET cc_start: 0.6399 (ttt) cc_final: 0.6037 (ttp) REVERT: D 40 MET cc_start: 0.7568 (ttp) cc_final: 0.7045 (ptm) REVERT: D 690 LYS cc_start: 0.6580 (tptt) cc_final: 0.5347 (tptp) REVERT: C 323 ASP cc_start: 0.6519 (p0) cc_final: 0.6263 (p0) REVERT: C 342 LEU cc_start: 0.2980 (OUTLIER) cc_final: 0.2457 (tp) outliers start: 47 outliers final: 29 residues processed: 291 average time/residue: 0.2837 time to fit residues: 133.3392 Evaluate side-chains 262 residues out of total 2210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 227 time to evaluate : 2.279 ------------------------------------------------------------------------------- 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 140 CYS Chi-restraints excluded: chain A residue 204 ILE 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 759 GLU Chi-restraints excluded: chain A residue 900 SER Chi-restraints excluded: chain A residue 983 LEU 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 740 ILE Chi-restraints excluded: chain D residue 741 THR Chi-restraints excluded: chain D residue 816 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 C residue 108 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 292 VAL Chi-restraints excluded: chain C residue 299 VAL 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 200 optimal weight: 0.7980 chunk 136 optimal weight: 0.9990 chunk 3 optimal weight: 3.9990 chunk 179 optimal weight: 5.9990 chunk 99 optimal weight: 0.9980 chunk 205 optimal weight: 7.9990 chunk 166 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 122 optimal weight: 0.2980 chunk 216 optimal weight: 7.9990 chunk 60 optimal weight: 0.8980 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 713 ASN D 869 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.2322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.097 20689 Z= 0.166 Angle : 0.557 15.929 28022 Z= 0.274 Chirality : 0.042 0.254 3199 Planarity : 0.004 0.059 3550 Dihedral : 7.938 100.930 3022 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 1.99 % Allowed : 14.25 % Favored : 83.76 % 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: -0.32 (0.17), residues: 2472 helix: 0.94 (0.15), residues: 1223 sheet: -0.43 (0.30), residues: 283 loop : -1.64 (0.20), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 441 HIS 0.003 0.001 HIS A 912 PHE 0.020 0.001 PHE D 473 TYR 0.015 0.001 TYR D1068 ARG 0.007 0.000 ARG A 997 *********************** 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 298 residues out of total 2210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 254 time to evaluate : 2.458 Fit side-chains revert: symmetry clash REVERT: A 124 GLU cc_start: 0.7727 (OUTLIER) cc_final: 0.7276 (mp0) REVERT: A 152 ASP cc_start: 0.7762 (t0) cc_final: 0.7411 (t0) REVERT: A 293 PHE cc_start: 0.8688 (OUTLIER) cc_final: 0.7086 (p90) REVERT: A 759 GLU cc_start: 0.8104 (OUTLIER) cc_final: 0.7462 (mp0) REVERT: A 1209 TYR cc_start: 0.5104 (m-80) cc_final: 0.4787 (m-80) REVERT: A 1278 ILE cc_start: 0.8420 (mm) cc_final: 0.7945 (pt) REVERT: A 1370 GLN cc_start: 0.7858 (OUTLIER) cc_final: 0.6849 (mp10) REVERT: A 1464 MET cc_start: 0.6397 (ttt) cc_final: 0.6010 (ttp) REVERT: D 40 MET cc_start: 0.7555 (ttp) cc_final: 0.7133 (ptm) REVERT: D 690 LYS cc_start: 0.6584 (tptt) cc_final: 0.5324 (tptp) REVERT: D 802 ILE cc_start: 0.8491 (mm) cc_final: 0.7717 (mm) REVERT: C 342 LEU cc_start: 0.3171 (OUTLIER) cc_final: 0.2507 (tp) outliers start: 44 outliers final: 27 residues processed: 286 average time/residue: 0.2899 time to fit residues: 133.7872 Evaluate side-chains 267 residues out of total 2210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 235 time to evaluate : 2.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 GLU Chi-restraints excluded: chain A residue 130 ILE 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 293 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 1370 GLN Chi-restraints excluded: chain A residue 1455 ILE Chi-restraints excluded: chain D residue 246 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 816 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 C residue 200 LEU Chi-restraints excluded: chain C residue 247 ILE 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 80 optimal weight: 2.9990 chunk 216 optimal weight: 8.9990 chunk 47 optimal weight: 0.8980 chunk 141 optimal weight: 3.9990 chunk 59 optimal weight: 7.9990 chunk 240 optimal weight: 20.0000 chunk 199 optimal weight: 5.9990 chunk 111 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 126 optimal weight: 3.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- 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** ** D 684 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 869 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.2551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.101 20689 Z= 0.296 Angle : 0.607 15.173 28022 Z= 0.304 Chirality : 0.044 0.241 3199 Planarity : 0.004 0.060 3550 Dihedral : 7.872 102.844 3022 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 2.44 % Allowed : 14.21 % Favored : 83.35 % 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: -0.41 (0.17), residues: 2472 helix: 0.90 (0.15), residues: 1214 sheet: -0.60 (0.31), residues: 270 loop : -1.66 (0.19), residues: 988 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 441 HIS 0.004 0.001 HIS A 544 PHE 0.021 0.002 PHE D 686 TYR 0.018 0.001 TYR D1068 ARG 0.005 0.000 ARG A 997 *********************** 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 fitting. rotamer outliers: 54 poor density : 243 time to evaluate : 2.255 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 124 GLU cc_start: 0.7792 (OUTLIER) cc_final: 0.7350 (mp0) REVERT: A 152 ASP cc_start: 0.7827 (t0) cc_final: 0.7467 (t0) REVERT: A 293 PHE cc_start: 0.8863 (OUTLIER) cc_final: 0.7198 (p90) REVERT: A 759 GLU cc_start: 0.8248 (OUTLIER) cc_final: 0.7578 (mp0) REVERT: A 983 LEU cc_start: 0.8865 (OUTLIER) cc_final: 0.8633 (mp) REVERT: A 1209 TYR cc_start: 0.5134 (m-80) cc_final: 0.4806 (m-80) REVERT: A 1370 GLN cc_start: 0.7956 (OUTLIER) cc_final: 0.6818 (mp10) REVERT: D 40 MET cc_start: 0.7537 (ttp) cc_final: 0.7113 (ptm) REVERT: D 671 LYS cc_start: 0.7776 (pttt) cc_final: 0.7480 (pttp) REVERT: D 690 LYS cc_start: 0.6587 (tptt) cc_final: 0.5350 (tptp) REVERT: C 342 LEU cc_start: 0.3339 (OUTLIER) cc_final: 0.2518 (tp) outliers start: 54 outliers final: 37 residues processed: 287 average time/residue: 0.2914 time to fit residues: 134.8709 Evaluate side-chains 275 residues out of total 2210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 232 time to evaluate : 2.198 ------------------------------------------------------------------------------- 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 293 PHE 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 755 LEU Chi-restraints excluded: chain A residue 759 GLU Chi-restraints excluded: chain A residue 763 THR Chi-restraints excluded: chain A residue 900 SER Chi-restraints excluded: chain A residue 983 LEU Chi-restraints excluded: chain A residue 1008 VAL Chi-restraints excluded: chain A residue 1271 THR Chi-restraints excluded: chain A residue 1370 GLN Chi-restraints excluded: chain A residue 1455 ILE Chi-restraints excluded: chain D residue 37 VAL 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 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 816 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 108 LEU Chi-restraints excluded: chain C residue 118 ILE Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 247 ILE 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 232 optimal weight: 8.9990 chunk 27 optimal weight: 3.9990 chunk 137 optimal weight: 0.7980 chunk 175 optimal weight: 4.9990 chunk 136 optimal weight: 0.9980 chunk 202 optimal weight: 4.9990 chunk 134 optimal weight: 5.9990 chunk 239 optimal weight: 10.0000 chunk 150 optimal weight: 0.9980 chunk 146 optimal weight: 1.9990 chunk 110 optimal weight: 9.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- 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 684 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 869 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.2671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 20689 Z= 0.248 Angle : 0.590 15.454 28022 Z= 0.294 Chirality : 0.043 0.243 3199 Planarity : 0.004 0.061 3550 Dihedral : 7.660 102.854 3022 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 2.22 % Allowed : 15.43 % 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: -0.38 (0.17), residues: 2472 helix: 0.90 (0.15), residues: 1218 sheet: -0.60 (0.31), residues: 271 loop : -1.63 (0.20), residues: 983 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 441 HIS 0.004 0.001 HIS A 544 PHE 0.024 0.001 PHE D 686 TYR 0.018 0.001 TYR D1068 ARG 0.006 0.000 ARG C 211 *********************** 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 291 residues out of total 2210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 242 time to evaluate : 2.380 Fit side-chains revert: symmetry clash REVERT: A 152 ASP cc_start: 0.7808 (t0) cc_final: 0.7461 (t0) REVERT: A 293 PHE cc_start: 0.8889 (OUTLIER) cc_final: 0.7258 (p90) REVERT: A 759 GLU cc_start: 0.8234 (OUTLIER) cc_final: 0.7620 (mp0) REVERT: A 983 LEU cc_start: 0.8856 (OUTLIER) cc_final: 0.8626 (mp) REVERT: A 1209 TYR cc_start: 0.5101 (m-80) cc_final: 0.4763 (m-80) REVERT: A 1370 GLN cc_start: 0.7962 (OUTLIER) cc_final: 0.6880 (mp10) REVERT: A 1464 MET cc_start: 0.6513 (ttt) cc_final: 0.6148 (ttp) REVERT: A 1553 LEU cc_start: 0.6537 (OUTLIER) cc_final: 0.6122 (tt) REVERT: D 40 MET cc_start: 0.7491 (ttp) cc_final: 0.7153 (ptm) REVERT: D 671 LYS cc_start: 0.7845 (pttt) cc_final: 0.7562 (pttp) REVERT: D 690 LYS cc_start: 0.6598 (tptt) cc_final: 0.5351 (tptp) REVERT: C 342 LEU cc_start: 0.3249 (OUTLIER) cc_final: 0.2433 (tp) outliers start: 49 outliers final: 38 residues processed: 282 average time/residue: 0.2891 time to fit residues: 130.5452 Evaluate side-chains 275 residues out of total 2210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 231 time to evaluate : 2.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 755 LEU Chi-restraints excluded: chain A residue 759 GLU Chi-restraints excluded: chain A residue 763 THR Chi-restraints excluded: chain A residue 900 SER Chi-restraints excluded: chain A residue 983 LEU 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 A residue 1544 VAL Chi-restraints excluded: chain A residue 1553 LEU 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 532 ILE Chi-restraints excluded: chain D residue 591 LEU Chi-restraints excluded: chain D residue 608 THR Chi-restraints excluded: chain D residue 667 CYS Chi-restraints excluded: chain D residue 816 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 118 ILE Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 220 ASP Chi-restraints excluded: chain C residue 247 ILE 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 148 optimal weight: 3.9990 chunk 95 optimal weight: 9.9990 chunk 143 optimal weight: 0.0570 chunk 72 optimal weight: 3.9990 chunk 47 optimal weight: 0.8980 chunk 46 optimal weight: 0.0970 chunk 152 optimal weight: 0.8980 chunk 163 optimal weight: 2.9990 chunk 118 optimal weight: 5.9990 chunk 22 optimal weight: 0.6980 chunk 188 optimal weight: 3.9990 overall best weight: 0.5296 ------------------------------------------------------------------------------- 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 D 703 ASN D 869 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.2767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.142 20689 Z= 0.166 Angle : 0.561 16.278 28022 Z= 0.276 Chirality : 0.042 0.260 3199 Planarity : 0.004 0.060 3550 Dihedral : 7.136 102.410 3019 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 1.67 % Allowed : 16.33 % Favored : 81.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.17), residues: 2472 helix: 1.09 (0.15), residues: 1225 sheet: -0.43 (0.31), residues: 283 loop : -1.56 (0.20), residues: 964 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A1269 HIS 0.007 0.001 HIS C 314 PHE 0.026 0.001 PHE D 686 TYR 0.016 0.001 TYR D 719 ARG 0.008 0.000 ARG A 997 *********************** 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 288 residues out of total 2210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 251 time to evaluate : 2.367 Fit side-chains revert: symmetry clash REVERT: A 152 ASP cc_start: 0.7742 (t0) cc_final: 0.7516 (t0) REVERT: A 293 PHE cc_start: 0.8686 (OUTLIER) cc_final: 0.7331 (p90) REVERT: A 759 GLU cc_start: 0.8195 (OUTLIER) cc_final: 0.7630 (mp0) REVERT: A 983 LEU cc_start: 0.8790 (OUTLIER) cc_final: 0.8587 (mp) REVERT: A 1209 TYR cc_start: 0.5057 (m-80) cc_final: 0.4749 (m-80) REVERT: A 1370 GLN cc_start: 0.7877 (OUTLIER) cc_final: 0.6848 (mp10) REVERT: A 1464 MET cc_start: 0.6415 (ttt) cc_final: 0.6086 (ttp) REVERT: D 40 MET cc_start: 0.7478 (ttp) cc_final: 0.7176 (ptm) REVERT: D 671 LYS cc_start: 0.7813 (pttt) cc_final: 0.7526 (pttp) REVERT: D 690 LYS cc_start: 0.6589 (tptt) cc_final: 0.5343 (tptp) REVERT: C 342 LEU cc_start: 0.3533 (OUTLIER) cc_final: 0.2752 (tp) outliers start: 37 outliers final: 27 residues processed: 279 average time/residue: 0.2790 time to fit residues: 127.2328 Evaluate side-chains 263 residues out of total 2210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 231 time to evaluate : 2.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 623 LEU Chi-restraints excluded: chain A residue 636 LEU Chi-restraints excluded: chain A residue 702 LEU Chi-restraints excluded: chain A residue 755 LEU Chi-restraints excluded: chain A residue 759 GLU Chi-restraints excluded: chain A residue 900 SER Chi-restraints excluded: chain A residue 983 LEU 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 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 816 ILE Chi-restraints excluded: chain D residue 818 VAL 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 247 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 218 optimal weight: 30.0000 chunk 229 optimal weight: 0.0000 chunk 209 optimal weight: 2.9990 chunk 223 optimal weight: 20.0000 chunk 134 optimal weight: 0.7980 chunk 97 optimal weight: 4.9990 chunk 175 optimal weight: 4.9990 chunk 68 optimal weight: 0.3980 chunk 202 optimal weight: 6.9990 chunk 211 optimal weight: 1.9990 chunk 222 optimal weight: 3.9990 overall best weight: 1.2388 ------------------------------------------------------------------------------- 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 869 ASN ** C 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.2837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.160 20689 Z= 0.212 Angle : 0.573 15.661 28022 Z= 0.283 Chirality : 0.043 0.249 3199 Planarity : 0.004 0.061 3550 Dihedral : 6.975 102.016 3019 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 1.72 % Allowed : 16.88 % Favored : 81.40 % 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: -0.10 (0.17), residues: 2472 helix: 1.15 (0.15), residues: 1211 sheet: -0.40 (0.31), residues: 281 loop : -1.53 (0.20), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A1474 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 *********************** 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 fitting. rotamer outliers: 38 poor density : 239 time to evaluate : 2.352 Fit side-chains revert: symmetry clash REVERT: A 152 ASP cc_start: 0.7763 (t0) cc_final: 0.7533 (t0) REVERT: A 293 PHE cc_start: 0.8817 (OUTLIER) cc_final: 0.7234 (p90) REVERT: A 759 GLU cc_start: 0.8179 (OUTLIER) cc_final: 0.7627 (mp0) REVERT: A 1209 TYR cc_start: 0.5084 (m-80) cc_final: 0.4770 (m-80) REVERT: A 1370 GLN cc_start: 0.7917 (OUTLIER) cc_final: 0.6843 (mp10) REVERT: D 40 MET cc_start: 0.7471 (ttp) cc_final: 0.7203 (ptm) REVERT: D 671 LYS cc_start: 0.7836 (pttt) cc_final: 0.7554 (pttp) REVERT: D 690 LYS cc_start: 0.6618 (tptt) cc_final: 0.5376 (tptp) REVERT: C 342 LEU cc_start: 0.3525 (OUTLIER) cc_final: 0.2668 (tp) outliers start: 38 outliers final: 28 residues processed: 269 average time/residue: 0.2906 time to fit residues: 126.9078 Evaluate side-chains 261 residues out of total 2210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 229 time to evaluate : 2.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 293 PHE Chi-restraints excluded: chain A residue 379 PHE 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 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 377 ASN 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 816 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 247 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 146 optimal weight: 0.7980 chunk 236 optimal weight: 6.9990 chunk 144 optimal weight: 0.9990 chunk 112 optimal weight: 2.9990 chunk 164 optimal weight: 2.9990 chunk 248 optimal weight: 5.9990 chunk 228 optimal weight: 20.0000 chunk 197 optimal weight: 6.9990 chunk 20 optimal weight: 0.9980 chunk 152 optimal weight: 0.8980 chunk 121 optimal weight: 0.1980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 863 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 869 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.2916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.115 20689 Z= 0.170 Angle : 0.570 16.023 28022 Z= 0.281 Chirality : 0.042 0.258 3199 Planarity : 0.004 0.060 3550 Dihedral : 6.811 101.690 3019 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 1.45 % Allowed : 17.33 % Favored : 81.22 % 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: -0.05 (0.17), residues: 2472 helix: 1.18 (0.15), residues: 1221 sheet: -0.36 (0.31), residues: 281 loop : -1.51 (0.20), residues: 970 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A1474 HIS 0.002 0.000 HIS C 314 PHE 0.025 0.001 PHE D 686 TYR 0.017 0.001 TYR D 719 ARG 0.007 0.000 ARG A 997 ********************** 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 274 residues out of total 2210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 242 time to evaluate : 2.265 Fit side-chains revert: symmetry clash REVERT: A 152 ASP cc_start: 0.7759 (t0) cc_final: 0.7551 (t0) REVERT: A 293 PHE cc_start: 0.8820 (OUTLIER) cc_final: 0.7294 (p90) REVERT: A 759 GLU cc_start: 0.8188 (OUTLIER) cc_final: 0.7642 (mp0) REVERT: A 1209 TYR cc_start: 0.5134 (m-80) cc_final: 0.4832 (m-80) REVERT: A 1269 TRP cc_start: 0.7666 (m100) cc_final: 0.7432 (m100) REVERT: A 1370 GLN cc_start: 0.7886 (OUTLIER) cc_final: 0.6848 (mp10) REVERT: A 1586 MET cc_start: 0.2408 (tpt) cc_final: 0.1611 (mpp) REVERT: D 40 MET cc_start: 0.7439 (ttp) cc_final: 0.7197 (ptm) REVERT: D 671 LYS cc_start: 0.7834 (pttt) cc_final: 0.7546 (pttp) REVERT: D 690 LYS cc_start: 0.6618 (tptt) cc_final: 0.5362 (tptp) REVERT: D 719 TYR cc_start: 0.7398 (t80) cc_final: 0.6822 (t80) REVERT: C 342 LEU cc_start: 0.3520 (OUTLIER) cc_final: 0.2683 (tp) outliers start: 32 outliers final: 24 residues processed: 268 average time/residue: 0.2919 time to fit residues: 125.9657 Evaluate side-chains 268 residues out of total 2210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 240 time to evaluate : 2.261 ------------------------------------------------------------------------------- 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 293 PHE Chi-restraints excluded: chain A residue 379 PHE 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 1276 ILE Chi-restraints excluded: chain A residue 1370 GLN Chi-restraints excluded: chain A residue 1455 ILE Chi-restraints excluded: chain D residue 54 VAL 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 532 ILE Chi-restraints excluded: chain D residue 591 LEU Chi-restraints excluded: chain D residue 740 ILE Chi-restraints excluded: chain D residue 816 ILE 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 247 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 156 optimal weight: 0.1980 chunk 210 optimal weight: 9.9990 chunk 60 optimal weight: 0.7980 chunk 182 optimal weight: 3.9990 chunk 29 optimal weight: 9.9990 chunk 54 optimal weight: 3.9990 chunk 197 optimal weight: 6.9990 chunk 82 optimal weight: 0.9990 chunk 203 optimal weight: 0.8980 chunk 25 optimal weight: 0.9980 chunk 36 optimal weight: 10.0000 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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 863 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 = 0.4061 r_free = 0.4061 target = 0.176623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.118113 restraints weight = 29477.893| |-----------------------------------------------------------------------------| r_work (start): 0.3247 rms_B_bonded: 2.73 r_work: 0.3054 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2925 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.2955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.156 20689 Z= 0.181 Angle : 0.572 17.557 28022 Z= 0.281 Chirality : 0.043 0.251 3199 Planarity : 0.004 0.060 3550 Dihedral : 6.743 101.043 3019 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 1.58 % Allowed : 17.15 % Favored : 81.27 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 0.01 (0.17), residues: 2472 helix: 1.24 (0.15), residues: 1214 sheet: -0.37 (0.30), residues: 281 loop : -1.48 (0.20), residues: 977 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A1474 HIS 0.002 0.000 HIS A 544 PHE 0.024 0.001 PHE D 686 TYR 0.016 0.001 TYR D1068 ARG 0.007 0.000 ARG A 997 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4722.66 seconds wall clock time: 84 minutes 27.39 seconds (5067.39 seconds total)